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QM/MM Discussion and Questions Jump to new posts
Reaction dynamcs with umbrella sampling ErandiUSJP 01/15/21 04:46 AM
Hi,

I'm trying to run umbrella sampling simulation with QM/MM and my reaction coordinate is simply a distance. The input script runs and gets a normal termination. I used umbrella.inp guide in CHARMM testcases to make the script. All other output files are written but rxn1.stt and rxn2.stt both have no data and there's a warning like given below in the umbrella.out file. Can someone please suggest the reason for this?

CHARMM> rxncor: statistics lowdelta 1.4 hidelta 3.8 deldel 0.2 -
CHARMM> start 500

***** LEVEL 2 WARNING FROM *****
***** NO NAME SPECIFIED: DEFAULTING TO FIRST COORDINATE
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5

CHARMM> rxncor: umbrella kumb 15.0 form 1 del0 1.4

***** LEVEL 2 WARNING FROM *****
***** NO NAME SPECIFIED: DEFAULTING TO FIRST COORDINATE
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5


Input
open write unit 18 form name rxn1.xyz
open write unit 19 form name rxn1.rst
open write unit 20 form name rxn1.ene
open write unit 21 form name rxn1.stt
open write unit 22 form name rxn1d12.trc

rxncor: define c1 point select atom R1 510 OD2 end
rxncor: define c2 point select atom H1 6 C1 end
rxncor: define rxn1d12 direction c1 c2
rxncor: set rxn1d12

rxncor: trace rxn1d12 unit 22

rxncor: statistics lowdelta 1.4 hidelta 3.8 deldel 0.2 -
start 500

DYNA leapfrog rest langevin rbuf @buf -
TIMEstep 0.001 NSTEp 1500 INBFrq -1 IHTFREQ 0 - ! was 50000 now 50 TESTING
IPRFrq 100 IEQFrq 0 NSAVC 50 NPRINT 50 ISVFRQ 100 ilbfrq 1 - !WE SAVE EVERY 50 fs
!Setting the temperature
firstt @TEMP finalt @TEMP tbath @TEMP -
!We assign velocities
IASORS 1 IASVEL 1 -
!File manager
IUNREAD 17 IUNWRITE 19 KUNIT 20 IUNVEL -1

rxncor: write unit 21
close unit 21

write coor card unit 18
* system after rxn1
*

! Phase 3: rxn2.inp
open read unit 17 form name rxn1.rst
open write unit 18 form name rxn2.xyz
open write unit 19 form name rxn2.rst
open write unit 20 form name rxn2.ene
open write unit 21 form name rxn2.stt
open write unit 22 form name rxn2d12.trc

rxncor: umbrella kumb 15.0 form 1 del0 1.4
rxncor: statistics lowdelta 1.4 hidelta 3.8 deldel 0.2 -
start 500

DYNA leapfrog rest langevin rbuf @buf -
TIMEstep 0.001 NSTEp 1500 INBFrq -1 IHTFREQ 0 -
IPRFrq 100 IEQFrq 0 NSAVC 50 NPRINT 50 ISVFRQ 100 ilbfrq 1 - !WE SAVE EVERY 50 fs
!Setting the temperature
firstt @TEMP finalt @TEMP tbath @TEMP -
!We assign velocities
IASORS 1 IASVEL 1 -
!File manager
IUNREAD 17 IUNWRI 19 KUNIT 20 IUNVEL -1

rxncor: write unit 21
close unit 21

write coor card unit 18
* reaction after rxn2
0 4 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Post Analysis of openMM trajctory rmv 01/14/21 04:27 PM
The energy doc file has a detailed list of energy terms available via ? substitutions, including ?ELEC and ?VDW, which can be used to write those values to a file:

open read unit 21 file name pff_8cell_10ns.dcd
OPEN UNIT 2 WRITE CARD NAME INTE.TXT
ECHU 2 ! see miscom doc file for echo usage
traj query unit 21
SET COUNT = ?NFILE
traj iread 21 nunit 1
set x 1
label loop
traj read
energy
update
SKIP ALL EXCL vdw Elec
interaction select resname phe .and. type C* end sele resname tip3 .and. type OH2 end
ECHO @X ?VDW ?ELEC
INCR X BY 1
IF X LE @COUNT GOTO LOOP


A more complete list of ? substitutions can be found in the subst doc file. Also, there is no need to read the PDB file for this, the PSF is sufficient for reading DCD files.
4 26 Read More
Installation and Testing Jump to new posts
Re: Installation of CHARMM on Ubuntu 18.04 rmv 01/14/21 03:49 PM
The error is very different. The CHARMM version and GCC versions are not up to date. There's not enough information to say more.
7 284 Read More
Molecular Dynamics Jump to new posts
Re: VV2 Dynamics rmv 01/12/21 11:17 PM
DOMDEC only supports the LEAPfrog Verlet integrator.

I don't have any answer for the VV2 and XYZ problem, it's not something I've done.
1 19 Read More
Energy terms, Constraints, Restraints, and Solvation Jump to new posts
Re: ENERGY CHANGE TOLERANCE EXCEEDED dengwenhao 01/11/21 04:29 AM
Okay´╝îthanks for your reply. I will try it. Thanks.

Wenhao
2 35 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: prepare drude initial coordinates rmv 01/07/21 06:12 PM
PDB is not a native CHARMM format, and there are a number of variations in the PDB format produced by different programs which can make import challenging at times.

I suggest using the UNIVersal I/O specification, as outlined in the second example in this post which reads a complex PDB file in a single pass.
1 43 Read More
Molecular Dynamics Jump to new posts
Re: cnt command in MD simulation input rmv 01/05/21 04:09 PM
It's not part of CHARMM per se, but a convention used by the CHARMM-GUI folks for their method of running dynamics. The user is expected to set a script variable named cnt on the command line, as indicated in the comment lines in the output you've posted.

There are alternative methods for creating numbered files for long MD runs in the Script Archive forum; for example, see this post
1 36 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: A selection problem rossi 12/31/20 05:59 PM
Dear Rick,

Thanks for helping me.

COR2 is a graphene molecule and flat.

Before the selection, I issue the command coor orient select resname COR2 end which ensures that it is in the xy-plane. It has a large radius so that a large .around. value allows molecules
interacting with it to be selected. Also, using prop Z is a way to select molecules above the xy-plane of the graphene.

The box size is x by y by z is 50 x 50 x 115 and has a complicated mix of molecules

How about this after the above selection:

format(I5)

calc ntest = ?nsel / 4

format

Now I have the number of molecules.

Can I somehow use .subset. to get the molecules I want? I am not sure.

I will try the following

set newnearby select nearby .subset 1:@ntest end

Regards,

Angelo
2 55 Read More
Parameter Set Discussion Jump to new posts
Parameterizing Borate cages AbhiAcharya 12/25/20 09:03 PM
Hi

I am interested in parameterizing dodecaborate cage [B12H12]2- and its halide derivatives [B12X12]2-, X=Cl,Br,I. I read the original paper on procedure, and did some literature survey. I have some idea how to go about it, but would like some sanity check on the methodology from more experienced members of the community.

The molecules are quite rigid and I think that for the most part it should be straightforward. This is what I planned:

a) LJ params for start can be adopted initially from CgenFF; I noticed the B201 atomtype available in the latest 2020 version. Luckily, bonded halides are well represented thanks to more recent efforts (although bonded to carbon, but I hope we can get away with this). So even in this case atom types are there.

b) Bonds, angles and torsions look simple as the molecule is rigid. So just setting parameters to match the QM optimized geometry should work.

c) Partial charges also do not look very tricky. But I am guessing this would require the most effort; dodecaborate has a negative charge on the hydrogens and forms dihydrogen bonds with water (B-H---H-O-H). [B12Cl12]2- (and Br derivatives) have a negative charge on the halide atoms, whereas Iodine is largely neutral. There is also the issue of sigma hole on halogen atoms and I am not sure if it is relevant in my case.

d) I The water interactions need to be modeled correctly. Maybe fitting the LJ and charges to fit the QM interaction energies would suffice.

Some suggestions and improvements on the aforesaid procedure would be highly appreciated.

Abhi
0 39 Read More
Molecular Dynamics Jump to new posts
Re: Trajectories in XYZ format rmv 12/17/20 09:30 PM
I've posted the fix here
3 96 Read More
Bug Reports & Fixes Jump to new posts
fix atom names for xyz trajectory rmv 12/17/20 09:27 PM
There is an issue with the XYZ format output for trajectories, in that it only writes the first character of the atom name. The snippet below from source/dynamc/dynio.F90 (or dynio.src for c43b2 and before) is the current code:

Code
  DO I=1,NATOM
     IF(MXYZ == 1) &
          WRITE(IUN,'(A1,1X,3E25.15)') ATYPE(I)(1:1),X(I),Y(I),Z(I)
     IF(MXYZ == 2) &
          WRITE(IUN,'(A1,1X,6E25.15)') ATYPE(I)(1:1),X(I),Y(I),Z(I), &
          VX(I),VY(I),VZ(I)
     IF(MXYZ == 3) &
          WRITE(IUN,'(A1,1X,9E25.15)') ATYPE(I)(1:1),X(I),Y(I),Z(I), &
          VX(I),VY(I),VZ(I),DX(I),DY(I),DZ(I)
     IF(MXYZ == 4) &
          WRITE(IUN,'(A1,1X,6E25.15)') ATYPE(I)(1:1),X(I),Y(I),Z(I), &
          DX(I),DY(I),DZ(I)
  ENDDO

Changing the array indices and format string in the four WRITE statements as shown below will write the full atom names for all output types.

Code
  DO I=1,NATOM
     IF(MXYZ == 1) &
          WRITE(IUN,'(A8,1X,3E25.15)') ATYPE(I)(1:8),X(I),Y(I),Z(I)
     IF(MXYZ == 2) &
          WRITE(IUN,'(A8,1X,6E25.15)') ATYPE(I)(1:8),X(I),Y(I),Z(I), &
          VX(I),VY(I),VZ(I)
     IF(MXYZ == 3) &
          WRITE(IUN,'(A8,1X,9E25.15)') ATYPE(I)(1:8),X(I),Y(I),Z(I), &
          VX(I),VY(I),VZ(I),DX(I),DY(I),DZ(I)
     IF(MXYZ == 4) &
          WRITE(IUN,'(A8,1X,6E25.15)') ATYPE(I)(1:8),X(I),Y(I),Z(I), &
          DX(I),DY(I),DZ(I)
  ENDDO
0 47 Read More
Parameter Set Discussion Jump to new posts
Re: Group definition for organic molecule rmv 12/17/20 02:29 PM
Other than the size restriction, the convention is that each group should have an integer net charge, i.e. the sum over partial charges for the group should be zero, +/- 1, etc.
1 52 Read More
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