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Installation and Testing Jump to new posts
Re: Installation of CHARMM on Ubuntu 18.04 rmv 10/24/20 07:51 PM
When did you download the CHARMM source?

What were the commands used to build CHARMM?

The threads you referenced were using the older, deprecated ./install.com procedure, while "installing CHARMM for Ubuntu" link uses the newer ./configure procedure, so those threads may not be relevant. If you used configure, there should be messages about any problems encountered. Did you install Ubuntu cmake first, or use the one that configure builds from source?

Please verify your compiler and cmake versions via

gcc --version
gfortran --version
cmake --version


The gfortran version should match gcc; gfortran and cmake may not be installed on Ubuntu by default.

Martin Karplus spent some time in Strasbourg, so perhaps there are people there you could ask for help.

From the main charmm directory (c45b1 in my case), I did the following:

mkdir ../BldTest
cd ../BldTest
../c45b1/configure
make -j6
3 4 Read More
Energy terms, Constraints, Restraints, and Solvation Jump to new posts
Re: syntax for simple restraint to box center lennart 10/23/20 05:15 PM
coor hbond can handle simple periodic boundary conditions (corman.info).
How good are the FF parameters for hydronium (a very rare species)?
4 73 Read More
Minimization, Normal modes, Monte Carlo,... Jump to new posts
GCMC simulation of crystal water Allen_123 10/23/20 10:40 AM
Hello Charmm users,

I'm currently using Grand canonical monte carlo ensemble to simulate crystal water by inserting and deleting water atoms inside a crystal. The crystal.crd contains position of crystal atoms as well as H2O. crystal atoms are fixed and set inactive. I got an error of
MC E ENR: Eval# ENERgy Delta-E GRMS
MC E INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
MC E EXTERN: VDWaals ELEC HBONds ASP USER
MC E IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
MC E EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
MC E PRESS: VIRE VIRI PRESSE PRESSI VOLUme
MC E LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
MC E> 0 28693807.808 0.000 39991243.434
MC E INTERN> 39.71400 71.43027 9.33503 125.67478 2.99950
MC E EXTERN> 157.74161 -227.80326 0.00000 0.00000 0.00000
MC E IMAGES> 28694837.626 -689.860 0.000 0.000 0.000
MC E EWALD> 43.99046 -3024.23481 2466.52214 0.00000 0.00000
MC E PRESS> -0.52165E+10 0.11479E+09 0.13065E+12 0.28750E+10 0.27377E+04
MC E LRCor> -5.32850 -10.65528
---------- --------- --------- --------- --------- ---------

***** LEVEL 2 WARNING FROM *****
***** REACHED GCMC LIMIT
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5

My scripts are like following:

*gcmc test simulation
*
!--- Read parameters, psf and coordinates
open read card name "top_all36_prot.rtf" unit 25
read rtf card unit 25
close unit 25
open read card name "par_all36m_prot.prm" unit 25
read parameter card unit 25 flex
close unit 25
stream toppar_water_ions.str

set cutnb 16.0 ! cutnb
set ctonnb 10.0 ! ctonnb
set ctofnb 12.0 ! ctofnb
set eatom atom
set etrun switch
set vatom vatom
set vtrun vswitch


OPEN UNIT 1 FORM READ NAME unit.psf
READ PSF CARD UNIT 1
CLOSe UNIT 1

! Read coordinates of starting structure
OPEN READ CARD UNIT 1 NAME crystal.crd
READ COOR CARD UNIT 1
CLOSE UNIT 1

!Set the active and blocking atoms
SCALar GCMC SET 0.0 SELEct IRES 1:12 END ! ires 1 to 12 is crystal
SCALar GCMC SET 1.0 SELEct IRES 13:42 END ! ires 13 to 42 is water
SCALar GCBLocker SET 1.0 SELEct all end
crystal define HEXAgonal 24.0709 24.0709 5.4560 90.00 90.00 120.00
crystal build noper 0 cutoff 30
update inbfrq -1 imgfrq -1 ihbfrq 0 imall -
ewald pmewald kappa 0.34 fftx 32 ffty 32 fftz 32 order 6 lrc -
@eatom @etrun @vatom @vtrun cutnb @cutnb ctonnb @ctonnb ctofnb @ctofnb -
cutim 999
ENERGY

! Create the MC move set
! Rigid translations
MOVE ADD MVTP RTRN BYREsidue WEIGht 1.0 DMAX 0.25 -
SELE (TYPE OH2) END LABEl DISP
! Rigid rotations
MOVE ADD MVTP RROT BYREsidue WEIGht 1.0 DMAX 30.0 -
SELE (TYPE OH2) END LABEl ROTA
! Insertion and deletion
MOVE ADD MVTP GCMC WEIGht 1.0 SELE (TYPE OH2) END LABEl GCMC

! Link the GCMC moves to the rotations and displacements to avoid moving
! inactive molecules.
MOVE LINK GCMC LAB1 GCMC LAB2 DISP
MOVE LINK GCMC LAB1 GCMC LAB2 ROTA

! Link the translations and rotations to each other for greater efficiency
MOVE LINK LAB1 DISP LAB2 ROTA

OPEN WRITE UNFOrmatted UNIT 32 NAME gcmc.dcd
! Do 1000000 steps at 298 K, writing energy 1000 steps.
! Grid-based insertions with 10 attempted orientations are used.
MC NSTEp 1000000 TEMPerature 298.0 ISEEd 302430 -
INBFrq -1 IECHeck 1000 IMGFrq -1 IUNC 32 NSAVc 1000 imall -
MUEX -5.8 DENS 0.03342 -
RGRId 0.25 GCCUt 2.5 NOTB 10 -
XMIN -12 YMIN -12 ZMIN -2.7 -
XMAX 12 YMAX 12 ZMAX 2.7

DELEte ATOM SELEct .BYRES. PROP X .GT. 9998.0 END
open write card unit 44 name gcmc.crd
write coor card unit 44 sele gcmc end


Could any one tell where the issue is?

Thank you.
0 10 Read More
Molecular Dynamics Jump to new posts
Re: Free energy between two graphenes with WHAM trying_MD 10/23/20 06:38 AM
Thanks to reply.


First, I didn't use the DOMDEC codes.

Second, the results seem to be that the restraints are well working by checking the configurations over time.

In my script, I just called/set the force fields/the crystal structure/the system information/nonbonded part before the restraint part.
Also, after the restraint part, there is the dynamics part.
I made 21 independent systems (windows) with the different distance (10~20 ang.) between two graphenes with 0.5 ang. interval.

The cylindrical restraints are just for making graphene impossible to translate with x, y-directions,
which means that the reaction coordinate in this system is only the z-direction distance between two graphenes.

The reason why I use the plane restraints, is that normal vector of the graphenes must be perpendicular (or close to) to xy-plane for my study.


My problem is that The free energy landscape looks good, but the free energy difference between local minimum and other regions (just 0.5 kcal/mol).
Do I need to product the number of atoms 88 (88 atoms in 1 graphene) to the free energy landscape? (if right, then the free energy scale is too large.)


Thank you to read my question.
2 28 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Error in structure after building pdb using ic build. rmv 10/21/20 04:11 PM
Possibly conflicting internal coordinates from using both the SETUP keyword of GENERATE, and using IC GENERATE; try omitting each separately, starting with IC GENERATE.
1 22 Read More
CHARMM-GUI Jump to new posts
Re: Parameterizing the heme in CHARMM-GUI rmv 10/01/20 06:43 PM
See the "Reporting CHARMM-GUI problems" post
1 44 Read More
Setup, I/O, and Basic questions Jump to new posts
Re: Missing donor specification in RTF Ripplet 09/28/20 01:21 AM
Thank you so much. I understand now.
4 85 Read More
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