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Problem with restarting REMD
#34234 07/31/14 04:26 AM
Joined: Oct 2012
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miracle Offline OP
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Hi, all,
I have trouble with restarting replica exchange MD simulation and hope to receive some advice on this problem.
I could run 5 ns REMD successfully. However, when I tried to restart REMD, continuing 5 ns simulation, the error message shown below appeared at first exchange attempt, followed by abrupt termination of MPI.

------------- Replica Exchange ------------
REX>EXCHANGE = 1 Step = 1000
REX>REPL = 15 Temp = 700.000 Epot = -2469.82315563
REX>NEIGHBOR = -1 Temp = 0.000 Epot = 0.00000000
REX>PROB = 0.00000 Rand = 0.55647 Tscale = 1.0000 Success = F
#REXSUM Rep# Tscale Sratio Temp NewTemp CurrTemp Epot
REXSUM> 15 1.000 0.000 700.000 0.000 673.762 -2469.8232
------------- Replica Exchange End --------
WRIDYN: RESTart file was written at step 5005000
WRIDYN: RESTart file was written at step 5005001

Writing RESTART FILE with previous and current coordinates,
which may be read by: READ COOR DYNR .... (see io.doc).
NOTE!! THIS FILE C A N N O T BE USED TO RESTART A RUN!!!

***** LEVEL -2 WARNING FROM *****
***** ENERGY CHANGE TOLERANCE EXCEEDED
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5

Would someone tell me why this error message popped up and how can I deal with this problem?
Thank you in advance.

PS - Here is the input script what I used for restart simulation.

set nreps ?numnode
set outname remd_ 2

open read card unit 15 name ../toppar/top_all22_prot.rtf
read rtf card unit 15

open read card unit 25 name ../toppar/par_all22_prot.prm
read parameter card unit 25

read psf card name ../setup/d_setup.psf
read coor card name ../ini_min/d_ini_min.crd

coor print sele (.not. INIT) .and. (.not. hydrogen) end

coor stat
coor orient
coor copy comp

define backbone sele type CA .or. type C .or. type N .or. type CO end

open read unit 10 card name ../scpism.inp

SCPI HYDR UISM 10

energy cutnb 14.0 ctofnb 12.0 ctonnb 10.0 atom fshift cdie vdw vshift

set node ?myrep
! Restart file of first replica exchange simulation
set oldrest remd_first.rst

repd nrep @nreps EXCHange FREQuency 1000 STEMp 300 MTEM 700 sump unit 17 -

open write form unit 17 name @outname.out
if ?MYNODE ne 0 outu 17

open write card unit 31 name @outname.rst
open write file unit 32 name @outname.dcd

open read unit 11 card name @oldrest

SCAL FBETA SET 8.0 SELE ALL END

energy cutnb 14.0 ctofnb 12.0 ctonnb 10.0 atom fshift cdie vdw vshift
update

! NOTE: Because of lang this will not produce the same results in parallel/parallel
dynamics lang leap rest -
timestep 0.001 nstep 4000000 nprint 100 -
iunwri 31 iunrea 11 iuncrd 32 iunvel -1 kunit -1 -
iprfrq 5000 firstt 300. finalt 300. tbath 300. -
iasors 1 iasvel 1 nsavc 100 nsavv 100 isvfrq 1000 ihtfrq 0 -
ieqfrq 0 inbfrq 0 ihbfrq 0 ntrfrq 0 -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 wmin 1.0 ato cdie fshift vdw vshift
echeck 10000.0 ichecw 0

open unit 28 write card name @outname.cor
write coor unit 28 card

open unit 29 write card name @outname.vel
write coor comp unit 29 card

stop

Last edited by miracle; 07/31/14 07:43 AM.
Re: Problem with restarting REMD
miracle #34235 08/01/14 08:58 PM
Joined: Oct 2004
Posts: 371
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tim Offline
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Joined: Oct 2004
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What version of CHARMM are you using? There were some bugs with restarting REPD simulations in versions earlier than c36 or thereabouts.

Your ECHECK is quite high (10000 kcal/mol) so it really shouldn't be getting exceeded if this is a well-equilibrated system. Is there anything suspicious looking in the previous 1000 steps of dynamics before the exchange?

Also, please use CODE tags when posting scripts (see the "read before posting" topic stickied in each forum) -- it will make your posts much easier to read.


Moderated by  BRBrooks, lennart, rmv 

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