[gmx-users] invacuo simulation

Kwee Hong jestan1985 at yahoo.com
Fri Jan 28 11:01:04 CET 2011

From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, January 28, 2011 17:51:41
Subject: Re: [gmx-users] invacuo simulation

On 28/01/2011 8:45 PM, Kwee Hong wrote: 
In John's "GROMACS tutorial for solvation study of spider           toxin 
peptide",I keep on getting an error message at the           production stage: 

>Step 12111  Warning: Pressure scaling more than 1%.
>Step 12121  Warning: Pressure scaling more than 1%.
>Step 12131  Warning: Pressure scaling more than 1%.
>Program mdrun, VERSION 4.5.1
>Source code file: ns.c, line: 2544
>Fatal error:
>One of the box vectors has become shorter than twice the           cut-off 
>length or box_yy-|box_zy| or box_zz has become smaller           than the 
>For more information and tips for troubleshooting, please           check the 
>website at http://www.gromacs.org/Documentation/Errors
>I've tried a few approaches after reading the mailing list yet           I'm 
>still getting the same error message.
>The command lined I used in this simulation is as follow:
>pdb2gmx -ignh -ff gtomos43a1 -f 1OMB.pdb -o fws.pdb -p fws.top           -water 
Typo there.

Sorry for the typo

editconf -bt cubic -f fws.pdb -o fws.pdb -d 1.0
>grompp -f em.mdp -c fws.pdb -p fws.top -o em.tpr -maxwarn 5
>mdrun -v -deffnm em
>grompp -f md.mdp -c em.gro -p fws.top -o md.tpr -maxwarn 3
>mdrun -v -deffnm md
Look at those warnings. Unless you know what they are and why     ignoring them 
is OK, don't use -maxwarn.

There is actually no warning but note:  

The optimal PME mesh load for parallel simulations is below 0.5  and for highly 
parallel simulations between 0.25 and 0.33, for higher performance, increase the 
cut-off and the PME grid spacing

I think this is not significant since I'm running the simulation on single 

>After getting the error above round step 2300, I increased the           tau_p 
>from 0.5 to 1.0.
>Yet I got the same error message at step  5400 though the           warning on 
>pressure scaling  more than 1% was gone. 
>Therefore, I inceased the -d option in editconf to 1.5.
>But once again, I got the same error message at step 7300 (no           warning 
>on pressure scaling). 
>So once again, I increased the -d option in editconf to 2.5.
>And I still got the same error message at step 11300.
>I'm now real lost in solving this.. I hereby attach my           full.mdp file, 
>hopefully to get some insight here.
>Any suggestions are appreciated.
.mdp file looks OK.



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