[gmx-users] Re: NPT MD Run Problem

teklebrh at ualberta.ca teklebrh at ualberta.ca
Thu Mar 11 21:22:58 CET 2010

Dear Justin.

I turned off the gen-vel to no. Yes you are right. But I got the same error.

I increase tau-p ( from 1 to 3) and it looks working fine so far.

One of the warnings is that the pressure is less 1%.

Thank you for your help Justine.


Remark from the previous request

The pdb2gmx is also working .... the reinstalled the .rtp file and it is ok!

I got the Toluene topology from the PHE.


I want the same for the n-heptane toplogy using the pdb2gmx.... is  
there any method I could get that from the gromos96 force filed. Just  
to avoid using PRODRG!


Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> teklebrh at ualberta.ca wrote:
>> Dear Gromacs users,
>> I have equilibration my system using the position restraint NVT  
>> simulation for 100ps, and it works well. and did not get any error  
>> until the end.
>> But as soon as I switch to NPT full production run, I got the  
>> following error. Can any body help me on this issue.
>> Program mdrun, VERSION 4.0.5
>> Source code file: constr.c, line: 136
>> Fatal error:
>> Too many LINCS warnings (6540)
>> If you know what you are doing you can adjust the lincs warning  
>> threshold in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>> gen-vel                  = yes ; assign velocities from Maxwell
> Re-generating velocities negates the purpose of any previous equilibration.
> -Justin
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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