[gmx-users] About Production MD run error

[Justin Lemkul]

On 5/20/13 11:42 AM, vidhya sankar wrote:
> Dear Justin Thank you for previous reply.
>                                                                            I am doing Carbon nano tubes Wrapped by Cyclic peptide .I am sure of that iher is no error in My topology of My system (CNT Wrapped by Cyclic peptide)

Cyclic peptides require manual changes; that can be problematic.

> After Successful  NPT and NVT equilibration  When i Run Production MD I have got The following Notes in terminal
>

Presumably restraints are on during NVT and NPT?  Restraints can mask underlying 
problems in the topology or with .mdp settings.

> NOTE 1 [file CNTCYCfull.mdp]:
>    nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>    nstcomm to nstcalcenergy
> NOTE 2 [file CNTCYCfull.mdp]:
>    You are using a cut-off for VdW interactions with NVE, for good energy
>    conservation use vdwtype = Shift (possibly with DispCorr)
> NOTE 3 [file CNTCYCfull.mdp]:
>    You are using a cut-off for electrostatics with NVE, for good energy
>    conservation use coulombtype = PME-Switch or Reaction-Field-zero
> NOTE 4 [file gfggZ.top, line 60]:
>    For energy conservation with LINCS, lincs_iter should be 2 or larger.
>
> if I ignore the Notes  I am Not Able to run . S I have Changed All options Accordingly in .mdp files Then

Posting a full .mdp file for the failing run (and ideally NVT and NPT as well) 
would be very useful.

> When I run I have got the following errors after few Minutes
>
> step 100, will finish Thu Oct 10 18:44:32 2013
> Step 153, time 0.0306 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.010047, max 0.158996 (between atoms 875 and 873)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>
> rms 37613.979597, max 954780.695847 (between atoms 1189 and 1190)
>     1157   1156   34.0    0.0997   0.1118      0.1000
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>     1171   1158   36.4    0.1542   0.1972      0.1530
>     1159   1158   34.8    0.1534   0.2022      0.1530
>     1178   1176   67.6    0.1528   2.4354      0.1530
>     1179   1177   79.1    0.1533   0.2981      0.1530
>     1046   1044   35.1    0.1489   0.3847      0.1470
> Fatal error:
> 3 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
>

None of this is particularly helpful as it's all information that has been 
posted before.  I would suggest that you follow what Mark suggested - simplify 
the system before proceeding.  Run your CNT in vacuo, then the peptide in vacuo, 
then both (by themselves) in water, then your full system.  Doing so will allow 
you to determine what element of the system fails first.

If you are still having trouble after doing all of that, please respond directly 
to the 4 points I posted before.  In the absence of that level of detail, no one 
can provide useful advice.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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