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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
