<br>Hi Justin and Jianguo, <br><br>Thank you for the suggestions. It makes sense to use the same velocities from the equilibration output instead of generating them and also to couple the groups separately. However they dont seem to work. <br>
<br>I changed the gen_vel to 0 and used the cpt files and equilibration tpr files to generate the tpr files for the replica exchange runs but still got the bad contacts error. <br><br>t = 2.010 ps: Water molecule starting at atom 21424 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br>Jul 5 23:10:10 2011 32736 4 7.04 handleTSRegisterTerm(): TS reports task <5> pid <10337> on host<cmp-43-5> killed or core dumped<br>
<br><br>I generated the tpr files with the following command:<br><br>/ifs1/apps/gromacs-405/bin/grompp -f remd.mdp -c eq_1ns.tpr -o cptremd0.tpr -t eq_1ns.cpt -p popc_mlt.top <br><br><br>I then coupled the components of the system separately and even that gave the same error.<br>
<br><br>t = 2.018 ps: Water molecule starting at atom 7015 can not be settled.<br>Check for bad contacts and/or reduce the timestep.<br>Wrote pdb files with previous and current coordinates<br>Jul 6 00:13:11 2011 7377 4 7.04 handleTSRegisterTerm(): TS reports task <1> pid <24584> on host<cmp-25-6> killed or core dumped<br>
<br>I attach the mdp file that I used. I would appreciate any other suggestions you might have. <br><br>Thanks<br><br>Sheeba<br><br><br><br><br><br><br><br><br><br><div class="gmail_quote">On Tue, Jul 5, 2011 at 7:22 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Sheeba Jem wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Dear Gromacs users,<br>
<br>
I am having trouble running REMD for a system containing one peptide molecule on the surface of a lipid membrane, the system contains the following:<br>
<br>
Protein 1<br>
POPC 128<br>
Water 4847<br>
Na+ 9<br>
Cl- 15<br>
<br>
The total number of atoms in the system is 21483. I have 50 replicas with temperatures distributed from 250 to 400 K. After setting up the system I minimized and equilibrated the system for 14 ns at three temperatures: 250 K, 300K and 350 K. I take the output file from the 250 K run and use that as the starting structure for the temperatures between 250 to 300 K; similarly the output file from 300 K as the starting structure for replicas between 300 to 350 K and for the replicas between 350 to 400 K I use the output from the 350 K run. I further equilibrate these structures at the replica temperature for 10 ns. The output from these 10 ns runs are then used as starting structures for the replica exchange simulation. However when the replica exchange simulation begins to run, it crashes after 2 ps with a bad contact error:<br>
<br>
</blockquote>
<br></div>
Your equilibration protocol doesn't make much sense. First, you're not equilibrating properly under all conditions, and then (in your .mdp file) you're re-generating velocities so you just end up destroying any equilibration you had previously achieved. Membranes are particularly sensitive to proper equilibration, so I suspect this is your root problem. Equilibrate each system at the desired temperature, maintaining the ensemble by passing the appropriate .cpt file to grompp (with "gen_vel = no" so as not to override the existing velocities).<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
t = 2.008 ps: Water molecule starting at atom 21421 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br>
Jul 4 18:07:21 2011 22666 4 7.04 handleTSRegisterTerm(): TS reports task <7> pid <15856> on host<cmp-13-9> killed or core dumped<br>
<br>
<br>
I use the Gromacs version 4.0.5 for all the simulations. Since the starting structure for each replica has been well equilibrated I am not sure how there could be hard contacts in the system. I looked at the <br>
</blockquote>
<br></div>
The configurations may be somewhat equilibrated, but you're killing that by generating velocities.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
input structures and the trajectories from the equilibration runs and I could not find anything strange with the system leading to hard contacts. Also the membrane remains intact for the high temperature replicas. Since I could not find anything to change in the system, I tried running REMD reducing the time step from 2 fs to 1 fs which also gave a similar error:<br>
<br>
</blockquote>
<br></div>
If you get the same problem, it's likely still the thermostatting/velocity generation that's the problem.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
t = 2.020 ps: Water molecule starting at atom 18919 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br>
<br>
I then tried with a timestep of 0.1 fs and got the same bad contacts error:<br>
<br>
t = 0.101 ps: Water molecule starting at atom 20251 can not be settled.<br>
Check for bad contacts and/or reduce the timestep.<br>
Wrote pdb files with previous and current coordinates<br>
Jul 4 18:34:17 2011 25639 4 7.04 handleTSRegisterTerm(): TS reports task <5> pid <17349> on host<cmp-4-5> killed or core dumped<br>
<br>
<br>
I am not sure if reducing the timestep further would help therefore I looked at the temperature and pressure coupling. For all the above simulations I had used nose-hoover thermostat and a parrinello-rahman barostat with semi-isotropic pressure coupling. I had previously 'successfully' ran a REMD simulation of the peptide in water with isotropic coupling, the difference in the two .mdp files were the type of pressure coupling and changes in the bond contraint parameters (I have attached both the mdp files). Since semi-isotropic pressure coupling reproduces membrane properties well, I had used it for the peptide-lipid system. To see if changing the coupling type made a difference, with the 0.1 fs time step, I changed the coupling type to isotropic and this time the job crashed with the lincs warning:<br>
<br>
</blockquote>
<br></div>
Membranes are more sensitive, especially to temperature and pressure coupling and the state of equilibration. Proteins in water are far more robust and take a lot of beating before they explode. Therefore, the comparison is not a particularly good one. Apples and oranges.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br><font color="#888888">
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</font></blockquote></div><br><br clear="all"><br>-- <br>with regards,<br>I. Sheeba Jem.<br>