On 10/02/2012 4:41 PM, vivek sharma wrote:
Hi Justin,
Thanks for your response. After posting my query, I tried running the
similar set with
NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p
= 0.5, compressibility = 4.5e-05, ref_p = 1.0)
On giving berendsen instead of Parrinello-Rahman for pressure
coupling, job finished successfully. Can you comment on this?
I suggest you read the manual section on pressure coupling, which likely
explains this observation.
Mark
As par the tutorial I am using simple vdW transformation only as mentioned below
---------
couple-moltype = Methane ; name of moleculetype to decouple
couple-lambda0 = vdw ; only van der Waals interactions
couple-lambda1 = none ; turn off everything, in this case only vdW
---------
Thanks,
Vivek
On 09/02/2012, Justin A. Lemkul<jalem...@vt.edu> wrote:
vivek sharma wrote:
Hi There,
I was trying to run a equilibrium run (npt) for system of "Methane in
1-octanol" (1 methane molecule with 200 1-octanol molecules with OPLS FF
parameters). Following is the series of steps I followed:
1. Energy minimization with steep integrator for 5000 steps
2. Energy minimization with l-bfgs integrator for 5000 steps
3. NVT run for 100 ps with sd integrator
4. NPT run for 100 ps with sd integrator (with Pcoupl =
Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0)
During the NPT run I am ending up with following error (too many LINCS
warning):
---------------------------------------------
Step 25406, time 50.812 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 11.778495, max 363.475445 (between atoms 2158 and 2157)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2152 2150 90.0 0.1090 1.3690 0.1090
2152 2151 90.0 0.1090 36.5266 0.1090
2158 2156 90.0 0.1091 0.5637 0.1090
2158 2157 90.0 0.2349 39.7278 0.1090
Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1#
Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault
------------------------------------------------------------
*.mdp files for above simulation are adapted from tutorial on free
energy calculation by Justin.
Please suggest me what could be wrong with above simulation.
The answer for LINCS warnings is always the same - the system has become
unstable due to inappropriate geometry, bad .mdp settings, or a combination
of
both. To troubleshoot, start by turning off the free energy code to make
sure
your system is actually stable. If it's not, refer here:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
If it is stable, turn back on whatever free energy settings you're using. I
assume, based on the tutorial, that this is a simple vdW transformation?
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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