Thanks. I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was "constraints = h-bonds ", however it was "constraints = all-bonds" for POPC/PROTEIN/WATER system.
You say insufficient minimization, I don't think so........ . I got a sensible potential energy as follow: Potential Energy = -1.2414742e+06 Maximum force = 9.8055229e+01 on atom 4719 Norm of force = 3.4904923e+00 Then what's wrong with the EM? Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <firstname.lastname@example.org> Cc: Sent: Tuesday, January 1, 2013 6:45 PM Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system On 1/1/13 8:56 AM, Shima Arasteh wrote: > Hi, > > I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD > simulation following the Justin's tutorial of kalp15-DPPC. > > The force field which I use, is charmm36. > > In NVT step, I get LINCS-warning as follow: > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 2.460224, max 54.696251 (between atoms 4719 and 4716) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > > Step 0, time 0 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.182707, max 15.613569 (between atoms 4725 and 4726) > > > When I checked the warning, I see the first warning is related to 2 atoms of > 71POPC, the chain of 71POPC residue is broken near these two atoms. And the > other warning is related to a bond between H and C in the other POPC residue. > > Some settings of nvt.mdp is as: > ns_type = grid > nstlist = 5 > rlist = 1.2 > rlistlong = 1.4 > rcoulomb = 1.2 > rvdw = 1.2 > pbc = xyz > vdwtype = switch > rvdw_switch = 0.8 > ; Parameters for treating bonded interactions > continuation = no > constraint_algorithm = LINCS > constraints = all-bonds > lincs_iter = 1 > lincs_order = 4 > > Do I need to increase the rlistlong? I have done a simulation of POPC-water > before with these settings, but everything was ok. So what's the problem? > Anybody may help me? > Don't haphazardly mess with cutoffs. Doing so usually makes your problem worse. Think about it scientifically - if POPC/water worked fine, but a POPC/protein/water system doesn't, what's the variable that changed? Moreover, look at when the failure is happening - it's failing at step zero. LINCS warnings always have the same causes: 1. Wrong .mdp settings (likely not the case, see above) 2. Insufficient equilibration (well, yours is failing outright, so probably not) 3. Insufficient minimization (hmmm...) -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 email@example.com 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