Hi Christopher & Mark, My simulation worked well with the parameters given by Christopher. The sd integrator & lincs-order was fit in this situation while md integrator still had lincs warnings. I'll continue my runs with sd. Thank you very much for your help!
Best wishes, Sidong Message: 4 > Date: Thu, 11 Aug 2016 15:51:55 +0000 > From: Mark Abraham <mark.j.abra...@gmail.com> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] LINCS warnings at high temperature md run > Message-ID: > <CAMNuMARr49_nYc9XTmdcL-bkAfopZrs0rFiJPJEeejwKT5f9cA@ > mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi, > > Fundamentally, at higher temperature you have higher atomic velocities, so > atoms move further in a step. Your simulation is only stable if you apply > constraints, but the default settings are chosen for normal temperatures > and thus displacements. So try the kinds of things Chris suggests. > > Mark > > On Tue, 9 Aug 2016 20:35 Christopher Neale <chris.ne...@alum.utoronto.ca> > wrote: > > > Try adding "lincs-order = 6" to your mdp file. > > > > The following settings don't give me lincs warnings at 500 K, though I > > presume that the lincs-order is the essential part. > > > > constraints = all-bonds > > lincs-iter = 1 > > lincs-order = 6 > > constraint_algorithm = lincs > > dt = 0.002 > > integrator = sd > > tc_grps = System > > tau_t = 1.0 > > ld_seed = -1 > > > > failing that, post your full .mdp file. > > > > > > > > > > ________________________________________ > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sidong > Tu > > <sido...@g.clemson.edu> > > Sent: 09 August 2016 14:49:03 > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Cc: Chandan K Choudhury > > Subject: [gmx-users] LINCS warnings at high temperature md run > > > > Dear all, > > > > I was trying to simulate lysozyme and polymer in water model tip3p using > > charmm36 force field at 500K on Gromacs 5.1.2. The software ran on GPU > and > > the system size was about 60,000 atoms. I have done equilibrium with > > Berendsen(B) and Parrinello-Rahman(PR), and then md. The thermal > coupling I > > used was v-rescale. > > I always got a LINCS warning and my job stopped during the md. Here's the > > parameter I have used: > > Stage Position_Constraint Pcoupl gen_vel LINCS dt > > nsteps > > 1 Protein & polymer B yes all bonds 0.002 > > 200,000 > > 2 Protein B yes all bonds > > 0.002 200,000 > > 3 None B yes all bonds > > 0.002 200,000 > > 4 None PR no all bonds > > 0.002 50,000 > > 5 None PR no h bonds > > 0.002 1.25e+8 > > > > At stage 5, the md run stopped at 149 steps and showed relative > constraint > > deviation after LINCS. > > > > I have searched for this warning and there is an explanation that it > might > > be introduced by the bad equilibrium. Then I added a equilibrium stage > with > > Berendsen pressure coupling after stage 3 with LINCS constraints of h > bonds > > for 50,000 steps without position constraints. > > > > This time there was still warings with LINCS and it stopped at step 79026 > > in md: > > > > Step 79026, time 158.052 (ps) LINCS WARNING > > relative constraint deviation after LINCS: > > rms 15.598468, max 1553.834961 (between atoms 15966 and 15968) > > bonds that rotated more than 30 degrees: > > atom 1 atom 2 angle previous, current, constraint length > > 15941 15943 40.7 0.2082 0.1109 0.1111 > > 15945 15946 75.6 0.2551 7.7014 0.1111 > > 15945 15947 90.0 0.2299 4.2042 0.1111 > > 15949 15950 67.8 0.1543 0.1150 0.1111 > > 15949 15951 86.2 0.1658 8.9758 0.1111 > > 15966 15967 90.0 0.1111 0.2587 0.1111 > > 15966 15968 143.1 0.1111 172.7422 0.1111 > > 15970 15971 90.0 0.1111 0.1405 0.1111 > > Wrote pdb files with previous and current coordinates > > > > The simulation worked well with dt=0.001 without LINCS. But I still want > to > > find if there is a way to simulate at high temperature(500K) with > dt=0.002 > > so that I can use less steps? > > > > > > -- > > Sidong Tu > > Department of Materials Science and Engineering > > Clemson University > > Phone: (213)265-6768 > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
