Re: [gmx-users] Fwd: tau-t effects on sd integrator

Thank you very much, Justin. I'll go and try with 2ps. Best wishes, Sidong On Mon, Aug 29, 2016 at 1:38 PM, Justin Lemkul wrote: > > > On 8/29/16 1:29 PM, Sidong Tu wrote: > >> Dear all, >> >> I was trying to simulate lysozyme and polymer in water model tip

[gmx-users] Fwd: tau-t effects on sd integrator

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 used sd as integrator and the tau-t option was 0.1. I wondered if there is any problem with this o

Re: [gmx-users] LINCS warnings at high temperature md run

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...@mail

[gmx-users] LINCS warnings at high temperature md run

ates 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 User