[gmx-users] More ATP errors
David van der Spoel
spoel at xray.bmc.uu.se
Mon Dec 8 12:13:01 CET 2003
On Mon, 2003-12-08 at 11:59, Raj Badhan wrote:
> Dear Sirs,
> After hours of trying to get my simulation to run with ATP as a
> ligand I have almost given up all hope.
> ATP is the ligand within my protein.
> I can run an em protocol with the protein alone and with the ligand
> alone, but not with both together, as MDRUN always crashes.
> I have checked for bad contacts and there are none.
> Any suggestions? I am running this on the windows ported version
> of gromacs, and below is my EM.MDP file.
> Has anyone been able to use ATP as a ligand and got the
> simulations to work? If so, I would appreciate any
> ideas/suggestions on how they got their simulation to work.
start by making it simpler: change PME to a cutoff
> title = FWS
> cpp = c:\gromacs\bin\cpp.exe
> constraints = none
> integrator = steep
> dt = 0.002 ; ps !
> nsteps = 400
> nstlist = 10
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 0.9
> pme_order = 4
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Energy minimizing stuff
> emtol = 1000.0
> emstep = 0.01
> Raj Badhan
> Postgraduate researcher
> School of Pharmacy and Pharmacetical Science
> The University of Manchester
> Manchester, UK.
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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