[gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory
jalemkul at vt.edu
Sat Jan 5 19:19:42 CET 2013
On 1/5/13 3:46 AM, Shima Arasteh wrote:
> Dear all,
> I have a system of POPC/Protein/water/ions to simulate. I am trying to simulate this system by getting ideas from Justin's tutorial of kalp15-dppc.
> I've passed all steps of EM, NVT, and NPT as I expected. But when I want to run mdrun, I get some errors about waters can not be settle. So, I tried to remove them from npt.gro, update the number of atoms in .gro file, and then update number of SOL molecules in top file.Finally I made a new index file to go on.
> Next, to start mdrun, I run this command:
> grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index-new.ndx -o md_0_1.tpr
> and get this fatal error:
> Number of atoms in Topology is not the same as in Trajectory.
> In fact, I thought of updating npt.cpt file, but it's a binary file and I guess it's impossible. Does anybody knows what should I do? Would you please give me advice?
Re-run equilibration with your altered system. You had a (maybe) equilibrated
system that you have now perturbed, so it's no longer equilibrated. If the
previous equilibration had been adequate (assuming your topology is stable and
your .mdp settings are correct), then you should not have had to make these
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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