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
modifications.
-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
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