Hello sir,<br><br>Thanks for your reply.<br>I have used this .mdp file. Is there anything wrong in the mdp file which I am using ?<br>To tell you in detail : First I have done energy minimization. Output of this step (box_em.pdb) is used to create an index group for sol and cl- ions using make_ndx. Then I am trying to run grompp using this particular .mdp file before position restraint mdrun.<br>
<br><b>pr.mdp file :</b><br>title = protein in popc bilayer<br>cpp = /usr/bin/cpp<br>
define = -DPOSRES -DPOSRES_LIPID<br>constraints = all-bonds<br>constraint-algorithm= Lincs<br>integrator = md<br>dt = 0.002 <br>nsteps = 5000 <br>nstcomm = 1<br>
nstxout = 50<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 10<br>nstenergy = 10<br>nstlist = 10<br>ns_type = grid<br>rlist = 1<br>
coulombtype = PME<br>rcoulomb = 1<br>vdw-type = Cut-off<br>rvdw = 1<br>; Berendsen temperature coupling is on in two groups<br>tcoupl = berendsen<br>tc_grps = Protein POPC SOL_CL-<br>
tau_t = 0.1 0.1 0.1 <br>ref_t = 300 300 300<br>; Energy monitoring<br>energygrps = Protein POPC SOL_CL-<br>; Pressure coupling is on<br>Pcoupl = berendsen<br>tau_p = 2.0 2.0<br>
compressibility = 4.5e-5 4.5e-5<br>ref_p = 1.0 1.0<br>Pcoupl_type = semiisotropic<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br>
<br>Thanking you,<br>Pawan<br><br><div class="gmail_quote">On Thu, Apr 9, 2009 at 10:38 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">Pawan Kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello Mark Sir,<br>
<br>
I have tried that way also.<br>
The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p topol.top -o box_pr.tpr<br>
But this time i get an error like this "Atom 1 defined in multiple groups (1 & 3). "<br>
How to overcome this error ?<br>
</blockquote>
<br></div>
You can't have the same atom in multiple groups used for the same purpose within mdrun (e.g. T-coupling or energy). I guess you've constructed your index file in a manner that is inconsistent with your use of it.<div>
<div></div><div class="h5"><br>
<br>
Mark<br>
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