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<p>First, sorry for the revival of this thread so late (maybe it should be better to start a new one).</p>
<p><br></p>
<p><span class=rvts6>> ----- Original Message -----</span></p>
<p><span class=rvts6>> From: Dmitri Dubov <</span><a class=rvts7 href="mailto:ddubov@ngs.ru">ddubov@ngs.ru</a><span class=rvts8>></span></p>
<p><span class=rvts6>> Date: Thursday, May 27, 2010 19:11</span></p>
<p><span class=rvts6>> Subject: Re[2]: [gmx-users] Non-conservation of total energy while</span></p>
<p><span class=rvts6>> using structure file to resume the simulation</span></p>
<p><span class=rvts6>> To: Discussion list for GROMACS users <</span><a class=rvts7 href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><span class=rvts8>></span></p>
<p><br></p>
<p><span class=rvts9>>> > I expect that either </span></p>
<p><br></p>
<p><span class=rvts9>>> > grompp -f new -o newtpr</span></p>
<p><span class=rvts9>>> > mdrun -s newtpr -cpi old_state.cpt</span></p>
<p><br></p>
<p><span class=rvts9>>> No, this way is unsuccessful, maybe due to somewhat contradictive instructions:</span></p>
<p><span class=rvts9>>> grompp supplies newtpr with usual options</span></p>
<p><span class=rvts9>>> tinit = 0</span></p>
<p><span class=rvts9>>> nsteps = 100000</span></p>
<p><span class=rvts9>>> simulation_part = 1</span></p>
<p><br></p>
<p><span class=rvts9>>> and from old_state.cpt the system finds itself on 100000th step already and stops.</span></p>
<p><br></p>
<p><span class=rvts6>> OK. Presumably some more cunning choice of .mdp options would work,</span></p>
<p><span class=rvts6>> or using grompp, tbconv -extend and then mdrun.</span></p>
<p><br></p>
<p><span class=rvts9>>> > grompp -f new -t old_state.cpt -o newtpr</span></p>
<p><span class=rvts9>>> > mdrun -s newtpr</span></p>
<p><span class=rvts9>>> > will do what you want. Please report back if one or both work :-)</span></p>
<p><br></p>
<p><span class=rvts9>>> And the latter variant is working! More precisely I use</span></p>
<p><span class=rvts9>>> grompp -f new -t old_state.cpt -c oldtpr -o newtpr </span></p>
<p><span class=rvts9>>> mdrun_d -s newtpr</span></p>
<p><br></p>
<p>> Mark</p>
<p><br></p>
<p>But I have noted just now that using grompp with -t option results in some bug: after simulation right size of my cubic box (last line of input structure file)</p>
<p> 10.00000 10.00000 10.00000</p>
<p>changes in confout.gro to meaningless</p>
<p> 0.00000 0.00000 0.00000</p>
<p>To analyse the output properly (e.g. with g_rdf tool) I have to correct this line manually.</p>
<p>And I'm worried whether this bug effects to my simulation itself, during md integration of NVE ensemble in vacuum? </p>
<p><br></p>
<p><span class=rvts10>-- </span></p>
<p><span class=rvts10>Rerards,</span></p>
<p><span class=rvts10> Dmitri </span><a class=rvts11 href="mailto:ddubov@ngs.ru">mailto:ddubov@ngs.ru</a></p>
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