Hi Mark, Justin,<br> Thanks for your help. <br>The details are helpful to improve my MD simulation. Also i need update my gromacs version from 4.5.1 to 4.5.3.<br><br>Thanks again,<br>Rama<br><br><div class="gmail_quote">
On Thu, Jan 13, 2011 at 3:47 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
Ramachandran G wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
thanks for your reply.<br>
Still i have the same problem.<br>
My aim is to extend my simulation from 6ns to 7ns.<br>
<br>
First i prepared the tpr as<br>
<br>
grompp_mpi -f nve.mdp -c nve6-g.tpr -o nve7-g.tpr -n crom.ndx<br>
<br>
where 'nve6-g.tpr' is my old 'tpr' . In the 'nve.mdp' file i have changed the option of storing the 'nstxout' from 1 to 100.<br>
That is the only change i have done.<br>
<br>
For simulation i do,<br>
<br>
mpirun -nolocal -np 8 -machinefile machine mdrun_mpi -nice 0 -v -s nve7-g.tpr -o nve-g.trr -c nve-g.gro -e nve-g.edr -cpi nve6-g.cpt -g md-g.log -append -cpo nve7-g.cpt -pd<br>
<br>
From the gromacs website, <a href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations" target="_blank">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations</a><br>
i understood that i need to use the option of 'tpbconv' also to extend the simulation. It says that<br></div>
'If your |old.cpt| is for a run that has finished, then use |tpbconv -extend |after grompp <<a href="http://www.gromacs.org/grompp" target="_blank">http://www.gromacs.org/grompp</a>> and before mdrun <<a href="http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun" target="_blank">http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun</a>>.'<br>
<br>
<br>
</blockquote>
<br>
The easiest thing for you to do is to simply extend your run with tpbconv and ignore grompp. If you just need to reduce output volume, post-process the trajectory with trjconv. Otherwise, you have 6 ns of coordinates at every step, then 1 ns of coordinates every 100 steps. The frame interval mismatch will likely cause numerous Gromacs tools to fail, anyway.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
My 'mdp' options are:<br>
<br>
title = production-dynamics<br>
;warnings = 10<br>
cpp = /lib/cpp<br>
;DEFINE = -DPOSRES<br>
DEFINE = -DFLEXIBLE<br>
</blockquote>
<br></div>
Flexible water should not be used for MD.<br>
<br>
<a href="http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html</a><div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
constraints = none<br>
;constraint_algorithm = shake<br>
integrator = md<br>
dt = 0.0005 ;<br>
nsteps = 2000000 ;<br>
;nstcomm = 1 ; reset c.o.m motion<br>
nstlist = 10<br>
ns_type = grid<br>
nstenergy = 1 ; print energies<br>
nstlog = 1 ; print to logfile<br>
nstvout = 0 ; write velocities<br>
nstxout = 100 ; collect data in fs (write coords)<br>
;nstxtcout = 0 ; to print corrdinates to xtc trajectory<br>
energygrps = Protein CROM HOH1 HOH2 SOL<br>
nstfout = 0<br>
coulombtype = shift<br>
fourierspacing = 0.12<br>
pme_order = 4<br>
vdwtype = switch<br>
rvdw = 1.0<br>
rvdw_switch = 0.9<br>
rlist = 1.2<br>
rcoulomb = 1.0<br>
rcoulomb-switch = 0.9<br>
pbc = xyz<br>
;dispcorr = Ener<br>
continuation = yes<br>
;Berendsen temperature coupling is on<br>
Tcoupl = no ; temperature bath (yes, no)<br>
;tau_t = 0.1<br>
;tc-grps = system<br>
;ref_t = 300<br>
;Berendsen Pressure coupling is on<br>
pcoupl = no ; pressure bath (yes, no)<br>
;pcoupltype = isotropic<br>
;tau_p = 0.5<br>
;compressibility = 4.5e-05<br>
;ref_p = 1.0<br>
;Generate velocities is on at 300<br>
gen_vel = no ; generate initial velocities<br>
;gen_temp = 300.0 ; initial temperature<br>
;gen_seed = 173529 ; random seeD<br>
<br>
</blockquote>
<br></div></div>
You haven't set the tinit parameter in this file. In conjunction with the fact that this .mdp file is for 1 ns, it will start at time zero and run to 1 ns. If you're trying to pick up from the end of a 6-ns simulation, you have two options:<br>
<br>
1. Set tinit=6000 and leave nsteps and dt alone. Pass the .cpt file to the -t flag of grompp and run it as if it were a new simulation, then concatenate the output.<br>
<br>
2. Set tinit=0 and set nsteps=350000 to generate a complete 7-ns .tpr file. Pass this to mdrun in conjunction with your .cpt file from the end of your 6-ns run.<br>
<br>
3. Use tpbconv and ignore grompp entirely, then post-process appropriately.<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4" target="_blank">http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
Please help.<br>
thank you,<br>
Rama<br>
<br>
<br>
<br></div><div><div></div><div class="h5">
On Wed, Jan 12, 2011 at 3:06 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Ramachandran G wrote:<br>
<br>
Hi gmx-users,<br>
I tried extending one of simulation with modified mdp option.<br>
First i used the command,<br>
<br>
grompp -f new.mdp -c old.tpr -o new.tpr<br>
<br>
then i used the command to extend<br>
<br>
tpbconv -s new.tpr -extend timetoextendby -o next.tpr<br>
<br>
<br>
Then,<br>
<br>
mdrun -s next.tpr -cpi previous.cpt<br>
<br>
<br>
I surprised to see the following simulation output,<br>
WARNING: This run will generate roughly 2059394074917430016 Mb<br>
of data<br>
<br>
starting mdrun 'GROningen MAchine for Chemical Simulation in water'<br>
<br>
2000000 steps, infinite ps (continuing from step 12000000, 6000.0 ps).<br>
step 12000000 performance: 0.3 ns/day step 12000100<br>
performance: 0.8 ns/day step 12000200 performance: 0.8 ns/day<br>
step 12000300 performance: 0.8 ns/day step 12000400 performance: 0.8 ns/day step 12000500<br>
performance: 0.8 ns/day step 12000600 performance: 0.8 ns/day<br>
step 12000700 performance: 0.8 ns/day step 12000800<br>
performance: 0.8 ns/day step 12000900 performance: 0.8 ns/day step 12001000<br>
performance: 0.8 ns/day step 12001100 performance: 0.8 ns/day<br>
--------------------------------------------------<br>
Is this correct? Why it needs to generate that much huge Mb of data?<br>
<br>
I have extended for 1000.0ps but it shows 'infinite ps'.<br>
can anybody help me if there is error made in my procedure?<br>
<br>
<br>
It seems like you're trying to extend your run using both grompp and<br>
tpbconv, which is not correct. Use one or the other.<br>
<br>
If you want a real answer to this question, please post real<br>
commands, not just the generic format of what should be correct.<br>
Also possibly useful is the contents of the .mdp file you used.<br>
<br>
-Justin<br>
<br>
Thank you<br>
Rama<br>
<br>
<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at<br>
<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<div class="im"><br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
<br>
<br>
<br>
<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br><br clear="all"><br><br>