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On 14/01/2011 10:27 AM, Ramachandran G wrote:
<blockquote
cite="mid:AANLkTinBBNFACCRjiqyqV2btnox7AV6Ep+SyGJV-+pcF@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
That should be sufficient. You can also try the wiki's suggestion of
grompp -t old.cpt.<br>
<br>
<blockquote
cite="mid:AANLkTinBBNFACCRjiqyqV2btnox7AV6Ep+SyGJV-+pcF@mail.gmail.com"
type="cite"><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 moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Extending_Simulations">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>
'If your <code>old.cpt</code> is for a run that has finished,
then use <code>tpbconv -extend </code>after <a
moz-do-not-send="true" title="grompp" rel="internal"
href="http://www.gromacs.org/grompp" class="new ">grompp</a> and
before <a moz-do-not-send="true" title="Documentation/Gromacs
Utilities/mdrun" rel="internal"
href="http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun">mdrun</a>.'
<br>
</blockquote>
<br>
I'd disagree with that last quoted statement, and have updated the
wiki accordingly.<br>
<br>
You need to tell us what GROMACS version you're using. There has
been at least one bug fixed in this area in my recent memory, so you
may do better with version 4.5.3.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:AANLkTinBBNFACCRjiqyqV2btnox7AV6Ep+SyGJV-+pcF@mail.gmail.com"
type="cite">
<br>
<br>
My 'mdp' options are:<br>
<br>
title = production-dynamics<br>
;warnings = 10<br>
cpp = /lib/cpp<br>
;DEFINE = -DPOSRES<br>
DEFINE = -DFLEXIBLE<br>
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>
<br>
Please help.<br>
thank you,<br>
Rama<br>
<br>
<br>
<br>
<div class="gmail_quote">On Wed, Jan 12, 2011 at 3:06 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
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;">
<div>
<div class="h5"><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;">
Hi gmx-users,<br>
I tried extending one of simulation with modified mdp
option.<br>
First i used the command,<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
grompp -f new.mdp -c old.tpr -o new.tpr<br>
</blockquote>
then i used the command to extend <br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
tpbconv -s new.tpr -extend timetoextendby -o next.tpr<br>
</blockquote>
<br>
Then,<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
mdrun -s next.tpr -cpi previous.cpt<br>
</blockquote>
<br>
I surprised to see the following simulation output,<br>
WARNING: This run will generate roughly
2059394074917430016 Mb 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
performance: 0.8 ns/day step 12000200 performance:
0.8 ns/day step 12000300 performance: 0.8 ns/day <br>
step 12000400 performance: 0.8 ns/day step 12000500
performance: 0.8 ns/day step 12000600 performance:
0.8 ns/day step 12000700 performance: 0.8 ns/day
step 12000800 performance: 0.8 ns/day <br>
step 12000900 performance: 0.8 ns/day step 12001000
performance: 0.8 ns/day step 12001100 performance:
0.8 ns/day
--------------------------------------------------<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>
</blockquote>
<br>
</div>
</div>
It seems like you're trying to extend your run using both
grompp and tpbconv, which is not correct. Use one or the
other.<br>
<br>
If you want a real answer to this question, please post real
commands, not just the generic format of what should be
correct. Also possibly useful is the contents of the .mdp
file you used.<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;">
Thank you<br>
Rama<br>
<br>
<br>
<br>
<br>
</blockquote>
<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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
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>
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