Dear Itamar and Justin,<div><br></div><div>Thank you for your responses. I will make the changes to the mdp files and see how easy or hard it is to make the shift from 4.0.5 to 4.5. </div><div><br></div><div>Sincerely,</div>
<div>Sapna<br><br><div class="gmail_quote">On Tue, Oct 18, 2011 at 10:28 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
Itamar Kass wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Sapna,<br>
<br>
It is a good question, but such of personal preferences. I found out that my simulations tend to crash more often when I am using 4.5.5. It might be the General-reaction -field I use or something else, I am not sure. Also, it seems I will not gain much from upgrading, so I stick to 4.0.7.<br>
<br>
</blockquote>
<br></div>
The general instabilities result from tweaks to the handling of temperature and pressure coupling. Simply setting nsttcouple and nstpcouple to 1 during the initial equilibration seems to give stable systems.<br>
<br>
I'd say there are many reasons for upgrading. Tons of new features, bug fixes, etc. But then too, that's my personal preference ;)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
All this is not to say that 4.5.5 is not a good simulation package. It is a good and useful MD package, and I highly appreciate all the time and effort put into it.<br>
<br>
Best,<br>
Itamat<br>
<br>
PS, there are still people around using 3.3.3 or even 3.2.1, so I am not that behind. <br>
On 19/10/2011, at 1:14 PM, Sapna Sarupria wrote:<br>
<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Dear Itamar,<br>
<br>
Thank you for your response. Why did you prefer to stick to 4.0.7? Is there something particularly difficult to transfer from 4.0.7 version to 4.5 version?<br>
<br>
Sapna<br>
<br></div><div><div></div><div class="h5">
On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass <<a href="mailto:itamar.kass@monash.edu" target="_blank">itamar.kass@monash.edu</a> <mailto:<a href="mailto:itamar.kass@monash.edu" target="_blank">itamar.kass@monash.edu</a><u></u>>> wrote:<br>
<br>
Hi Sapna,<br>
<br>
I had the same problem few weeks ago.<br>
<br>
Apparently, some parameters are different (eg. nstpcouple).<br>
<br>
Cheers,<br>
Itamar<br>
<br>
PS I found out that I prefer to stick to 4.0.7.<br>
<br>
<br>
<br>
<br>
On 19/10/2011, at 12:08 PM, Sapna Sarupria wrote:<br>
<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div></div><div class="h5">
Dear All,<br>
<br>
I have a simulation set up for a mixture of carbon dioxide and<br>
water system which runs perfectly on Gromacs 4.0.5 version. I<br>
have run these simulations at different temperatures and<br>
pressures, from the same starting configuration and the<br>
simulation proceeds smoothly in the 4.0.5 version. However, when<br>
I use exactly the same files to run the simulation in 4.5.4<br>
version, the system crashes and writes out several pdb files. I<br>
was wondering if there is anything specific that has been changed<br>
between the two versions. I have pasted the mdp file of the<br>
simulations below. Any input will be much appreciated.<br>
<br>
MDP File <br>
title = 100% occupancy CO2 hydrate ; a string<br>
cpp = /lib/cpp ; c-preprocessor<br>
dt = 0.002 ; time step<br>
nsteps = 15000000 ; number of steps<br>
nstcomm = 10 ; reset c.o.m. motion<br>
nstxout = 0000 ; write coords<br>
nstvout = 0000 ; write velocities<br>
nstlog = 25000 ; print to logfile<br>
nstenergy = 500 ; print energies<br>
xtc_grps = OW_HW1_HW2_CO2 nstxtcout = 1000<br>
nstlist = 10 ; update pairlist<br>
ns_type = grid ; pairlist method<br>
coulombtype = PME<br>
rvdw = 1.2 ; cut-off for vdw<br>
rcoulomb = 1.2 ; cut-off for coulomb<br>
rlist = 1.2 ; cut-off<br>
for coulomb<br>
DispCorr = EnerPres<br>
Tcoupl = Nose-Hoover<br>
ref_t = 270 tc-grps = System<br>
tau_t = 0.5 Pcoupl = Parrinello-Rahman<br>
Pcoupltype = semiisotropic ; pressure geometry<br>
tau_p = 1.0 1.0 ; p-coupoling time<br>
compressibility = 4.5e-5 4.5e-5 ; compressibility<br>
ref_p = 30.5 30.5 ; ref pressure<br>
gen_vel = yes ; generate<br>
initial vel<br>
gen_temp = 260 ; initial<br>
temperature<br>
gen_seed = 372340 ; random seed<br>
constraint_algorithm = shake<br>
constraints = all-bonds <br>
-------<br>
<br>
<br>
Thank you,<br>
<br>
Sincerely,<br>
Sapna<br>
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<br>
==============================<u></u>=============<br>
| Itamar Kass, Ph.D.<br>
| Postdoctoral Research Fellow<br>
|<br>
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-----<br>
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut<br>
<br>
==============================<u></u>=============<br>
| Itamar Kass, Ph.D.<br>
| Postdoctoral Research Fellow<br>
|<br>
| Department of Biochemistry and Molecular Biology<br>
| Building 77 Clayton Campus<br>
| Wellington Road<br>
| Monash University,<br>
| Victoria 3800<br>
| Australia<br>
|<br>
| Tel: <a href="tel:%2B61%203%209902%209376" value="+61399029376" target="_blank">+61 3 9902 9376</a><br>
| Fax: <a href="tel:%2B61%203%209902%209500" value="+61399029500" target="_blank">+61 3 9902 9500</a><br></div>
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==============================<u></u>==============<br>
<br>
</blockquote>
<br>
-- <br>
==============================<u></u>==========<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> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<div><div></div><div class="h5"><br>
-- <br></div></div></blockquote></div>
</div>