Hello,<div><br></div><div>I did change nsttcouple and nstpcouple but the simulations that run in 4.0.5 are still crashing in 4.5.4. I think it is related to constraints but I am unable to figure out exactly what is different. I have pasted both my topology and mdp (updated for 4.5.4) files. Any ideas? I have read through the manual and it seems like the mdp files does not need any changes, but perhaps I am missing something.</div>
<div><br></div><div>Thank you for your help!</div><div><br></div><div>Sincerely,</div><div>Sapna</div><div><br></div><div>@@@@ MDP File @@@@</div><div><div>title = 100% occupancy CO2 hydrate ; a string</div>
<div>cpp = /lib/cpp ; c-preprocessor</div><div>integrator = md</div><div>dt = 0.002 ; time step</div><div>nsteps = 15000000 ; number of steps</div>
<div>nstcomm = 10 ; reset c.o.m. motion</div><div>nstxout = 0000 ; write coords</div><div>nstvout = 0000 ; write velocities</div><div>
nstlog = 25000 ; print to logfile</div><div>nstenergy = 500 ; print energies</div><div>xtc_grps = OW_HW1_HW2_CO2 </div><div>nstxtcout = 1000</div>
<div>nstlist = 10 ; update pairlist</div><div>ns_type = grid ; pairlist method</div><div>coulombtype = PME</div><div>rvdw = 1.2 ; cut-off for vdw</div>
<div>rcoulomb = 1.2 ; cut-off for coulomb</div><div>rlist = 1.2 ; cut-off for coulomb</div><div>DispCorr = EnerPres</div><div>Tcoupl = Nose-Hoover</div>
<div>ref_t = 270 </div><div>tc-grps = System</div><div>tau_t = 0.5 </div><div>nsttcouple = 1</div><div>Pcoupl = Parrinello-Rahman</div><div>Pcoupltype = semiisotropic ; pressure geometry</div>
<div>tau_p = 1.0 1.0 ; p-coupoling time</div><div>compressibility = 4.5e-5 4.5e-5 ; compressibility</div><div>ref_p = 30.5 30.5 ; ref pressure</div>
<div>nstpcouple = 1</div><div>gen_vel = yes ; generate initial vel</div><div>gen_temp = 260 ; initial temperature</div><div>gen_seed = 372340 ; random seed</div>
<div>constraint_algorithm = shake</div><div>constraints = all-bonds </div></div><div>@@@@ end MDP File @@@@</div><div><br></div><div>@@@@ Topology file @@@@</div><div><br></div><div><div>[ defaults ]</div><div>; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ</div>
<div> 1 2 no 1.0 1.0</div><div><br></div><div>[ atomtypes ]</div><div>; name mass charge ptype sigma epsilon</div><div>; Water parameters are those of Vega TIP4P/Ice Model</div>
<div> OWT4 15.9994 0.0000 A 0.31668 0.882164429</div><div> HW 1.008 0.5897 A 0.000 0.000</div><div> MW 0.000 -1.1794 V 0.000 0.000</div>
<div><br></div><div><br></div><div>; TraPPE rigid</div><div> M2 22.0000 0.00 A 0.000 0.000000 ; </div><div> M1 22.0000 0.00 A 0.000 0.000000 ; </div><div> DO 00.0000 -0.35 V 0.305 0.656806 ; oxygen</div>
<div> DC 00.0000 0.70 V <span class="Apple-tab-span" style="white-space:pre"> </span> 0.280 0.224478 ; carbon</div><div><br></div><div><br></div><div>[ moleculetype ]</div><div>; molname nrexcl</div>
<div> SOL 2</div><div><br></div><div>[ atoms ]</div><div>1 OWT4 1 SOL OW 1 0.0000</div><div>2 HW 1 SOL HW1 1 0.5897</div><div>3 HW 1 SOL HW2 1 0.5897</div>
<div>4 MW 1 SOL MW 1 -1.1794</div><div><br></div><div>[ bonds ]</div><div>; i<span class="Apple-tab-span" style="white-space:pre"> </span>j<span class="Apple-tab-span" style="white-space:pre"> </span>funct<span class="Apple-tab-span" style="white-space:pre"> </span>length<span class="Apple-tab-span" style="white-space:pre"> </span>force.c.</div>
<div>1<span class="Apple-tab-span" style="white-space:pre"> </span>2<span class="Apple-tab-span" style="white-space:pre"> </span> 1<span class="Apple-tab-span" style="white-space:pre"> </span> 0.09572 502416.0 </div>
<div>1<span class="Apple-tab-span" style="white-space:pre"> </span>3<span class="Apple-tab-span" style="white-space:pre"> </span> 1 0.09572 502416.0 </div><div>2 3 1 0.15139 502416.0 </div>
<div><br></div><div>[ exclusions ]</div><div>1 2 3 4</div><div>2 1 3 4</div><div>3 1 2 4</div><div>4 1 2 3</div><div><br></div><div>; The position of the dummy is computed as follows:</div>
<div>;</div><div>;<span class="Apple-tab-span" style="white-space:pre"> </span>O</div><div>; <span class="Apple-tab-span" style="white-space:pre"> </span> </div><div>;<span class="Apple-tab-span" style="white-space:pre"> </span> <span class="Apple-tab-span" style="white-space:pre"> </span>D</div>
<div>;<span class="Apple-tab-span" style="white-space:pre"> </span> </div><div>;<span class="Apple-tab-span" style="white-space:pre"> </span>H<span class="Apple-tab-span" style="white-space:pre"> </span>H</div><div>;</div>
<div>; const = distance (OD) / [ cos (angle(DOH)) <span class="Apple-tab-span" style="white-space:pre"> </span>* distance (OH) ]</div><div>;<span class="Apple-tab-span" style="white-space:pre"> </span> 0.01577 nm<span class="Apple-tab-span" style="white-space:pre"> </span>/ [ cos (52.26 deg)<span class="Apple-tab-span" style="white-space:pre"> </span>* 0.09572 nm<span class="Apple-tab-span" style="white-space:pre"> </span>]</div>
<div><br></div><div>; Dummy pos x4 = x1 + a*(x2-x1) + b*(x3-x1)</div><div><br></div><div>[ virtual_sites3 ]</div><div>; Dummy from<span class="Apple-tab-span" style="white-space:pre"> </span>funct<span class="Apple-tab-span" style="white-space:pre"> </span>a<span class="Apple-tab-span" style="white-space:pre"> </span>b</div>
<div>4<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>2<span class="Apple-tab-span" style="white-space:pre"> </span>3<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>0.13458335087 0.13458335087</div>
<div><br></div><div>[ moleculetype ]</div><div>; molname nrexcl</div><div> TIP 2</div><div><br></div><div>[ atoms ]</div><div>1 OWT4 1 TIP OW 1 0.0000</div><div>2 HW 1 TIP HW1 1 0.5897</div>
<div>3 HW 1 TIP HW2 1 0.5897</div><div>4 MW 1 TIP MW 1 -1.1794</div><div><br></div><div>[ bonds ]</div><div>; i<span class="Apple-tab-span" style="white-space:pre"> </span>j<span class="Apple-tab-span" style="white-space:pre"> </span>funct<span class="Apple-tab-span" style="white-space:pre"> </span>length<span class="Apple-tab-span" style="white-space:pre"> </span>force.c.</div>
<div>1<span class="Apple-tab-span" style="white-space:pre"> </span>2<span class="Apple-tab-span" style="white-space:pre"> </span> 1<span class="Apple-tab-span" style="white-space:pre"> </span> 0.09572 502416.0 </div>
<div>1<span class="Apple-tab-span" style="white-space:pre"> </span>3<span class="Apple-tab-span" style="white-space:pre"> </span> 1 0.09572 502416.0 </div><div>2 3 1 0.15139 502416.0 </div>
<div><br></div><div>[ exclusions ]</div><div>1 2 3 4</div><div>2 1 3 4</div><div>3 1 2 4</div><div>4 1 2 3</div><div><br></div><div>[ virtual_sites3 ]</div><div>; Dummy from<span class="Apple-tab-span" style="white-space:pre"> </span>funct<span class="Apple-tab-span" style="white-space:pre"> </span>a<span class="Apple-tab-span" style="white-space:pre"> </span>b</div>
<div>4<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>2<span class="Apple-tab-span" style="white-space:pre"> </span>3<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>0.13458335087 0.13458335087</div>
<div><br></div><div><br></div><div>[ moleculetype ]</div><div>; molname nrexcl</div><div> CO2 2</div><div><br></div><div>[ atoms ]</div><div>1 M1 1 CO2 M1 1 0.00 22.00</div><div>
2 M2 1 CO2 M2 1 0.00 22.00</div><div>3 DC 1 CO2 CO 1 0.70 0.000</div><div>4 DO 1 CO2 OC1 1 -0.35 0.000</div>
<div>
5 DO 1 CO2 OC2 1 -0.35 0.000</div><div><br></div><div><br></div><div>[ constraints ]</div><div>1 2 1 0.19785026</div><div><br></div><div><br></div><div>[ virtual_sites2 ]</div>
<div>; ai aj ak funct a</div><div> 3 1 2 1 0.50</div><div> 4 1 2 1 -0.086327900</div><div> 5 1 2 1 1.086327913 </div><div><br></div><div>[ exclusions ]</div>
<div>3 4 5</div><div>4 5 3</div><div>5 4 3</div><div><br></div><div>[ system ]</div><div>Hydrate with cages filled with carbon dioxide</div><div><br></div><div>[ molecules ]</div><div>
SOL 2944</div>
<div>CO2 512</div><div>TIP 3641</div></div><div><br></div><div>@@@@ End topology file @@@@</div><div><br></div><div><br></div><div><br><br><div class="gmail_quote">On Wed, Oct 19, 2011 at 7:17 AM, Sapna Sarupria <span dir="ltr"><<a href="mailto:sapna.sarupria@gmail.com">sapna.sarupria@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">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<div><div></div><div class="h5"><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" target="_blank">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><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>
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>
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>
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>
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>
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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>
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</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>
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<br>
==============================<u></u>==========<div><div></div><div><br>
-- <br></div></div></blockquote></div>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Sapna Sarupria<br>Post-doctoral Researcher<br>Princeton University<br>New Jersey 08540<br>U.S.A.<br><br>Life isn't about finding yourself. Life is about creating yourself. -- George Bernard Shaw. <br>
Dare to Dream<br>
</div>