Hi Itamar and Mark, <div><br></div><div>The error message is pasted below. I tried both running minimization and then running the MD; and using a configuration from a previous simulation (that was run using Gromacs 4.0.5). In both these case the simulations are crashing. The error message is similar. </div>
<div><br></div><div>Mark, Yes there is no reason as such to have TIP and SOL defined but it is for the purpose of my simulations. It helps me differentiate between water phases at the beginning of the simulation (SOL is in solid and TIP is in liquid phase). Indeed, they are exactly the same, as they are supposed to be. </div>
<div><br></div><div>I also tried using the Berendsen coupling for both temperature and pressure, but the simulations still crash. Like I mentioned, all of these simulations work perfectly in 4.0.5 Gromacs version with Nose-Hoover and PR starting from the exact same configuration (except initial velocity) that I am using in 4.5 version. </div>
<div><br></div><div>Thank you all for your suggestions and help.</div><div><br></div><div>Sapna.</div><div><br></div><div>@@@@ Error Message from Gromacs @@@@</div><div><br></div><div><div>starting mdrun 'Hydrate with cages filled with carbon dioxide'</div>
<div>15000000 steps, 30000.0 ps.</div><div>step 0Inner product between old and new vector <= 0.0!</div><div>constraint #1 atoms 25869 and 25871</div><div>Wrote pdb files with previous and current coordinates</div><div>
Inner product between old and new vector <= 0.0!</div><div>constraint #1 atoms 145 and 147</div><div>Wrote pdb files with previous and current coordinates</div><div>Segmentation fault</div></div><div><br></div><div>@@@@@</div>
<div><br></div><div><br></div><br><div class="gmail_quote">On Wed, Oct 19, 2011 at 6:19 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 20/10/2011 8:40 AM, Sapna Sarupria wrote:
<blockquote type="cite">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>
</blockquote>
<br></div>
P-R P-coupling is not well-suited to equilibration if you are not
close to equilibrium. Since you are generating velocities, you are
likely not close to equilibrium.<br>
<br>
I don't see that it is causing a problem, but there is no reason to
have both SOL and TIP molecule type. They're identical.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
<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 style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>j<span style="white-space:pre-wrap"> </span>funct<span style="white-space:pre-wrap"> </span>length<span style="white-space:pre-wrap"> </span>force.c.</div>
<div>1<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span> 1<span style="white-space:pre-wrap"> </span>
0.09572 502416.0 </div>
<div>1<span style="white-space:pre-wrap"> </span>3<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>O</div>
<div>; <span style="white-space:pre-wrap"> </span>
</div>
<div>;<span style="white-space:pre-wrap"> </span>
<span style="white-space:pre-wrap"> </span>D</div>
<div>;<span style="white-space:pre-wrap"> </span>
</div>
<div>;<span style="white-space:pre-wrap"> </span>H<span style="white-space:pre-wrap"> </span>H</div>
<div>;</div>
<div>; const = distance (OD) / [ cos (angle(DOH)) <span style="white-space:pre-wrap"> </span>*
distance (OH) ]</div>
<div>;<span style="white-space:pre-wrap"> </span>
0.01577 nm<span style="white-space:pre-wrap"> </span>/ [ cos (52.26 deg)<span style="white-space:pre-wrap"> </span>*
0.09572 nm<span style="white-space:pre-wrap">
</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 style="white-space:pre-wrap"> </span>funct<span style="white-space:pre-wrap"> </span>a<span style="white-space:pre-wrap"> </span>b</div>
<div>4<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>3<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>j<span style="white-space:pre-wrap"> </span>funct<span style="white-space:pre-wrap"> </span>length<span style="white-space:pre-wrap"> </span>force.c.</div>
<div>1<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span> 1<span style="white-space:pre-wrap"> </span>
0.09572 502416.0 </div>
<div>1<span style="white-space:pre-wrap"> </span>3<span style="white-space:pre-wrap"> </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 style="white-space:pre-wrap"> </span>funct<span style="white-space:pre-wrap"> </span>a<span style="white-space:pre-wrap"> </span>b</div>
<div>4<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>3<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </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>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></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>