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On 20/10/2011 8:40 AM, Sapna Sarupria wrote:
<blockquote
cite="mid:CAMUW_Mks-oQYDB47ts-gEY2eA5Orm6P-q-1uhhwmM+Fy6nKS8Q@mail.gmail.com"
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>
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>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAMUW_Mks-oQYDB47ts-gEY2eA5Orm6P-q-1uhhwmM+Fy6nKS8Q@mail.gmail.com"
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
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>
<br>
</blockquote>
<br>
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