<br clear="all"><div>On Wed, Mar 14, 2012 at 7:40 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Today's Topics:<br>
<br>
1. Re: Importance of -rcon and -dd options when using mdrun with<br>
mpi. (Mark Abraham)<br>
2. clashes (Dariush Mohammadyani)<br>
3. Re: clashes (Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 14 Mar 2012 23:21:34 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Importance of -rcon and -dd options when<br>
using mdrun with mpi.<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F608D4E.10905@anu.edu.au">4F608D4E.10905@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 14/03/2012 9:54 PM, PAVAN PAYGHAN wrote:<br>
><br>
> Dear Gromacs Users,<br>
><br>
> I am running mdrun on single node with 8 CPU and getting following error<br>
><br>
> Fatal error:-<br>
><br>
> D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are<br>
> connected via constraints from the neighbouring cells.<br>
><br>
> This probably means your constraint length are too long compared to<br>
> the domain decomposition cell size.<br>
><br>
> Decrease the number of domain decomposition grid cells or lincs order.<br>
><br>
<br>
The .log file has a detailed analysis of how DD is setting things up.<br>
You need to make sure that this output is sensible for your system.<br>
<br>
You should also desist from using P-R pressure coupling during<br>
equilibration (i.e. with velocity generation), as warned in the manual<br>
section on pressure coupling. Perhaps your system is blowing up.<br>
<br>
Mark<br>
<br></blockquote><div> Dear Mark,</div><div><br></div><div>Thanks for the reply.</div><div> I have successfully done the equilibration run ,while doing production run I am gettiing above error (almost after 10 ns run).</div>
<div> Also It would be worth working if you explain the importance -rcon value and other things that I have asked .</div><div><br></div><div>Regards,</div><div><br></div><div>Pavan</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
> For solving this problem following are the attempts by me.<br>
><br>
> *1] Decreasing grid cell size:-*<br>
><br>
> As per the suggestion in error, I tried to decrease the grid cells by<br>
> option -dd from 8 1 1 to 6 1 1 , it has thrown following error..<br>
><br>
> Fatal error:-The size of the DD grid (6) does not match the number of<br>
> nodes(8).<br>
><br>
> Can you please suggest any better way to overcome this for decreasing<br>
> grid cell size.<br>
><br>
> *2] -rcon option:*<br>
><br>
> What is the correlation between the -rcon value with DD cell<br>
> size(Directly or inversely proportional ) , for the problem entitled<br>
> above what should be the strategy (to decrease or to increase rcon value).<br>
><br>
> If one changes the -rcon value will it affect the lincs accuracy, or<br>
> in other words the run will hold the same continuation or any change<br>
> in it.<br>
><br>
> For changing the -rcon value the reference of previous log file i.e.<br>
> Estimated maximum distance required for p-lincs say 0.877, so one can<br>
> increase than what has been estimated.<br>
><br>
> *3] lincs_order and lincs_iter :*<br>
><br>
> **<br>
><br>
> If we don't want to deteriorate the lincs accuracy (1+<br>
> lincs_iter)*lincs_order has to remain constant , In my case<br>
><br>
> With lincs_order = 4 and lincs_iter =1 I got above error. So I<br>
> decreased lincs _order (2) and increased lincs_iter(3) proportionally.<br>
> What I am following is right or I have misunderstood it. If so please<br>
> correct it. Can this value be fraction?<br>
><br>
> Values which I have tried are relevant or very bad?**<br>
><br>
> Please explain it.<br>
><br>
> If the same problem can be solved by any other methodology please<br>
> explain it.<br>
><br>
> *Please see the mdp file details.*<br>
><br>
><br>
> integrator = md<br>
><br>
> nsteps = 10000000<br>
><br>
> dt = 0.002 ; 2 fs<br>
><br>
> ; Output control<br>
><br>
> nstxout = 1000 ; save<br>
> coordinates every 2 ps<br>
><br>
> nstvout = 1000 ; save<br>
> velocities every 2 ps<br>
><br>
> nstxtcout = 1000 ; xtc compressed<br>
> trajectory output every 2 ps<br>
><br>
> nstenergy = 1000 ; save energies every 2 ps<br>
><br>
> nstlog = 1000 ; update log file<br>
> every 2 ps<br>
><br>
> ; Bond parameters<br>
><br>
> continuation = yes ; Restarting after NPT<br>
><br>
> constraint_algorithm = lincs ; holonomic constraints<br>
><br>
> constraints = all-bonds ; all bonds (even heavy atom-H<br>
> bonds)<br>
><br>
> lincs_iter = 1 ; accuracy of LINCS<br>
><br>
> lincs_order = 4<br>
><br>
> ; Neighborsearching<br>
><br>
> ns_type = grid<br>
><br>
> nstlist = 5<br>
><br>
> rlist = 1.2<br>
><br>
> rcoulomb = 1.2<br>
><br>
> rvdw = 1.2<br>
><br>
> ; Electrostatics<br>
><br>
> coulombtype = PME<br>
><br>
> pme_order = 4<br>
><br>
> fourierspacing = 0.16<br>
><br>
> ; Temperature coupling is on<br>
><br>
> tcoupl = Nose-Hoover<br>
><br>
> tc-grps = Protein P SOL_NA_CL ; three<br>
> coupling groups - more accurate<br>
><br>
> tau_t = 0.5 0.5 0.5<br>
><br>
> ref_t = 323 323 323<br>
><br>
> group, in K<br>
><br>
> ; Pressure coupling is on<br>
><br>
> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT<br>
><br>
> pcoupltype = semiisotropic ; uniform<br>
> scaling of x-y box vectors, independent z<br>
><br>
> tau_p = 2.0 ; time<br>
> constant, in ps<br>
><br>
> ref_p = 1.0 1.0 ; reference<br>
> pressure, x-y, z (in bar)<br>
><br>
> compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1<br>
><br>
> ; Periodic boundary conditions<br>
><br>
> pbc = xyz ; 3-D PBC<br>
><br>
> ; Dispersion correction<br>
><br>
> DispCorr = EnerPres ; account for cut-off vdW scheme<br>
><br>
> ; Velocity generation<br>
><br>
> gen_vel = yes<br>
><br>
> **<br>
><br>
> Pavan<br>
><br>
><br>
<br>
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<br>
Message: 2<br>
Date: Wed, 14 Mar 2012 10:03:31 -0400<br>
From: Dariush Mohammadyani <<a href="mailto:d.mohammadyani@gmail.com">d.mohammadyani@gmail.com</a>><br>
Subject: [gmx-users] clashes<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<CAAk3nxd6rq2Y2QD5be9sK+b=<a href="mailto:ay9Nb6Z%2B1Nc-UfSHPiMLMv7uRw@mail.gmail.com">ay9Nb6Z+1Nc-UfSHPiMLMv7uRw@mail.gmail.com</a>><br>
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<br>
Dear user,<br>
<br>
When I am using:<br>
genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro<br>
<br>
to add water in a coarse grained system, after running mdrun I am getting<br>
"Syntax error" and it shows maybe the distances are so close or there are<br>
some clashes.<br>
<br>
Do you know how can I figure it out?<br>
Or actually if we have some clashes in system how we can correct them?<br>
<br>
Thanks,<br>
Dariush Mohammadyani<br>
Department of Structural Biology<br>
University of Pittsburgh School of Medicine<br>
Biomedical Science Tower 3<br>
3501 Fifth Avenue<br>
Pittsburgh, PA 15261<br>
USA<br>
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<br>
Message: 3<br>
Date: Wed, 14 Mar 2012 10:08:49 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] clashes<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4F60A671.4030105@vt.edu">4F60A671.4030105@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Dariush Mohammadyani wrote:<br>
> Dear user,<br>
><br>
> When I am using:<br>
> genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro<br>
><br>
> to add water in a coarse grained system, after running mdrun I am<br>
> getting "Syntax error" and it shows maybe the distances are so close or<br>
> there are some clashes.<br>
><br>
<br>
I've never heard of mdrun throwing a syntax error. Can you please copy and<br>
paste the complete error message from your terminal?<br>
<br>
> Do you know how can I figure it out?<br>
> Or actually if we have some clashes in system how we can correct them?<br>
><br>
<br>
Better energy minimization typically solves bad atomic clashes.<br>
<br>
-Justin<br>
<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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a 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>
<br>
<br>
------------------------------<br>
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</font></span></blockquote></div><br>