On Wed, Mar 14, 2012 at 7:40 PM, <[email protected]> wrote:
> Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: Importance of -rcon and -dd options when using mdrun with > mpi. (Mark Abraham) > 2. clashes (Dariush Mohammadyani) > 3. Re: clashes (Justin A. Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 14 Mar 2012 23:21:34 +1100 > From: Mark Abraham <[email protected]> > Subject: Re: [gmx-users] Importance of -rcon and -dd options when > using mdrun with mpi. > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > On 14/03/2012 9:54 PM, PAVAN PAYGHAN wrote: > > > > Dear Gromacs Users, > > > > I am running mdrun on single node with 8 CPU and getting following error > > > > Fatal error:- > > > > D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are > > connected via constraints from the neighbouring cells. > > > > This probably means your constraint length are too long compared to > > the domain decomposition cell size. > > > > Decrease the number of domain decomposition grid cells or lincs order. > > > > The .log file has a detailed analysis of how DD is setting things up. > You need to make sure that this output is sensible for your system. > > You should also desist from using P-R pressure coupling during > equilibration (i.e. with velocity generation), as warned in the manual > section on pressure coupling. Perhaps your system is blowing up. > > Mark > > Dear Mark, Thanks for the reply. I have successfully done the equilibration run ,while doing production run I am gettiing above error (almost after 10 ns run). Also It would be worth working if you explain the importance -rcon value and other things that I have asked . Regards, Pavan > > For solving this problem following are the attempts by me. > > > > *1] Decreasing grid cell size:-* > > > > As per the suggestion in error, I tried to decrease the grid cells by > > option -dd from 8 1 1 to 6 1 1 , it has thrown following error.. > > > > Fatal error:-The size of the DD grid (6) does not match the number of > > nodes(8). > > > > Can you please suggest any better way to overcome this for decreasing > > grid cell size. > > > > *2] -rcon option:* > > > > What is the correlation between the -rcon value with DD cell > > size(Directly or inversely proportional ) , for the problem entitled > > above what should be the strategy (to decrease or to increase rcon > value). > > > > If one changes the -rcon value will it affect the lincs accuracy, or > > in other words the run will hold the same continuation or any change > > in it. > > > > For changing the -rcon value the reference of previous log file i.e. > > Estimated maximum distance required for p-lincs say 0.877, so one can > > increase than what has been estimated. > > > > *3] lincs_order and lincs_iter :* > > > > ** > > > > If we don't want to deteriorate the lincs accuracy (1+ > > lincs_iter)*lincs_order has to remain constant , In my case > > > > With lincs_order = 4 and lincs_iter =1 I got above error. So I > > decreased lincs _order (2) and increased lincs_iter(3) proportionally. > > What I am following is right or I have misunderstood it. If so please > > correct it. Can this value be fraction? > > > > Values which I have tried are relevant or very bad?** > > > > Please explain it. > > > > If the same problem can be solved by any other methodology please > > explain it. > > > > *Please see the mdp file details.* > > > > > > integrator = md > > > > nsteps = 10000000 > > > > dt = 0.002 ; 2 fs > > > > ; Output control > > > > nstxout = 1000 ; save > > coordinates every 2 ps > > > > nstvout = 1000 ; save > > velocities every 2 ps > > > > nstxtcout = 1000 ; xtc compressed > > trajectory output every 2 ps > > > > nstenergy = 1000 ; save energies every 2 ps > > > > nstlog = 1000 ; update log file > > every 2 ps > > > > ; Bond parameters > > > > continuation = yes ; Restarting after NPT > > > > constraint_algorithm = lincs ; holonomic constraints > > > > constraints = all-bonds ; all bonds (even heavy atom-H > > bonds) > > > > lincs_iter = 1 ; accuracy of LINCS > > > > lincs_order = 4 > > > > ; Neighborsearching > > > > ns_type = grid > > > > nstlist = 5 > > > > rlist = 1.2 > > > > rcoulomb = 1.2 > > > > rvdw = 1.2 > > > > ; Electrostatics > > > > coulombtype = PME > > > > pme_order = 4 > > > > fourierspacing = 0.16 > > > > ; Temperature coupling is on > > > > tcoupl = Nose-Hoover > > > > tc-grps = Protein P SOL_NA_CL ; three > > coupling groups - more accurate > > > > tau_t = 0.5 0.5 0.5 > > > > ref_t = 323 323 323 > > > > group, in K > > > > ; Pressure coupling is on > > > > pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT > > > > pcoupltype = semiisotropic ; uniform > > scaling of x-y box vectors, independent z > > > > tau_p = 2.0 ; time > > constant, in ps > > > > ref_p = 1.0 1.0 ; reference > > pressure, x-y, z (in bar) > > > > compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, > bar^-1 > > > > ; Periodic boundary conditions > > > > pbc = xyz ; 3-D PBC > > > > ; Dispersion correction > > > > DispCorr = EnerPres ; account for cut-off vdW scheme > > > > ; Velocity generation > > > > gen_vel = yes > > > > ** > > > > Pavan > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120314/64be9330/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Wed, 14 Mar 2012 10:03:31 -0400 > From: Dariush Mohammadyani <[email protected]> > Subject: [gmx-users] clashes > To: [email protected] > Message-ID: > <CAAk3nxd6rq2Y2QD5be9sK+b=ay9nb6z+1nc-ufshpimlmv7...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear user, > > When I am using: > genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro > > to add water in a coarse grained system, after running mdrun I am getting > "Syntax error" and it shows maybe the distances are so close or there are > some clashes. > > Do you know how can I figure it out? > Or actually if we have some clashes in system how we can correct them? > > Thanks, > Dariush Mohammadyani > Department of Structural Biology > University of Pittsburgh School of Medicine > Biomedical Science Tower 3 > 3501 Fifth Avenue > Pittsburgh, PA 15261 > USA > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120314/4d8dafec/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Wed, 14 Mar 2012 10:08:49 -0400 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] clashes > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Dariush Mohammadyani wrote: > > Dear user, > > > > When I am using: > > genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro > > > > to add water in a coarse grained system, after running mdrun I am > > getting "Syntax error" and it shows maybe the distances are so close or > > there are some clashes. > > > > I've never heard of mdrun throwing a syntax error. Can you please copy and > paste the complete error message from your terminal? > > > Do you know how can I figure it out? > > Or actually if we have some clashes in system how we can correct them? > > > > Better energy minimization typically solves bad atomic clashes. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 95, Issue 92 > ***************************************** >
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