On Fri, Jun 12, 2009 at 8:46 AM, Mark Abraham <[email protected]>wrote:
> Manik Mayur wrote: > >> Hi, >> >> The last mail supposedly bounced from the server due to attachments. So >> please excuse in case you find this as a repetition. >> >> I am trying to simulate a system where I want to exclude all nb >> interactions between frozen groups. So I followed the manual and defined >> them in energygrp_excl. But upon doing that it throws the following warning. >> >> WARNING 1 [file topol.top, line 1583]: >> Can not exclude the lattice Coulomb energy between energy groups >> >> What is the reason of the warning and should I be worried about it or >> safely ignore it. >> > > So, what algorithm are you using for your long-ranged electrostatic > interactions? Do you know roughly how it works? Does it then make sense to > try to exclude some of the long-range interactions? I am using PME. I honestly do not have much idea about its implementation details but I will definitely look into it. Here I was trying to remove all interactions between the frozen group so that I can speedup my simulation a little bit. Also since the atoms in the frozen group are uncharged, my basic concern was to remove even the LJ interaction calculation. Till now I have ignored the warning. So is it ok? > > Next, I am facing a strange problem with mdrun_mpi. If I run it on 4 nodes >> then it throws up the following error. Which I traced to md.log where I saw: >> >> There are: 15923 Atoms >> Charge group distribution at step 0: 0 3264 3185 0 (why these zeroes?) >> > > You have atoms that are not part of a charge group (or, probably, are part > of one of size one and charge zero. > In my topology file, All the atoms that I have defined within a molecule do belong to a charge group. Could you please elaborate on the second part of your statement? Grid: 3 x 4 x 5 cells >> >> However with 2 nodes it has and runs fine: >> >> There are: 15923 Atoms >> Charge group distribution at step 0: 3226 3223 >> Grid: 4 x 5 x 25 cells >> >> The error- >> > > No, that's the dump from MPI after the error. You need to consult both the > stdout and the .log file. > > Mark > > Making 1D domain decomposition 1 x 1 x 4 >> starting mdrun 'TransverseElectrode' >> 100000 steps, 200.0 ps. >> step 0 >> >> NOTE: Turning on dynamic load balancing >> >> [md-comp1:32374] *** Process received signal *** >> [md-comp1:32377] *** Process received signal *** >> [md-comp1:32377] Signal: Segmentation fault (11) >> [md-comp1:32377] Signal code: Address not mapped (1) >> [md-comp1:32377] Failing at address: (nil) >> [md-comp1:32374] Signal: Segmentation fault (11) >> [md-comp1:32374] Signal code: Address not mapped (1) >> [md-comp1:32374] Failing at address: (nil) >> [md-comp1:32377] [ 0] [0xb7fd8440] >> [md-comp1:32374] [ 0] [0xb7ef0440] >> [md-comp1:32374] *** End of error message *** >> [md-comp1:32377] *** End of error message *** >> >> I would be extremely thankful, if somebody points me to the source of the >> error and the workaround. >> >> Thanks, >> >> Manik Mayur >> Graduate student >> Microfluidics Lab >> Dept. of Mechanical Engg. >> IIT Kharagpur >> INDIA >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA
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