[gmx-users] Re: Issues regarding exclusions and Charge group distribution

[Manik Mayur]

On Fri, Jun 12, 2009 at 8:46 AM, Mark Abraham <Mark.Abraham at anu.edu.au>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    gmx-users at gromacs.org
>> 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 gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090612/60b6d428/attachment.html>