[gmx-users] Warnings while grompp_d

[Jochen Hub]

vivek sharma wrote:
> Hi there,
> while running gromacs in parallel with double precision, during 
> grompp_d I am getting following warning in output file along with 
> other status..
>
>
> ...
> ...
> ...
> WARNING 1 [file 1XU9_A.top, line unknown]:
>   The largest charge group contains 12 atoms.
>   Since atoms only see each other when the centers of geometry of the 
> charge
>   groups they belong to are within the cut-off distance, too large charge
>   groups can lead to serious cut-off artifacts.
>   For efficiency and accuracy, charge group should consist of a few atoms.
>   For all-atom force fields use: CH3, CH2, CH, NH2 NH, OH, CO2, CO, etc.
Just what it says, you have a large charge group which may cause 
artifacts. Check the [ atoms ] section in your topology, there is a 
charge goup column. (And have a look at Chapter 5 of the manual.) If you 
generated the topology with pdb2gmx, check the appropriate rtp-file.

> ...
> ...
> ...
> ...
> ...
> WARNING 2 [file aminoacids.dat, line 1]:
>   T-Coupling group protein has fewer than 10% of the atoms (2626 out of
>   45599)
If you couple too few atoms to a thermostat you get artifacts. Use 
larger tc-groups.

Best,
Jochen

>   Maybe you want to try Protein and Non-Protein instead?
> WARNING 3 [file aminoacids.dat, line 1]:
>   T-Coupling group NDP has fewer than 10% of the atoms (61 out of 45599)
>   Maybe you want to try Protein and Non-Protein instead?
> ......
> .
> .
> .
> .
> .
> What these warnings indicates and how can they be rectified ?
>
> just a guess, Is there any relation with tau_t mentioned in .mdp file 
> corresponding to protein and NDP i.e. 0.1 (for warning 2 and 3)
> if it is, then how can we reduce the number of sol atoms i.e. very 
> high 43000(approx).
>
> Any idea of this would be of great help.
>
> With Thanks,
> Vivek
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.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


-- 
************************************************
Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
************************************************