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 [email protected]
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 [EMAIL PROTECTED]
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
************************************************
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
