On Sat, 12 Jan 2008 15:04:40 +0530 (IST)
[EMAIL PROTECTED] wrote:
Hi All,
Myself Kinshuk from IIT-Bombay.I have gone through gromacs mailing list
there i came to know about you while searching the solution of the problem
while running minimization using .tpr in position restraints steps of MD
run.I have been performing simulation of guanidium ion & phosphate ion by
gromacs.
i hope i will be getting answer of my problem .
In my case no problem is coming while running the grompp, no warning is
coming. i could able to generate .tpr file without any error.
problem cames only while running the minimization using the .tpr file
For convenience, as mention earlier, following was the problem :
...................
#Warning: 1-4 interaction between 1 and 9 at distance 8.443 which is larger
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file#
The message gives you two possible solutions:
1) your system is exploding: which suggests that the starting structure
is somehow unrealistic and the minimization is not able to fix it. Check
you starting configuration, atoms 1 and 9 ...
2) increase the size of the table in the mdp file to be able to describe
the distances up to 8.443 nm. The way to do this is certainly described
in the manual. However this is a very large distance and the case 1) is
probably what is happening.
XAvier
I will be thankful if i'll be getting solution of this problem.
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
-----------------------------------------------------
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