Moeed wrote:
Dear Justin,
1- Could you please check if I have grouped atoms properly? Lastly, I
could generate the tpr file for PR step. Since I am getting segmentation
fault in the next step I though maybe there is sth wring with charge
groups..
I don't know how your labeling is set up. If your CH3 and CH2 groups are all
your charge groups, then you should be fine. In fact, this is what grompp
suggested in the note. You can get a sense of what might be appropriate by
looking at your force field's .rtp file and looking at the functional groups.
However, I have a funda,mental question. I am to compute interaction
parameters for ternary system of hexane/polyethylene/ethylene. Sofar I
have only hexane as solvent, later polyethylene and ethylene will be
added. My questions is for this apolar system, do I need to worry about
electrostatic interactions between atoms? I mean could I skip buildig
charge groups if I am interested in cacluation of interaction parameters
BETWEEN hexane, polyethylene and ethylene?
Your atoms have partial charges, do they not? Then you certainly need to
consider proper electrostatics treatment.
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 opls_157 1 HEX C1 1 -0.18 12.011 ;
qtot -0.18
2 opls_158 1 HEX C2 2 -0.12 12.011 ;
qtot -0.3
3 opls_158 1 HEX C3 3 -0.12 12.011 ;
qtot -0.42
4 opls_158 1 HEX C4 4 -0.12 12.011 ;
qtot -0.54
5 opls_158 1 HEX C5 5 -0.12 12.011 ;
qtot -0.66
6 opls_157 1 HEX C6 6 -0.18 12.011 ;
qtot -0.84
7 opls_140 1 HEX H1 1 0.06 1.008 ;
qtot -0.78
8 opls_140 1 HEX H2 1 0.06 1.008 ;
qtot -0.72
9 opls_140 1 HEX H3 1 0.06 1.008 ;
qtot -0.66
10 opls_140 1 HEX H4 2 0.06 1.008 ;
qtot -0.6
11 opls_140 1 HEX H5 2 0.06 1.008 ;
qtot -0.54
12 opls_140 1 HEX H6 3 0.06 1.008 ;
qtot -0.48
13 opls_140 1 HEX H7 3 0.06 1.008 ;
qtot -0.42
14 opls_140 1 HEX H8 4 0.06 1.008 ;
qtot -0.36
15 opls_140 1 HEX H9 4 0.06 1.008 ;
qtot -0.3
16 opls_140 1 HEX H10 5 0.06 1.008 ;
qtot -0.24
17 opls_140 1 HEX H11 5 0.06 1.008 ;
qtot -0.18
18 opls_140 1 HEX H12 6 0.06 1.008 ;
qtot -0.12
19 opls_140 1 HEX H13 6 0.06 1.008 ;
qtot -0.06
20 opls_140 1 HEX H14 6 0.06 1.008 ;
qtot 0
2- I tried to run the position restrained simulation. VERSION 4.0.7
with "mdrun -s Hexane_pr.tpr -o Hexane_pr.tpr -c Hexane_b4md -v >&
output.mdrun_pr". After a few seconds I get segmentation fault error. I
did a thorough search on mailing list and found a smilar situation where
Mr. MArck Abraham introduced
http://oldwiki.gromacs.org/index.php/blowing_=up but link is not
working. Do I need to change the constraint algorithm? Could you please
tell me why I am getting segmentation error? Does it have to do with
kinetic energy?
Did you do energy minimization? Usually instabilities like this arise because
either the system is energetically unstable due to atomic clashes, or something
about the underlying model physics is broken. You haven't mentioned how you
built your system or if you energy minimized it, so I assume that you simply
haven't resolved the clashes in your system.
<snip>
define = -DPOSRES
If your system is just a box of hexane, restraining anything doesn't make sense
to me. One usually employs position restraints on a solute (like a protein) to
relax the solvent (usually water) around it. If you're trying to equilibrate a
hexane system, you're just wasting your time by restraining any or all of the
molecules.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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