Juliette N. wrote:
Hello Justin,
I am using tpbconv to set zero charges after em and after doing grompp_md.
grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr
tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq
mdrun -s *-ZERO_md -o -c -e -x -v
Do I need to use tpbconv after grompp_em? (before mdrun_em)
If you want to do energy minimization with zero charges, then yes.
-Justin
Regards,
On 28 July 2011 14:53, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Juliette N. wrote:
Hi again,
I am wondering if using tpbconv to set zero charges (case 1)
works similar to when one sets zero atom charges in topology
file from the very beginning (case 2). Do these two cases work
similarly?
They should work identically.
I checked tpr file and I see that charges are set to zero.
Can you please tell me what these lines mean?
Does it refer to exclusion which is set to 3 in top file?
Yes.
excls[0][0..10]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10}
excls[1][11..18]={0, 1, 2, 3, 4, 5, 6, 7}
The number of these lines corresponds to atom numbers in the system.
They refer to the atom indices of the atoms in the [moleculetype],
not the consecutive numbering of the system (for the first molecule
this will be the same, but I thought I'd point that out).
-Justin
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==============================__==========
Justin A. Lemkul
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ICTAS Doctoral Scholar
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Virginia Tech
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Thanks,
J. N.
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========================================
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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