Juliette N. wrote:
sorry Justin to get back to you gain. This means I have to set zero
charges twice ( after grompp EM and grommp MD), since in grompp_md I am
using topology file which sets actual charges again to all atoms. Do
atoms charges affect EM configuration ?
Anything that affects the potential will affect the outcome of EM. Think about
what you're doing - EM seeks to find the potential energy minimum, which is
affected by charges according to whatever Coulombic scheme you've employed.
-Justin
Regards,
On 28 July 2011 17:44, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
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 <[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>> 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
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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