On 2/15/15 9:29 AM, nazli kashani javid wrote:
thank you
so I have to run different times !?
For any given simulation, you just use mdrun -rerun as many times as needed,
with whatever groups are of interest. Interaction energies are just
post-processing measures, really. They can be specified during the run or after
the fact.
-Justin
On Sun, Feb 15, 2015 at 5:46 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/15/15 9:12 AM, nazli kashani javid wrote:
Thank you very much.
what do you mean of " multiple energy evaluations " ?
do you mean I should change my .mdp file like this:
energygrps = chaina chainb chainc chaind
is it ok?
This will give you nonbonded energy decomposition of:
A-B
A-C
A-D
B-C
B-D
C-D
e.g. all possible (non-redundant) combinations of individual chains.
if I want to calculate interaction energy between ac and bd chains, what
should I do?
Then you need groups that are chains AC and chains BD in two groups.
-Justin
could you help me with more details about .mdp and .ndx files?
On Sun, Feb 15, 2015 at 5:23 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/15/15 8:51 AM, nazli kashani javid wrote:
Hi all
I want to calculate interaction energy of my protein that includes 4
individual chains(a,b,c and d). at first I define an index file. It
contains:
[ chaina ]
1 2 3 4 ...454
[ chainb ]
455 456 457 ...919
[ chainc ]
920 921 922 .... 1373
[ chaind ]
1374 1375 1376 ....1838
[ chainsab ]
1 2 3....919
[ chainsac ]
1 2 3 ...454 920....1373
[ chainsad ]
......
[ chainsbc ]
.....
[ chainsbd ]
..........
[ chainscd ]
........
[ chainsabc]
1 2 3 .... 1373
[ chainsacd ]
1 2 3 .....454 920 ...1838
[ chainsabd ]
......
[ chainsbcd ]
........
I add these groups to .mdp file as following:
energygrps = chaina chainb chainc chaind chainsab chainsac chainsad
chainsbc chainsbd chainscd chainsabc chainsacd chainsabd chainsbcd
when I use grompp command ( grompp -f md.mdp -c npt.gro -p topol.top -n
chains.ndx -o mda.tpr) , and face with this error :
Fatal error:
Atom 1 in multiple Energy Mon. groups (1 and 5)
For more information and tips for troubleshooting, please check the
GROMACS
dose my index file need any modifications? is there any wrong with my
mdp
file?
how could I solve my problem?
You can't have overlapping groups. You'll have to do multiple energy
evaluations to achieve what you want.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
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Support/Mailing_Lists/GMX-Users_List before posting!
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* For (un)subscribe requests visit
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send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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