On 7/6/17 8:42 AM, Hermann, Johannes wrote:
Dear Justin,
I think you were referring to amitabhjayas...@gmail.com Mails, right? You posted
the link as answer to his question but now my object is in the object line.
Yes, because it was important to correct the record and because failing to
change the subject and replying to the whole digest is incorrect list etiquette.
However, I am still looking for an answer to my question.
Is there anyone, who can tell me something about my dual topology of my MG ions
or point me to some literature? I really did my google search before...
Your approach is fine.
-Justin
I will highly appreciate it!
Thanks!
Johannes
-----------------------
This was my orginal message:
Dear all,
I am doing a FEC via alchemical transformation. In order to keep the charge
constant I plan to mutate ions at the same time. In particular, I want to change
the charge of MG ions. My question is did I manipulate the .top .itp and .gro
file in the right way:
In the topology.top file I added:
#include "topol_MG_Hybrid.itp"
in the beginning and included in the [molecules] section
MG_HBRID 26
at the place where my hybrid MGs begin in the .gro file. In the .tip file I
defined the new moleculetype and the atom:
[ moleculetype ]
; Name nrexcl
MG_HBRID 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB
massB
1 MG 1 MGX MGHBR 1 2 24.305 MG
2.30769 24.305
In the gro file I changed the (formaly regular) MGs to:
8702MGX MGHBR55183 -1.480 0.077 2.991
I.e. I changed the residue name to MGX and the atom name to MGHBR. I ran grompp
and it compiles without errors. However, I want to make sure, that this is
consistent with gromacs files and that I will change the charge in the simulation.
Thank you very much for your help!
All the best
Johannes
-----------------------
On 06.07.2017 14:24, Justin Lemkul wrote:
On 7/6/17 12:56 AM, amitabh jayaswal wrote:
... well, this URL under ans.2 (http://www.bevanlab.biochem.
vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is what I'm
repeatedly getting.
Please rectify/improve.
Because you haven't copied the whole URL, which is split across two lines in
that message.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html
-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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