[gmx-users] Carbon monoxide topology- Charges & non-bonded interaction values usage
jalemkul at vt.edu
Fri Jun 27 03:43:00 CEST 2014
On 6/26/14, 9:38 PM, 라지브간디 wrote:
> Thank you for your suggestion.
> Moreover, it has been used by many publication.
> What i want to know is " since the charges and LJ written for charmm force field, shall i directly use this values in gromacs -charmm27 force filed (ffnonbonded.itp) section? or need any manual conversion?
Units need to be converted from CHARMM standard to what Gromacs expects. The
expected units are all in the manual and conversion between different formats
has been covered extensively in past mailing list posts; it's quite simple to do.
> Date: Thu, 26 Jun 2014 13:41:21 +0200
> From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Carbon monoxide topology
> <CAPXdD+aXx5MhguROMifX5qH1CnSVGTH3uEaLk55i1PumtPV=3Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> In my opinion, it is an acceptable solution to take these parameters as is.
> Especially, if you write some wise words about philosophy of FF
> compatibility/trasferability and pairwise interactions for your
> methodology section.
> Dr. Vitaly V. Chaban
> On Wed, Jun 25, 2014 at 8:02 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>> If you're happy that such parameters might work with your intended force
>> field, then you only need to build them into a topology. Assuming you have
>> some GROMACS experience, check out the relevant parts of chapters 4 and 5
>> of the manual.
>> On Jun 25, 2014 4:01 AM, "?????" <rajiv at kaist.ac.kr> wrote:
>>> Dear Dr. Vitaly V. Chaban,
>>> The charges and non-bonded interactions of Carbon monoxide are set to give
>>> approximate agreement with the experimental dipole & quardrupole moments (
>>> J.E. Straub, M. Karplus, Chemical Physics, 1991).
>>> According to this article, with the specific point charges and LJ
>>> parameters fit to give good agreement with the multipole moments of CO as
>>> well as lattice constant for the Myoglobin with CO structure ( Written for
>>> Charmm ff)
>>> Hence, i would like to know how do i interpret this values in charmm27 ff
>>> in gromacs? Thank you for your concern.
>>> Msg: 3
>>> Date: Tue, 24 Jun 2014 11:26:02 +0200
>>> From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
>>> To: gmx-users at gromacs.org
>>> Subject: Re: [gmx-users] Charges & non-bonded interaction values usage
>>> in different force fields
>>> <CAPXdD+Y4fndZeeL-D+WECT_TmFjkq0Co28DMHbsGcxgDRvCk+A at mail.gmail.com>
>>> Content-Type: text/plain; charset=UTF-8
>>> Can you perhaps kindly explain us how "charges and non-bonded
>>> interaction values" were "experimentally determined"?
>>> Dr. Vitaly V. Chaban
>>> On Tue, Jun 24, 2014 at 10:37 AM, Rj <rajiv at kaist.ac.kr> wrote:
>>>> Dear all,
>>>> Experimentally determined charges and non-bonded interaction values for
>>> ligand atoms ( Written in charmm) can be used directly in gromacs provided
>>> charmm27.ff ? or does it need any conversion to use it in gromacs based
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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