[gmx-users] Re:Carbon monoxide topology- Charges & non-bonded interaction values usage
rajiv at kaist.ac.kr
Fri Jun 27 03:38:45 CEST 2014
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?
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>
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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
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
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