[gmx-users] Re:Carbon monoxide topology- Charges & non-bonded interaction values usage

[라지브간디]

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 
Message-ID: 
<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. 
> 
> Mark 
> 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 
>> Message-ID: 
>> <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 
>> charmm27.ff? 
>> >