[gmx-users] Adding new residue to the the force field
rameshgromacs at gmail.com
Fri Feb 24 07:20:18 CET 2012
I am very thank ful to you for your valuble suggestion. I
have verified my results by changing the sigma and epsilon values in
[atomtypes ] directive of the ffnonbonded.itp . Results were uneffected by
changing these values.
Here i have one another doubt regarding [ pairtypes ] directive, As I am
using buckingham potential for the nonbonded interactions and have only A,
B & C values can i use zeros for the sigma and epsilon values in this
directive. What i observed is results will change by changing the sigma
and epsilon values in this directive.
Please suggest me how can i use correct values for the sigma and epsilon in
[ pairtypes ] directive.
Thank you in advance.
On Thu, Feb 23, 2012 at 7:32 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> On 23/02/2012 6:02 AM, ramesh cheerla wrote:
>> Dear gromacs users,
>> I am adding a new residue to the existing
>> force field in gromacs for that i am using some new atom types i added
>> these atom types to the atomtypes.atp file and ffnonbonded.itp and I am
>> using Buckingham potential for the non-bonded interactions for that i have
>> only A,B&C values, but in the [atomtype] directive of the ffnonbonded.itp
>> file one has to specify the sigma and epsilon values. How can i get these
>> values ? or can i specify these values as zeros ?
> You will be able to use zeroes. You can verify that there's no effect by
> changing the values to ludicrous ones and observing that the simulation is
> the same.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users