[gmx-users] Adding new residue to the the force field
rameshgromacs at gmail.com
Fri Feb 24 13:56:23 CET 2012
Thanks for your reply. I am not using both LJ and
Buckingham in the same simulation, but trying to use only Buckingham . As
my system is a polymer which is made of the monomer unit that's what i am
adding to the force field. Our polymer system uses the parameters only from
the residue which i have added to the forcefield through buckingham A,B &
I would like to ask the previous question again, Which values can i use for
the [ pairtypes ] directive in the ffnonbonded.itp can i use arbitrary
values or zeroes what i noticed from my simulations is by changing the
sigma and epsilon values in the [ pairtypes ] directive energy values are
if i try to comment out the pairtypes 'grompp' is generating the
following errors( here i am sending only one error message )
ERROR 411 [file topol.top, line 862]:
No default LJ-14 types
i am a little bit confused why grompp is giving this error message though
i am using the bucking potential by specifying the nbfunc as 2 in the [
default ] directive and providing the A,B,C values through [nonbond_params
if it is mandatory to use pair types how can i get these values for this
Thanks in advance.
On Fri, Feb 24, 2012 at 12:15 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> On 24/02/2012 5:20 PM, ramesh cheerla wrote:
> Dear Mark
> 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.
> As I understand things, pairs for special 1-4 interactions are not used
> with Buckingham interactions.
> Looking closer at your original post, you claim to be adding a residue
> using Buckingham to an existing force field. No force fields distributed
> with GROMACS use Buckingham, so if you're trying to make both LJ and
> Buckingham work in the same simulation, you will be unable to succeed.
> 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.
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