Re: [gmx-users] distance_restraints with flexible angle

2012-07-23 Thread tarak karmakar
Exactly so. But in the ffbonded.itp file there are two columns, equilibrium bond length and Kb . So evenif I give zero then it won't affect the bond . Thanks a lot for the reply, it's working fine now . On Mon, Jul 23, 2012 at 6:02 PM, Justin Lemkul wrote: > > > On 7/23/12 8:31 AM, tarak karmakar

Re: [gmx-users] distance_restraints with flexible angle

2012-07-23 Thread Justin Lemkul
On 7/23/12 8:31 AM, tarak karmakar wrote: Thanks for the reply. But then what should I give as Kb [ bond stretching constant ] in the ffbonded.itp file ? should I give 00.000 there or something else ??? Constraints make bonds rigid. The force constant is irrelevant. -Justin On Mon, Jul 2

Re: [gmx-users] distance_restraints with flexible angle

2012-07-23 Thread tarak karmakar
Thanks for the reply. But then what should I give as Kb [ bond stretching constant ] in the ffbonded.itp file ? should I give 00.000 there or something else ??? On Mon, Jul 23, 2012 at 4:11 PM, Justin Lemkul wrote: > > > On 7/23/12 2:39 AM, tarak karmakar wrote: >> >> Dear All, >> >> >>In my

Re: [gmx-users] distance_restraints with flexible angle

2012-07-23 Thread Justin Lemkul
On 7/23/12 2:39 AM, tarak karmakar wrote: Dear All, In my simulation I want to fix the S=O bond length of SO2, but the angle has to be kept flexible. So I search for the distance restraints in gromacs mailing list and accordingly I have incorporated the distant_restraints block in the topo

[gmx-users] distance_restraints with flexible angle

2012-07-22 Thread tarak karmakar
Dear All, In my simulation I want to fix the S=O bond length of SO2, but the angle has to be kept flexible. So I search for the distance restraints in gromacs mailing list and accordingly I have incorporated the distant_restraints block in the topology file. After a short equilibration, when I