Re: [gmx-users] Distance restraint and pull code

hi, I included this bond assignment right after [bonds] in the topology. [ bonds ] ; i j func b0 kb 1354 3852 6 0.214000 1390 3852 6 0.214000 1721 3852 6 0.214000 1520 3852 6 0.404000 It seems the type 6 works now,

Re: [gmx-users] Distance restraint and pull code

On 6/9/16 11:21 AM, Hong Tham wrote: hi Justin, in the manual, the [distance restraint] will add flat-bottom harmonic potential to keep distance between 2 atoms. The low, up1, up2 is corresponds to ro, r1, r2 in the equation 4.83 (manual 5.0.7). I understand if rij < r low, up1 up2, mdrun

Re: [gmx-users] Distance restraint and pull code

hi Justin, in the manual, the [distance restraint] will add flat-bottom harmonic potential to keep distance between 2 atoms. The low, up1, up2 is corresponds to ro, r1, r2 in the equation 4.83 (manual 5.0.7). I understand if rij < r low, up1 up2, mdrun will add the harmonic potential, if rij

Re: [gmx-users] Distance restraint and pull code

On 6/9/16 8:54 AM, HongTham wrote: Hi, I have another question. I applied 4 pull codes (3 to keep Zn ion in coordination with 3 HIS, 1 to keep Zn ion in coordination with the ligand). The pull code worked effectively. With the same system, when applying 3 distance restraints (to keep Zn ion in

Re: [gmx-users] Distance restraint and pull code

Hi, I have another question. I applied 4 pull codes (3 to keep Zn ion in coordination with 3 HIS, 1 to keep Zn ion in coordination with the ligand). The pull code worked effectively. With the same system, when applying 3 distance restraints (to keep Zn ion in coordination with 3 HIS) and 1 pull

Re: [gmx-users] Distance restraint and pull code

Hi Justin, I got it. Thank you for your explanation. :D Hongtham On Wed, Jun 1, 2016 at 7:38 PM, Justin Lemkul wrote: > > > On 6/1/16 5:16 AM, HongTham wrote: > >> Hi, >> Im now applying 4 pull codes to keep the Zn coordination. the script is >> like below. >> ; Pull code >>

Re: [gmx-users] Distance restraint and pull code

On 6/1/16 5:16 AM, HongTham wrote: Hi, Im now applying 4 pull codes to keep the Zn coordination. the script is like below. ; Pull code pull = umbrella pull-ngroups = 5 pull-ncoords = 4 pull-group1-name = ZN pull-group2-name = a_3862 pull-group3-name = a_1354 pull-group4-name = a_1390

Re: [gmx-users] Distance restraint and pull code

Hi, Im now applying 4 pull codes to keep the Zn coordination. the script is like below. ; Pull code pull = umbrella pull-ngroups = 5 pull-ncoords = 4 pull-group1-name = ZN pull-group2-name = a_3862 pull-group3-name = a_1354 pull-group4-name = a_1390 pull-group5-name = a_1721 pull-geometry =

Re: [gmx-users] Distance restraint and pull code

On 5/26/16 9:20 PM, HongTham wrote: Dear Gromacs users, Im running a Zn bound protein - ligand complex system. Zn makes coordinations with 3 HIS and NH- of ligand. in the itp file, Zn and protein in the same [molecule] but not ligand. because it cant be applied distance restraint ZN and