Re: [gmx-users] Oleic acid.....topology problem...

whenever I am running the pd2gmx it is giving me an error OLA not found in residue topology database On Sun, Mar 29, 2015 at 10:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/28/15 11:33 PM, Kamalesh Roy wrote: Dear all, I am using gromacs latest version in Ubuntu... I am trying to

Re: [gmx-users] Feature wishlist

Hi, I suspect you can do this already with a COM virtual site upon which you place a position restraint. Mark On Sun, Mar 29, 2015 at 1:02 AM, Sridhar Kumar Kannam srisri...@gmail.com wrote: Dear Gromacs developers, A feature on constraining the CM of a molecule using harmonic potentials in

Re: [gmx-users] About g_enemat tool

On 3/29/15 6:27 AM, vidhya sankar wrote: Dear Justin Thank you for your previous reply I want to calculate interaction energies (such as Coulombic and Vandeewaal's interaction , LJ interaction ) between groupsCNT and Cyclic peptide for that I set energygrps = CNT peptide1 petide2

Re: [gmx-users] Oleic acid.....topology problem...

On 3/28/15 11:33 PM, Kamalesh Roy wrote: Dear all, I am using gromacs latest version in Ubuntu... I am trying to simulate oleic acid in a box with some protein. Have made the .itp from prodrg server... incorporate the same still not recognizing OLA residue. PRODRG parameters always require

[gmx-users] About g_enemat tool

Dear Justin Thank you for your previous reply I want to calculate interaction energies (such as Coulombic and Vandeewaal's interaction , LJ interaction ) between groups    CNT and Cyclic peptide  for that I set energygrps = CNT  peptide1 petide2                     in mdp file When i extract 

[gmx-users] Error while using pbc = xy Segmentation fault (core dumped)

Hi everyone, I want to use PBC only in xy direction but get error Segmentation fault (core dumped) during energy minimization. I am using CHARM36 force field and my .mdp file is integrator= steep emtol= 1000.0 emstep = 0.01 nsteps= 5 nstlist= 20

Re: [gmx-users] Setting custom atoms in FF

On 3/29/15 4:07 PM, Alex wrote: Hi all, I am messing with the OPLS/AA forcefield. The idea is to functionalize graphene edge atoms beyond passivation with hydrogen. At the functionalization region, there is a C atom with two C-C bonds (from graphene), while the third bond is formed with the

Re: [gmx-users] Setting custom atoms in FF

Wha, that's a huge blow, and it explains a bunch of other issues. I was thinking the difference had to be around 2-3% and set my pdb files very precisely. I actually think that either the tolerance is even larger, or there's something on top of that in the code. Setting CJ opls_9960

[gmx-users] Setting custom atoms in FF

Hi all, I am messing with the OPLS/AA forcefield. The idea is to functionalize graphene edge atoms beyond passivation with hydrogen. At the functionalization region, there is a C atom with two C-C bonds (from graphene), while the third bond is formed with the functional group. The particular atom

Re: [gmx-users] Setting custom atoms in FF

Yeah, I know there's that disclaimer. I wonder if this http://software-lisc.fbk.eu/obgmx/ could be useful. Any comment on this UFF? First time I'm hearing about it, to be honest. The system I have in mind isn't much beyond CNTs and nucleotide chains. Well, and water. Thanks. Alex JL g_x2top

Re: [gmx-users] Setting custom atoms in FF

On 3/29/15 5:01 PM, Alex wrote: Wha, that's a huge blow, and it explains a bunch of other issues. I was thinking the difference had to be around 2-3% and set my pdb files very precisely. I actually think that either the tolerance is even larger, or there's something on top of that in the

Re: [gmx-users] Setting custom atoms in FF

Another question about x2top: in the previous discussion, the atom type was determined from its environment and the element type. What if I set up my PDB with atom labels (i think that's the third field from the left in the PDB format), say CJ1 and CJ2 (instead of just C), while the force field