Re: [gmx-users] Adding ions

The problem I was facing earlier: in the force field files (I am ussing ffG53a6) the ions are named NA+, CL-, for example, so with capital letters. Genion will add to the topology the ions named by default Na or Cl, unless you use the options -pname and/or -nname to name the ions. I do so and I hav

Re: [gmx-users] Dealing with non-aminoacid residues

Hi Pablo, I would write .rtp entries and so on for each monomer. You copy the modified files into your working directory. Have a great day, Andrea 2009/10/6 Englebienne, P. > Hi all, > > > > I’m looking to perform simulations on a series of synthetic co-polymers > containing a variety of bui

Re: [gmx-users] is there a possibility to convert .gro files directly to PDB?

Hi Andrew, I would do it with editconf with the same options. Regards Andrea 2009/3/11 Andrew Voronkov : > Dear GROMACS users, > is there a possibility to convert .gro files directly to PDB? Or I can do it > only with .tpr? > I've tried gro2pdb -f conf.gro -o conf.pdb > but it doesn't work. >

Re: [gmx-users] Rtp for polymer.

I connect the monomers by adding a bond in the rtp entry, in which the first atom of the next residue is given with + (you can also connect with the previous residue with - in front of the last atom). Sorry to explain this in a very confuse way. Better look at the example bellow (for polystyrene):

Re: [gmx-users] PBC only in xy direction

Hi Berk, that is a good idea. Thank you for your answer. Cheers, Andrea 2008/12/11 Berk Hess <[EMAIL PROTECTED]>: > Hi, > > This is not possible in 3.3. > > But in practice you almost never need this, > since it is far more efficient to use pbc=xyz and have a slab of vacuum > in between the peri

[gmx-users] PBC only in xy direction

Hi gmx-users, We are using the version 3.3.3. Is there also a posibility to have pbc only in xy direction (as I saw it is possible in Gromacs 4.0)? The manual says nothing about that. Thank you in advance. Best regards, Andrea ___ gmx-users mailing lis

Re: [gmx-users] system explodes

Thank you. I will do so. kind regards, Andrea 2008/11/11 Justin A. Lemkul <[EMAIL PROTECTED]>: > > > Andrea Muntean wrote: >> >> I am simulating one chain of PS. The box is produced by pdb2gmx. If I >> run simulations with timestep 0.1 fs up to 0.4 fs every

[gmx-users] system explodes

I am simulating one chain of PS. The box is produced by pdb2gmx. If I run simulations with timestep 0.1 fs up to 0.4 fs everything seem to be ok. With 1 fs (which should be a normal time for my system) I would get the following warning: Warning: 1-4 interaction between 290 and 299 at distance 108.

Re: [gmx-users] .mdp file

I thought so. Thank you very much! Cheers Andrea 2008/11/10 Justin A. Lemkul <[EMAIL PROTECTED]>: > > > Andrea Muntean wrote: >> >> Hello there, >> >> I have a practical question regarding the mdp file, regardless the >> system to simulate. Before I

[gmx-users] .mdp file

Hello there, I have a practical question regarding the mdp file, regardless the system to simulate. Before I would run a md simulation, usually we have to run grompp in order to preprocess the system. So I obtain, among other files, the mdout.mdp, based on the input mdp file. My question: If I wa

[gmx-users] Box size

Hi all, I have my box defined at the end of my pdb file as (lenghts in Angstrom) AXAYAZt 70.70. 112.0777 5800. In the gro file (produced by pdb2gmx) I get 2.51900 2.84400 6.80610 on the last line. Is this my box reduced to the size of the molecule? Or what does

[gmx-users] Re: dihedrals again

Remark: if I change that dihedral with -CHCH2 CH CBgd_17, that it gives again 2 9 10 11 , but this time with gd_17, as it should do. But why it does not work with the other definition? Does it have to do with the fact that in the dihedral I have atoms belonging to 3 residu

[gmx-users] dihedrals again

Hi all, I did some work on thise dihedrals for polystyrene, and I simplified my version now, using also the inspiration from PHE residue. My problem now is that for the dihedral around the CH2-CH bond in the inner monomer (PS thus) I define in the rtp -CH CH2 CH +CH2gd_17 but in

Re: [gmx-users] Dihedral not counted?

3 8 7 1 > > Makes sense that they'd be missing. If you're dealing with polystyrene, > maybe consider basing the dihedrals off of those contained in the PHE > sidechain in the Gromos force field you appear to be using. > > -Justin > > Andrea Muntean wrot

Re: [gmx-users] Dihedral not counted?

Sorry, once again for everybody in the list: Here are the .rtp entries: [PS1] [atoms] CH3 CH3 0 0 CH CH1 0 0 CB C 0 0 CG1 CR1 0 0 CG2 CR1 0 0 CG3 CR1 0 0 CG4 CR1 0 0 CG5 CR1 0 0

Re: [gmx-users] Dihedral not counted?

Hi Justin, here are the relevant parts, as pdf files. I miss a dihedral between the atoms 2, 9, 10 and 17, which corresponds to the -CH CH2 CH +CH2 dihedral in the PS residue in the RTP entry. For the trimer I should have 26 dihedrals, but in the TOP file I get only 25 (I mean only the prop

[gmx-users] Dihedral not counted?

Hi all, I defined my residues for Polystyrene (first, last and inner monomers), with the coresponding bonds, angles, dihedrals and impropers, including also the conectivities (as + and - atoms of the next or previous residue). Pdb2gmx runs without error or warning, but it counts less dihedrals the

Re: [gmx-users] monomer's conectivity

It did work. Thank you! Cheers, Andrea 2008/10/23 Mark Abraham <[EMAIL PROTECTED]> > Andrea Muntean wrote: > >> Thank you for your answer. >> If I am looking at the PDB standard format and my file, I observe that I >> have only one number between the type of

Re: [gmx-users] monomer's conectivity

Thank you. I hope this helps me further. My system is 32 polystyrene chains of 80 monomers. Andrea 2008/10/23 Mark Abraham <[EMAIL PROTECTED]> > Andrea Muntean wrote: > >> Thank you for your answer. >> If I am looking at the PDB standard format and my file, I observe

Re: [gmx-users] monomer's conectivity

hanks again for your help. Best regards, Andrea 2008/10/22 Mark Abraham <[EMAIL PROTECTED]> > Andrea Muntean wrote: > >> I have a *pdb file for a polymer box which I want to use. I defined the >> residues (the first, the last and the inner monomers). >> Pdb2gmx runs

[gmx-users] monomer's conectivity

I have a *pdb file for a polymer box which I want to use. I defined the residues (the first, the last and the inner monomers). Pdb2gmx runs, but I obtain a "soup" of monomers instead of N chains a M monomers each. My problem now is how to connect the monomers. What is the best way to do so? Regard

[gmx-users] .tdb entries for polystyrene (or other linear polymer)

Sorry for the trivial question, but I am new in Gromacs. I try to simulate a polystyrene film and I want to use a 8.pdb file from an equilibrated film of 32 chains, 80 monomers each. I unterstand that I should enter the residues (for the first, inner and last monomer(s)) and maybe to define the cor

[gmx-users] Preparing polystyrene

I am trying to use a .pdb for a polystyrene film (32 chains with 80 monomers each). The problem is that when I start running pdb2gmx I get the error that it can not find the residues (which are of course different from those in Gromacs). What would be the best thing to do? Have somebody a pdb or rt

[gmx-users] help with installation

I want to install fftw and gromax in my directory. Everything went ok, fftw was installed without errors. When I configure gromacs I have the error: cannot find fftw3f library. I did use the CPPFLAGS and LDFLAGS. Can somebody help me? Thank you kindly in advance! Andrea

[gmx-users] Polystyrene box

Hello, we are trying to generate a polystyrene box. We have a homemade pdb file, but the residues are not recognised. Have somebody a good pdb file or can tell me what are the standard residues in Gromax? Any other good hints are welcome. Thanks a lot, Andrea _