[gmx-users] last line in .gro file

Dear gmx-users, I am new to GROMACS. Can anyone tell me what does the last line in .gro file stands for ? The manual mentions "box[X][X],box[Y][Y],box[Z][Z], box[X][Y],box[X][Z],box[Y][X],box[Y][Z],box[Z][X],box[Z][Y]" Can anyone explain what each of these mean in terms of cell parameters ? Tha

Re: [gmx-users] last line in .gro file

Dear Justin, Thanks for replying. The table mentions only a few unit cell type. I am using a monclinic unit cell. Do you know how these box vectors have been derived. thanks vishal On Tue, Feb 2, 2010 at 11:26 AM, Justin A. Lemkul wrote: > > > Vishal Agarwal wrote: > >&

Re: [gmx-users] last line in .gro file

2, 2010 at 11:52 AM, Justin A. Lemkul wrote: > > > Vishal Agarwal wrote: > >> Dear Justin, >> >> Thanks for replying. The table mentions only a few unit cell type. I am >> using a monclinic unit cell. Do you know how these box vectors have been >> derive

Re: [gmx-users] last line in .gro file

. Lemkul wrote: > > > Vishal Agarwal wrote: > >> Dear Justin, >> >> I am trying to set up calculations for a cellulose structure. The >> allomorph of cellulose which I want to study has a monoclinic structure. I >> have a .cif file of the XRD structure. I think

Re: [gmx-users] last line in .gro file

You'll > > have to do the math and reading yourself to find out how this translates > to > > a .gro box. The manual is your friend here. > > > > Good luck, > > > > Erik > > > > Vishal Agarwal skrev: > >> > >> Dear Justin, > >&

[gmx-users] making topology file for infinite crystal

). When I try running pdbgmx, I get an error for extra hydrogens (which is not there in itp file but is actually there in the original structure which I am using) and missing oxygen (-O). -- Regards *** Vishal Agarwal Research Scholar University of

Re: [gmx-users] making topology file for infinite crystal

14:52, Vishal Agarwal wrote: > >> Dear All, >> >> Can anyone help me how can I go about preparing the topology file for an >> infinite crystal of cellulose. I have prepared the .gro file for 5X5X5 >> unit cells of cellulose II using GROMACS utility and intend to

Re: [gmx-users] making topology file for infinite crystal

tin A. Lemkul wrote: > > > Vishal Agarwal wrote: > >> Dear Mark, >> >> What I meant over here is the missing oxygen (-O) which pdbgmx complains >> about is not a part of .rtp entry. There is no such type of oxygen specified >> in any of the .atp entry of the f

Re: [gmx-users] making topology file for infinite crystal

hat carbon as a separate residue ? Again thanks for replying. Best, Vishal -Justin > > Your help is appreciated. >> Thanks, >> Vishal >> >> On Sun, Feb 7, 2010 at 11:35 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>

Re: [gmx-users] making topology file for infinite crystal

correct or another typo ? Vishal On Sun, Feb 7, 2010 at 1:18 PM, Justin A. Lemkul wrote: > > > Vishal Agarwal wrote: > >> Dear Justin, >> >> Thanks for replying. >> >>pdb2gmx -f cellulose.gro >> >> >>So then your "ce

Re: [gmx-users] making topology file for infinite crystal

Dear Justin, Thanks for replying. I really appreciate this. Thanks, Vishal On Sun, Feb 7, 2010 at 3:58 PM, Justin A. Lemkul wrote: > > > Vishal Agarwal wrote: > >> Dear Justin, >> >> Thanks for replying. I guess it should be -O4 from the convention but have &g

[gmx-users] extracting coordinates

Dear All, I am new to using GROMACS. I have done some NVT simulation on glucose molecule. Can one anyone tell me how to extract the coordinates of atoms for each frame from the output trajectory file. Thanks, Vishal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailm

[gmx-users] hessian.mtx----> readable format

Dear Gromacs Users, Is there a way to convert the hessian.mtx file into a readable format using any of the gromacs utilities? Any help on this would be highly apprecaited.. Thanks, Vishal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] hessian.mtx----> readable format

Thanks Justin On Tue, Sep 7, 2010 at 5:14 PM, Justin A. Lemkul wrote: > > > Vishal Agarwal wrote: > >> Dear Gromacs Users, >> Is there a way to convert the hessian.mtx file into a readable format >> using any of the gromacs utilities? >> > > gmx