Re: [gmx-users] A few general questions on Gromacs

Am Dienstag, 26. Juni 2007 schrieb Corina Stratan: > I would like to thank you and David for the answers. By "multiple > programs", I meant batch scripts that contain other Oh yes, we have runtime limitation of 144h on serial and 24 or 48h on the large machines. I had to setup several runs over

Re: [gmx-users] rtp entry

David van der Spoel wrote: ASHWINI JAYAPRAKASH wrote: Hi Mark, I have used pdb2gmx to create the topology file with the option of -missing,also I have deleted the HEATOM that were there in the pdb file. Will these be a problem later? Now when I run grompp I am getting the error "Atomtype

Re: [gmx-users] rtp entry

ASHWINI JAYAPRAKASH wrote: Hi Mark, I have used pdb2gmx to create the topology file with the option of -missing,also I have deleted the HEATOM that were there in the pdb file. Will these be a problem later? Now when I run grompp I am getting the error "Atomtype 'opls_135' not found!"

Re: [gmx-users] rtp entry

Hi Mark, I have used pdb2gmx to create the topology file with the option of -missing,also I have deleted the HEATOM that were there in the pdb file. Will these be a problem later? Now when I run grompp I am getting the error "Atomtype 'opls_135' not found!" .

Re: [gmx-users] producing top and gro files for the molecule with metal ions.

Anna Reymer wrote: Hi! I am running GROMACS for DNA with Ruthenium (II) complex. Please have a look into pdb file below. There is no parameters for any of transitional metals to produce topology and coordinates for it. The Dundee PRODRG server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/

Re: [gmx-users] rotational fit in XY plane only

Naser, Md Abu wrote: > > I implemented an xy only fitting option for trjconv in the development > > branch. > > > > Berk. In reference to the above replay of Berk, I was trying to get into CVS to get a copy of it. When I click on the "instructions on how to access our CVS repository", it s

Re: [gmx-users] Re: mk_angndx

Fabio Affinito wrote: angle multiplicity force constant so, does it refer to the angle values contained in the topology files? tpr file. Thank you, Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo

[gmx-users] rotational fit in XY plane only

> > I implemented an xy only fitting option for trjconv in the development > > branch. > > > > Berk. In reference to the above replay of Berk, I was trying to get into CVS to get a copy of it. When I click on the "instructions on how to access our CVS repository", it says not authorised to acce

Re: [gmx-users] producing top and gro files for the molecule with metal ions.

Hi Anna, Interesting compound you have. In addition to the link sent by Mark, I'd say that this compound is a bridge too far. It's a heavily conjugated system with transitional metal. For parameterization you should perform QM calculations, and because of the conjugation, you can't really do it "

Re: [gmx-users] producing top and gro files for the molecule with metal ions.

Anna Reymer wrote: Hi! I am running GROMACS for DNA with Ruthenium (II) complex. Please have a look into pdb file below. There is no parameters for any of transitional metals to produce topology and coordinates for it. The Dundee PRODRG server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/

[gmx-users] producing top and gro files for the molecule with metal ions.

Hi! I am running GROMACS for DNA with Ruthenium (II) complex. Please have a look into pdb file below. There is no parameters for any of transitional metals to produce topology and coordinates for it. The Dundee PRODRG server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ ) has parameters on

Re: [gmx-users] DNA simulations with GROMACS???

Hi! Thank you all very much for the help! The problem was in correct usage of water models. I used amber_tip3p.gro and gromacs_tip3p.itp. So, it is necessary to use both tip3p.gro and tip3p.itp from either amber or gromacs. regards /anna On 6/19/07, Anna Reymer <[EMAIL PROTECTED]> wrote: Hi a

Re: [gmx-users] A few general questions on Gromacs

> Hi, > > I would like to thank you and David for the answers. By "multiple > programs", > I meant batch scripts that contain other preprocessing/postprocessing > programs besides mdrun (like grompp, pdb2gmx,...) - so this would be a > case > in which the processing is done in multiple steps. I as

[gmx-users] Re: mk_angndx

angle multiplicity force constant so, does it refer to the angle values contained in the topology files? Thank you, Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] A few general questions on Gromacs

Corina Stratan a écrit : Hi, I would like to thank you and David for the answers. By "multiple programs", I meant batch scripts that contain other preprocessing/postprocessing programs besides mdrun (like grompp, pdb2gmx,...) - so this would be a case in which the processing is done in mult

Re: [gmx-users] A few general questions on Gromacs

Hi, I would like to thank you and David for the answers. By "multiple programs", I meant batch scripts that contain other preprocessing/postprocessing programs besides mdrun (like grompp, pdb2gmx,...) - so this would be a case in which the processing is done in multiple steps. I asked this becau

Re: [gmx-users] Gromacs website broken

pim schravendijk wrote: Hi People!, The Gromacs website is seriously broken. I wanted to copy-paste the line for cvs checkout as I usually do, but following the link to the CVS page via either the download or the developer menu gives me a page saying I don't have access and need to log in. Usin

Re: [gmx-users] mk_angndx

Fabio Affinito wrote: Hi everybody, what's the meaning of the labels in the angle.ndx generated by the mk_angndx? For example, I've got groups named [ Phi=0.0_3_3.77 ].. what does that mean? Thanks, Fabio ___ gmx-users mailing listgmx-users@gr

Re: [gmx-users] Gromacs website broken

pim schravendijk wrote: Hi People!, The Gromacs website is seriously broken. I wanted to copy-paste the line for cvs checkout as I usually do, but following the link to the CVS page via either the download or the developer menu gives me a page saying I don't have access and need to log in. Usin

[gmx-users] Gromacs website broken

Hi People!, The Gromacs website is seriously broken. I wanted to copy-paste the line for cvs checkout as I usually do, but following the link to the CVS page via either the download or the developer menu gives me a page saying I don't have access and need to log in. Using the website search func

[gmx-users] mk_angndx

Hi everybody, what's the meaning of the labels in the angle.ndx generated by the mk_angndx? For example, I've got groups named [ Phi=0.0_3_3.77 ].. what does that mean? Thanks, Fabio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gr

Re: [gmx-users] A few general questions on Gromacs

Am Montag, 25. Juni 2007 schrieb Corina Stratan: Hi Cornia, these are my experiences, so others might differ from mine: > 1) Which is the typical size of the input/output files for Gromacs > programs? The ones included in the tutorial are below 50K; are the files > larger in "real" situations? A

Re: [gmx-users] Re: WCA and free energy calculations

From: "David Mobley" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "Discussion list for GROMACS users" Subject: Re: [gmx-users] Re: WCA and free energy calculations Date: Mon, 25 Jun 2007 09:32:05 -0700 Berk, Nearly anything can be done now in Gromacs :) (although so