Re: [gmx-users]D Gsol from g_sas calculation

limei zhang wrote: Hi to all, I did surface calculation on a protein either with or without Cu-binding, using g_sas with exactly the same parameter setting. For the delta solvation energy from the output file (the the 5th column in the output file with a label of D Gsol), non-Cu bound prote

[gmx-users] Re: Removal of pbc for analysis

Hi All, I am doing a 5 peptide simulation, and i want to analyze some of the basic properties like radius of gyration, distance between peptides etc. but i wanted to do it in a situation when all my peptides are inside the box. Due to pbc i am getting artifacts. i tried all the -pbc option (inbox,

[gmx-users] Zinc (Zn) parameters

Dear Gromacs users, I am planing to do MD of an enzyme that has a Zn in its active site. Up to now I have used QM/MM or ONIOM approaches but now I need to perform a long MD and would like to model the Zn with MM, preferably in OPLS. I know that there are three possible approaches: Bonded, nonbonded

Re: [gmx-users] Re: Removal of pbc for analysis

[EMAIL PROTECTED] wrote: Hi All, I am doing a 5 peptide simulation, and i want to analyze some of the basic properties like radius of gyration, distance between peptides etc. but i wanted to do it in a situation when all my peptides are inside the box. Due to pbc i am getting artifacts. i trie

Re: [gmx-users] energy groups

rams rams wrote: Dear Users, I have a question about separating a system into energy groups. In my system, I have a metal atom and a few residues close to the metal atom (catalytic center). I ran the simulation with out any restraints. In the most representative structure, the catalytic cen

[gmx-users] How to do CGMD in GROMACS?

Hi All, I am interested in doing Coarse Grained MD in GROMACS. Is there any module in GROMACS with which I can do this? Please tell me the procedure of doing CGMD in GROMACS. Thanks a lot. Regards,   Anirban Ghosh M.Tech Bioinformatics University of Hyderabad Explore your hobbies and int

Re: [gmx-users] Zinc (Zn) parameters

Hi Ramon, Zinc should be considered as one of those "exotic species" (http://wiki.gromacs.org/index.php/Exotic_Species). It's almost impossible to give a set of parameters which will work for all zinc binding sites. Actually, it's best to parameterize based on the environment. Now, if you have QM/

Re: [gmx-users] How to do CGMD in GROMACS?

Read just about any of the papers from Marrink's group. -Justin Anirban Ghosh wrote: Hi All, I am interested in doing Coarse Grained MD in GROMACS. Is there any module in GROMACS with which I can do this? Please tell me the procedure of doing CGMD in GROMACS. Thanks a lot. Regards,

[gmx-users] (no subject)

Hi all I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2. so check i tried to to do speptide tutorial in /usr/local/gromacs/share/gromacs/tutor/speptide But when i m running grompp for position restraint with the command grompp -f pr -o pr -c after_em -r after_em -p speptide i

Re: [gmx-users] (no subject)

Check the information on the gromacs wiki about this: http://wiki.gromacs.org/index.php/Errors#T-Coupling_group_XXX_has_fewer_than_10.25_of_the_atoms Cheers /Per 17 jul 2008 kl. 14.38 skrev [EMAIL PROTECTED]: Hi all I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2. so c

Re: [gmx-users] (no subject)

For warnings/errors, etc. please check the archive and wiki before posting. I just responded to a similar issue a few days ago: http://www.gromacs.org/pipermail/gmx-users/2008-June/034786.html -Justin [EMAIL PROTECTED] wrote: Hi all I have installed gromacs 3.3.3 in one of my 32 machine fedo

[gmx-users] How to do CGMD in GROMACS?

Also check Prof. Marrink's website: http://md.chem.rug.nl/~marrink/science.html There are good instructions to get started, for both lipids (2004 FF) and proteins (MArtini) > > Message: 6 > Date: Thu, 17 Jul 2008 07:55:19 -0400 > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > Subject: Re: [gmx-u

[gmx-users] [Fwd: questions about surface tension]

Original Message Subject: questions about surface tension Date: Thu, 17 Jul 2008 21:27:28 +0800 From: Li Yang <[EMAIL PROTECTED]> To: David van der Spoel <[EMAIL PROTECTED]> Dir Sir I must apologize if I've disturbed you. I have been learning the molecular dyn

[gmx-users] how to measure the surface tension of membrane by inclusion

Hi I have some questions about the surface tension calculations: 1. For the formula, \gamma_m=(P_N - P_L) * L_z / 2, is it only available for a flat surface, like a lipid bilayer in water ? For example, the surface fluctuation of lipid bilayer often occur in the simulation, sometimes,

[gmx-users] Constraint Pulling - Oscillating Forces

Hello, I am running constraint pulling on a peptide chain. After the run, the pull.pdo file outputs the time, along with the force (in kJ/(mol nm)). The problem is that the forces are oscillating between almost 1000 pN. I tried to reduce the constraint tolerance, but it does not help that m

[gmx-users] CHARMM FF

Hi all, who has the CHARMM FF working with Gromacs? I heard that Erik's group has something working. Is this correct? My impression is that all force terms are supported in the CVS version including CMAP. But obviously converting the files in the itp format is not trivial. Which converters do you

[gmx-users] Re: CHARMM FF

Hi Roland, We have it working with pdb2gmx, but not CMAP yet, but we're working on integrating that. I'll see what I can do about pushing things into CVS when I'm back from vacation in two weeks! Cheers, Erik On Thu, Jul 17, 2008 at 6:57 PM, Roland Schulz <[EMAIL PROTECTED]> wrote: > Hi all, >

[gmx-users] Re: gmx-users Digest, Vol 51, Issue 70

Hi Erik, Despite ffamber seems more developed for GMX, can you tell us if pdb2gmx (for next release) is also working for amber or we still need to tweak the pdb input file (Nxxx and Cxxx terms, CYN etc.)? Many thanks in advance, Alan > Date: Thu, 17 Jul 2008 21:49:56 +0200 > From: "Erik Lindahl"

[gmx-users] Re: CHARMM FF

Hi Erik, Despite ffamber seems more developed for GMX, can you tell us if pdb2gmx (for next release) is also working for amber or we still need to tweak the pdb input file (Nxxx and Cxxx terms, CYN etc.)? Many thanks in advance, Alan > Date: Thu, 17 Jul 2008 21:49:56 +0200 > From: "Erik Lindahl"

Re: [gmx-users] CHARMM FF

We also have a implementation of CHARMM(27) for Gromacs, but without CMAP as well. The main limitation is the computational cost due to the CHARMM TIP3P water model (it cannot be treated by the special code dedicated to water). IIRW the Gromacs 4 publication, the authors said there is no partic

Re: Re: [gmx-users] (no subject)

I think, setting tc groups = system will solve this issue. On Thu, 17 Jul 2008 Justin A.Lemkul wrote : >For warnings/errors, etc. please check the archive and wiki before posting. I >just responded to a similar issue a few days ago: > >http://www.gromacs.org/pipermail/gmx-users/2008-June/

[gmx-users] Biomolecular Modelling Retreat 8-12th September 2008

Stradbroke Island, Brisbane Australia A small school/retreat on classical molecular dynamics simulation techniques will be held from the 8th to the 12th of September 2008. The retreat has been organized as a satellite setting the WATOC (World Organization for Theoretically Orientated Chemists