Re: [gmx-users] Re: Locally Enhanced Sampling with Gromacs

2010-01-26 Thread David van der Spoel
On 1/27/10 7:49 AM, swa...@ncbs.res.in wrote: Dear Dr. Spoel, I am garduate student in National Centre for Biological Sciences(NCBS-TIFR), India. I am willing to do Locally Enhanced Sampling(LES) in one my research project.I saw few webpages on LES using GROMACS but not able to find any proper d

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

2010-01-26 Thread Mark Abraham
On 27/01/10 15:58, vivek sharma wrote: Hi Dallas, I am trying to run MD simulation over a docked complex (protein+ligand), to confirm their dynamic stability in water media. For the same I am using PRODRG server to generate topologies for ligand molecule as gromacs can generate topology for 20 st

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

2010-01-26 Thread Tsjerk Wassenaar
Hi Vivek, Either 1. Use the original ligand coordinates with the PRODRG topology or 2. Fit the structure obtained from PRODRG to the original structure Cheers, Tsjerk On Wed, Jan 27, 2010 at 5:58 AM, vivek sharma wrote: > Hi Dallas, > I am trying to run MD simulation over a docked complex (

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

2010-01-26 Thread vivek sharma
Hi Dallas, I am trying to run MD simulation over a docked complex (protein+ligand), to confirm their dynamic stability in water media. For the same I am using PRODRG server to generate topologies for ligand molecule as gromacs can generate topology for 20 standard residues. As mentioned in tutorial

[gmx-users] Re: Steered Molecular Dynamics (SMD) in Gromcas-4.0.5(toby10222...@sina.com)

2010-01-26 Thread toby10222224
Dear all: These days, I am trying to pull a slab of griphene moving along the Z direction at a constant speed. The slab of griphene contains 700 atoms. After several times of  E-mail communication with the Gromacs users, the simulation can run. However, the run didn't produce the results which I

Re: [gmx-users] Problem in g_rms

2010-01-26 Thread Mark Abraham
On 27/01/10 15:11, rituraj purohit wrote: I want get rmsd deviation between NMR structure and the simulated result, but i am getting following error in following command. g_rms -s em.tpr -f md.trr -o rsmd_Calpha.xvg WARNING: topology has 50772 atoms, whereas trajectory has 22899 ---

[gmx-users] Problem in g_rms

2010-01-26 Thread rituraj purohit
I want get rmsd deviation between NMR structure and the simulated result, but i am getting following error in following command. g_rms -s em.tpr -f md.trr -o rsmd_Calpha.xvg WARNING: topology has 50772 atoms, whereas trajectory has 22899 --- Pro

[gmx-users] Problems with gromacs-openMM

2010-01-26 Thread jorge_quintero
Hello everybody, I tried to install gromacs 4.0.7 + openMM on Fedora core 10 x86_64, but I had lots of problems with that. I typed the configure options below to obtain a Makefile: $ ./configure --enable-shared --prefix=/opt/gromacs_openmm CPPFLAGS="-I/opt/openmm/include/openmm/ -I/opt/openmm/i

Re: [gmx-users] Potential Energy

2010-01-26 Thread Mark Abraham
- Original Message - From: Yanmei Song Date: Wednesday, January 27, 2010 10:58 Subject: Re: [gmx-users] Potential Energy To: jalem...@vt.edu, Discussion list for GROMACS users > Dear Justin: > > I finally figure out that the problem comes from the Coulomb 1-4 interactions > defined b

Re: [gmx-users] Potential Energy

2010-01-26 Thread Yanmei Song
Dear Justin: I finally figure out that the problem comes from the Coulomb 1-4 interactions defined by [pairs] part. When I remove this parts, the energy minimization ends with a big negative number. Thanks for your help. On Tue, Jan 26, 2010 at 4:24 PM, Justin A. Lemkul wrote: > > > Yanmei Song

Re: [gmx-users] Potential Energy

2010-01-26 Thread Justin A. Lemkul
Yanmei Song wrote: Dear Justin: Sorry, that itp is the original one generated by PRODRG. Also I have modified it based on a optimized force field of the molecule. (See attached file and the literature of the force field). But still the potential energy is positively 1e2 and why the system c

[gmx-users] stretched exponential

2010-01-26 Thread Ramachandran G
Dear gromacs users: I have a couple of questions: While doing auto correlation function under what condition i need to use polynomials? Apart from the fit functions existing in the gromacs how can i use different functions like stretched exponential in the form P(t)=ex

Re: [gmx-users] the solvent group SOL is not continuous

2010-01-26 Thread Justin A. Lemkul
nce, for systems in such size, the potential energy is usually a big negative number? Does this mean that my force field parameter or molecule structure have problems? Thanks in advance! -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Ariz

[gmx-users] Re: gmx-users Digest, Vol 69, Issue 133

2010-01-26 Thread Miguel Quiliano Meza
-0700 > From: Yanmei Song > Subject: [gmx-users] Potential Energy > To: Discussion list for GROMACS users > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Users: > > I am in the process of setting up a new system. I have a 8.

Re: [gmx-users] Potential Energy

2010-01-26 Thread Justin A. Lemkul
Yanmei Song wrote: Dear Justin: Thanks for your response. I got my force field parameters from PRODRG. The system run well and I got a very reasonable density profile. Just can not figure out what is the problem. I attached my itp file and gro file. Would you please help me check what is th

Re: [gmx-users] Potential Energy

2010-01-26 Thread Justin A. Lemkul
Yanmei Song wrote: Dear Users: I am in the process of setting up a new system. I have a 8.0*8.0*8.0 nm3 system which include 27800 molecules. When the system approach equilibrium, I found the potential energy is +3e5 (big positive number). Is this normal? Since based on my experience, for

[gmx-users] RE : gmx-users Digest, Vol 69 , Issue 132

2010-01-26 Thread ABEL Stephane 175950
atal error: The solvent group SOL is not continuous: index[9]=1732, index[10]=1747 --- "Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is." (Jackie Brown) *I do not know the reason,the number of residues in top f

[gmx-users] Potential Energy

2010-01-26 Thread Yanmei Song
Dear Users: I am in the process of setting up a new system. I have a 8.0*8.0*8.0 nm3 system which include 27800 molecules. When the system approach equilibrium, I found the potential energy is +3e5 (big positive number). Is this normal? Since based on my experience, for systems in such size, the

Re: [gmx-users] the solvent group SOL is not continuous

2010-01-26 Thread Justin A. Lemkul
Miguel Quiliano Meza wrote: *Hi everyone. I have a problem when I try to run GENION, GROMACS says: * WARNING: turning of free energy, will use lambda=0 Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision) Using a coulomb cut-off of 0.9 nm Will try to add 0 Na ions and 15 NA+ ions.

[gmx-users] the solvent group SOL is not continuous

2010-01-26 Thread Miguel Quiliano Meza
*Hi everyone. I have a problem when I try to run GENION, GROMACS says: * WARNING: turning of free energy, will use lambda=0 Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision) Using a coulomb cut-off of 0.9 nm Will try to add 0 Na ions and 15 NA+ ions. Select a continuous group of so

RE: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

2010-01-26 Thread Dallas B. Warren
So, what EXACTLY are you doing? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the o

Re: [gmx-users] Re: Obtain a pre-version of gromacs 4.1 without git

2010-01-26 Thread Justin A. Lemkul
Stephane Abel wrote: Thank you Roland for your response I have effectively downloaded from the http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version of gmx Unfortunately, the unpacked directory does not contain a configure file, I have only an configure.ac. So my question

[gmx-users] Re: Obtain a pre-version of gromacs 4.1 without git

2010-01-26 Thread Stephane Abel
Thank you Roland for your response I have effectively downloaded from the http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version of gmx Unfortunately, the unpacked directory does not contain a configure file, I have only an configure.ac. So my question is: how to obtain a ful

Re: [gmx-users] xtc file

2010-01-26 Thread Carla Jamous
Thank you . Carla On Tue, Jan 26, 2010 at 11:53 AM, Carsten Kutzner wrote: > > On Jan 26, 2010, at 11:48 AM, Carla Jamous wrote: > > > Hi everyone, > > > > Please I'm having a problem with mdrun: > > If I type: > > mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g > test.lo

Re: [gmx-users] xtc file

2010-01-26 Thread Carsten Kutzner
On Jan 26, 2010, at 11:48 AM, Carla Jamous wrote: > Hi everyone, > > Please I'm having a problem with mdrun: > If I type: > mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g > test.log > > I never get the .xtc file. Can anyone tell me why & what can I do to have an > .x

[gmx-users] xtc file

2010-01-26 Thread Carla Jamous
Hi everyone, Please I'm having a problem with mdrun: If I type: mdrun -v -s test.tpr -o test.trr -c test.pdb -x test.xtc -e test.edr -g test.log I never get the .xtc file. Can anyone tell me why & what can I do to have an .xtc file? Thank you Carla -- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] MARTINI-CG updated web site

2010-01-26 Thread Krzysztof Mlynarczyk
I wish G96 force fields had a similar website with so much useful information. It would be good if authors posted anything on the forum cause it's completely empty right now. 2010/1/26 XAvier Periole > > Dears, > > the MARTINI CG force field web site has been remodeled. > > It now includes FAQs,

[gmx-users] MARTINI-CG updated web site

2010-01-26 Thread XAvier Periole
Dears, the MARTINI CG force field web site has been remodeled. It now includes FAQs, tutorials, a forum and much more ... http://md.chem.rug.nl/cgmartini Enjoy. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] PLUMED tutorial announcement

2010-01-26 Thread Giovanni Bussi
Dear all, We are proud to announce a CECAM tutorial on PLUMED. PLUMED is an open source plugin for free-energy calculations in molecular systems that can be interfaced, through a simple patch procedure, with some of the most popular classical molecular dynamics codes, including AMBER, GROMACS, NA