[gmx-users] FeS cluster

Hello We dont have the parameters for Fe4S4 cluster in any of the the gomacs force fields but if we able to make the .itp file for the cluster manually with the help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in the include section of the  protein .top file later as

Re: [gmx-users] FeS cluster

subarna thakur wrote: Hello We dont have the parameters for Fe4S4 cluster in any of the the gomacs force fields but if we able to make the .itp file for the cluster manually with the help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in the include section of the

[gmx-users] PLUMED release 1.1.0 available

The PLUMED Developers Team is proud to announce that the NEW version of PLUMED 1.1.0 is available at http://merlino.mi.infn.it/plumed PLUMED is a plugin for free-energy calculations in molecular systems that can be interfaced, through a simple patch procedure, with some of the most popular

[gmx-users] Position-restraint

Dear gmx-users, I am trying to create a tpr file using grompp. My system has a protein with four identical chains, 288 POPC molecules, SOL, and ions. I am trying to restrain the lipid molecules. When running grompp, I get the following message: Program grompp, VERSION 3.3 Source code file:

Re: [gmx-users] Position-restraint

On Jul 28, 2009, at 9:50 AM, Morteza Khabiri wrote: Dear gmx-users, I am trying to create a tpr file using grompp. My system has a protein with four identical chains, 288 POPC molecules, SOL, and ions. I am trying to restrain the lipid molecules. When running grompp, I get the

[gmx-users] reg mopac.gromacs installations

dear gmx user thanks in advance  i have sucessfully installed the folowing version of fft files from src fftw-3.2.2 but when i install the gromacs-4.0.5 by giving the following command LIBS=-lmopac LDFLAGS=-L/usr/lical/lib ./configure --with-qmmm-mopac i got the error as follows configure:

[gmx-users] RE:appropriate values fot tau_t and tau_p

Hi, thank you for your help, Berk. The propertie I am looking for is the partial molar volume which can be calculated with this equation and a test particle insertion: vi=V^2exp(-bU)/Vexp(-bU) - V To find out the right mdp parameters I made test runs with a pure box of argon as vapour, so I

Re: [gmx-users] Huge acceleration needed to reproduce results!

Hi, Yes I realised that gromacs works in ps. I converted my force in kj mol-1 A-1 to acceleration in nm/ps2. I also took into account that the msd.xvg is plotted in nm and ps-2 and the calculated gradient printed at the top of the msd.xvg file is in cm2/s. One strange thing that I do

Re: [gmx-users] reg mopac.gromacs installations

vidhya sankar wrote: dear gmx user thanks in advance i have sucessfully installed the folowing version of fft files from src fftw-3.2.2 but when i install the gromacs-4.0.5 by giving the following command LIBS=-lmopac LDFLAGS=-L/usr/lical/lib ./configure --with-qmmm-mopac This command is

[gmx-users] question about continuation using tpbconv and mdrun -cpi

Hi all, Recently I made some tests on the continuation of gmx 4.0.5. Firstly, I run a complete simulation as the reference. In the full.mdp file, gen_seed=123456 continuation=yes are used to build the same initial structure. In all the simulations, mdrun -dlb no is used because I want to

[gmx-users] Re: openmm

Dear all, Zephyr (https://simtk.org/home/zephyr) is released, although only for Mac and Windows so far, and it comes with examples, pretty neat. Even though there's some apparently fixes compared to the usual release of openmm and gromacs-openmm, my molecule didn't work with it yet.

[gmx-users] linking

Dear gromacs users Can anyone of you please tell me as to how I can link ligands or chemical compounds onto proteins at specific locations or active sites and not just randomly placing it? Thank you. Love Cricket? Check out live scores, photos, video highlights and more. Click here

Re: [gmx-users] Huge acceleration needed to reproduce results!

Title indicates you think that you have CH4 in MCM: [ system ] ; Name CH4 in MCM Actual system is MCM in CH4: [ molecules ] ; Compound#mols MCM1 CH4340 .mdp accelerates the CH4: acc-grps = CH4 Now I'm not sure if this is the source

Re: [gmx-users] linking

P.R.Anand Narayanan wrote: Dear gromacs users Can anyone of you please tell me as to how I can link ligands or chemical compounds onto proteins at specific locations or active sites and not just randomly placing it? ... by doing it. Unfortunately, linking is too vague a verb to get you real

Re: [gmx-users] Huge acceleration needed to reproduce results!

Hi Chris, Thanks for the input-its good to get another person's perspective. Let me explain a bit more about my system... MCM stands for MCM-41, a mesoporous silica which consits of 1071 atoms so even though it is only 1 molecule, it is the more massive group. I am purposely accelerating

Re: [gmx-users] Huge acceleration needed to reproduce results!

As for your posted problem, I don't think that I can be of any more assistance. I picked the low-hanging fruit, but probably you need some assistance from somebody who has actually done constant acceleration simulations. I will take this opportunity to note, though, that you will never get

[gmx-users] energy of individual protein residues

Hello: I am interested in plotting the (kinetic) energy of the individual residues of a protein that I am working with. Is there a straight forward way to do this? Any suggestions would be greatly appreciated! Thank you, Kristina ___ gmx-users

[gmx-users] MD Simulation of DPPC Lipid Bilayer

Hello, I am new to Gromacs, but have prior experience with MD simulations. I'd like to setup and run a simulation of hydrated dipalmitoylphosphatidylcholine (DPPC) lipid bilayers at room temperature (~298 K). Are there tutorials that provide step-by-step instructions on how to do this? Thank

Re: [gmx-users] MD Simulation of DPPC Lipid Bilayer

Quoting Nancy nancy5vi...@gmail.com: Hello, I am new to Gromacs, but have prior experience with MD simulations. I'd like to setup and run a simulation of hydrated dipalmitoylphosphatidylcholine (DPPC) lipid bilayers at room temperature (~298 K). Are there tutorials that provide

Re: [gmx-users] MD Simulation of DPPC Lipid Bilayer

I tried to follow the Membrane Protein tutorial at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html I downloaded the properly oriented PDB file of the KALP-15 model peptide:

Re: [gmx-users] MD Simulation of DPPC Lipid Bilayer

This is a bug that has been reported some time ago (by me). To fix the issue, in the .rtp entry for [ NH2 ], change the improper line: N H H -C gi_1 to N H1 H2 -C gi_1 -Justin Nancy wrote: I tried to follow the Membrane Protein tutorial at:

[gmx-users] building C-Ter residues : automated

Hi all, I have a bunch of 200 pdb structures with missing C terminal residues , namely OC1 and OC2 due to which I am unable to build a topology file . I would appreciate if anyone knows of a tool or program which is capable of automatically adding these residues in a batch mode rather than

Re: [gmx-users] building C-Ter residues : automated

lorna mendonca wrote: Hi all, I have a bunch of 200 pdb structures with missing C terminal residues , namely OC1 and OC2 due to which I am unable to build a topology file . I would appreciate if anyone knows of a tool or program which is capable of automatically adding these residues in a batch

Re: [gmx-users] energy of individual protein residues

Kristina Woods wrote: Hello: I am interested in plotting the (kinetic) energy of the individual residues of a protein that I am working with. Is there a straight forward way to do this? Any suggestions would be greatly appreciated! g_traj -h. You may need to supply an index file with groups

Re: [gmx-users] question about continuation using tpbconv and mdrun -cpi

Baofu Qiao wrote: Hi all, Recently I made some tests on the continuation of gmx 4.0.5. Firstly, I run a complete simulation as the reference. In the full.mdp file, gen_seed=123456 continuation=yes are used to build the same initial structure. In all the simulations, mdrun -dlb no is used