[gmx-users] Averege structure

I have done 15ns MD simulations at 300k temp for a protein finally obtained an average structure from g_rmsf. so please tell me is output average structure is a sampled structure? is there no need of remd or sampling further because I got plateau in RMSD calculation at last? I have strongly energy

[gmx-users] topology builiding

Hi There, I am using x2top to build topology for a molecule using oplsaa forcefield from a pdb file. I have added a few entries in the n2t file but i have got a wrong topology as some additional bonds are made in the molecule. As far as I know x2top ignores the connect information of the atoms. Is

Re: [gmx-users] charmmff

Hi, The gromacs version in git master, please see the directory share/top/charmm27.ff That directory contains whole gromacs charmm files. Furthermore, please see the reference below which explain more details about these parameters. Bjelkmar, Larsson, Cuendet, Hess, and Lindahl, JCTC 2010 I hop

Re: [gmx-users] Need For a Script

Hi Justin, I am trying to perform umbrella sampling following your link. But when I put the command grompp -f md_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o umbrella0.tpr I found the the following error No molecules were defined in the system Could you please suggest please? S

[gmx-users] charmmff

Hi, If one has to make a version of gromacs charmm compatible, which files from the charmm compatible version must be looked at? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

Re: [gmx-users] extracting coordinates

What do you want to do with the coordinates? Look-up 'trjconv' -Gaurav On Tue, Jul 20, 2010 at 11:32 AM, Vishal Agarwal wrote: > 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 > eac

[gmx-users] Free Energy Calculation Using Tabulated Potentials

Hi, I am having some troubles calculating free energies. Can someone please tell me if I have tabulated potentials, can I calculate free energy using the gromacs options in the mdp file for free energies. (If someone has done it, can you please provide a sample topology file.) Thanks, Nimesh -

[gmx-users] I wonder if anyone has a "gmx2lmp" tool

Hi Does anyone also use LAMMPS? I want to ask if anyone has written a tool which transfers Gromacs input files (.itp, .top, and .gro files) into a lammps ".data" input file. Thank you! Shuo Li Ph.D. Candidate in Chemical Engineering Department of Chemical & Materials Engineering University of

[gmx-users] Segmentation Fault with g_dielectric

Hello, I am trying to calculate the dielectric constant for pure tetrahydrofuran (THF) at 298K. I keep running into problems though. I have looked through the gmx user list to see if others have had these problems, but I didn't see any mention of them (although I did see that others were asked t

[gmx-users] Heme_Grompp_error

Dear All I used the following command sequentially to prepare file for energy minimization and subsequent MD run. 1. pdb2gmx -f *.pdb -o seq.gro -p seq.top 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic 3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top 4. grompp -c s

[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] translation

Hi, all: I am running dynamics with PBC in xyz direction. Now I got a problem. Since PBC is applied, some atoms will move to the other side of the box and this will change the polarization. I need the results of polarization, so I do not hope that the polarization changed during the dynamics. Do

Re: [gmx-users] frezzing a bond

Justin A. Lemkul wrote: > Nilesh Dhumal wrote: >> How can I freeze a bond? > How about distance restraints instead? That raises some kind of off-topic question: In Cerius2, we use position constraints to reduce the calculation complexity, because forces between constrained atoms need not to be eva

[gmx-users] LINC warning but reasonable potential energy and force

Dear experts, I am trying to build up a polymer system. To do so I took a chain with 60 repeating units (ethylene) and compressed the system to attain the desired box volume (density). I took the following approach since after one week work on this problem I believe that is the only way of achievi

[gmx-users] Re: Help needed with ACPYPI

Hi there, I didn't have time to improve opls generation in ACPYPE. I need to put a Wiki about it for the moment, but to get the Opls atomtypes, use MKTOP: http://labmm.iq.ufrj.br/mktop/ Good luck, Alan On Tue, Jul 20, 2010 at 14:42, wrote: > Hello all > > I want to study protein-ligand using

[gmx-users] Re: gmx-users Digest, Vol 75, Issue 107

help. Shahid Nayeem -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100720/9f365e5f/attachment-0001.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.

[gmx-users] Re: gmx-users Digest, Vol 75, Issue 107

help. Shahid Nayeem -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100720/9f365e5f/attachment-0001.html -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.

Re: [gmx-users] Replica exhange - no. of processors

On 19/07/10 17:25, Sai Pooja wrote: Thanks Lanyuan. Can one use fewer processors than the number of replicas? My 0.02 £: I never did REMD, but, as far as I know, putting more processes on the same processor in any kind of parallel computing is asking for your performance to grind to a halt.

Re: [gmx-users] Tabulated potentials and performance

On 19/07/10 23:18, Lanyuan Lu wrote: From our group's experience, there is a critical point for dramatic performance drop when one uses two many tables. The possible reason is that the size of tables exceeds the cache size. However, this only happens when the number of tables is beyond something

Re: [gmx-users] Potential of mean force

The tutorial to which you refer should give you all the necessary background to apply pulling to a variety of systems. In general, the procedure is the same. -Justin Quoting abdul wadood : > > Dear gmx user > > First of all I am very thankful to all of you in helping me in the running of > nor

[gmx-users] Potential of mean force

Dear gmx user First of all I am very thankful to all of you in helping me in the running of normal simulation using gromacs. Now, I want to calculate pmf for enzyme ligand complex. I search for correct direction but not found anywhere. There is tutorial on the gromacs website but it is for pept

[gmx-users] Help needed with ACPYPI

Hello all I want to study protein-ligand using OPLS ff of Gromacs. For Ligand topology preparation, I am using ACPYPI where I am getting "9 opls_x 1 <1> C9__9 0.056600 0.0 ; qtot -0.253" in .itp file of ligand. And thus, atomtype opls_x is not recognised which leads to falal