[gmx-users] gmx dipoles and gmx potential output files detail

Hello gromacs user I am trying to calculate the various properties from the membrane simulation. As I am trying to explore the various properties which I can calculate from the trajectory using various module given in the gromacs. But I felt difficulties in understanding the various output

Re: [gmx-users] CH3CN solvents breaking the periodic box

Hi Debashis, I haven't looked at your trajectory but I suspect this will answer your question: http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Cara Date: Fri, 15 May 2015 12:02:31 +0530 From: debashis.sah...@gmail.com To: gmx-us...@gromacs.org Subject: Re:

[gmx-users] RMSD distribution calculation using g_cluster

During calculation of RMSD distribution using *g_cluster*, the Y axis of the XVG file showing the RMSD distribution denotes a.u. i.e arbitrary unit which I think probably the frequency. But it is not clear which frequency it exactly is and also kindly let me know how the calculation happened. --

Re: [gmx-users] CH3CN solvents breaking the periodic box

Dear Justin, I have decreased the box size than previous box case. Now I have mentioned coupling between the system and the rest of mix solvent and ion. The trajectory of the MD is better than the earlier in this new box (water 345 and acetonitrile 48) cases. But there is a

[gmx-users] (no subject)

Dear All, can anyone send me the GROMACS Script file to run in cluster. Email id: sivanandam...@gmail.com M.SIVANANDAM Research Scholar Department of Physics Periyar University Salem-636 011 Mobile- 9965582730, 9042066076

Re: [gmx-users] Protein+ligand complex

On 5/15/15 1:36 AM, Kashif wrote: I have done MD simulation of my protein and ligand docked complex. My protein is having 900 amino acids. When I use g_rms to analyse rmsd, the graph is too short. Currently I am simulating my protein for 5 ns. Should I increase my ns for such big protein and

Re: [gmx-users] energy minimization problem

On 5/14/15 10:02 PM, Ming Tang wrote: Hi Justin Here is the .mdp file with position restraints, which I downloaded from the martini tutorial website. It works well with the tutorial and my small triple helix, and the grompp process does not give any warnings. Please help to have a look.

Re: [gmx-users] Sanjay (REg. Grompp error CA ATOM NOT FOUND)

On 5/15/15 6:29 AM, sanjay choubey wrote: HI, Thanks for your cooperation. Last time i asked about grompp error in running membrane dynamics simulation. THe error was atom type CA Not found. You suggested me to remove CA from DPPC.itp. But no effect still i am getting I did not suggest

Re: [gmx-users] energy minimization problem

On 5/15/15 9:32 AM, Ming Tang wrote: Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be reasonable according to gromacs website. So ijust kept trying 0.02ps The time step will depend on the stability of the system, which in turn depends on how well equilibrated it is.

Re: [gmx-users] Why h_bond can not form

I'm so glad to tell that the question seemed to be solved after I refine the charge of Zn atom and the atoms around it. +2 may be too much for the Zn atom, and reduce the positive charge according to the results of resp calculation. Also I think the simulation could be further refined after

Re: [gmx-users] energy minimization problem

Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be reasonable according to gromacs website. So ijust kept trying 0.02ps Sent from my Huawei Mobile Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 10:02 PM, Ming Tang wrote: Hi Justin Here is the .mdp file with position

Re: [gmx-users] Error 'Atomtype NTL not found'

On 5/15/15 4:15 PM, Ta-Chou 黃大周 wrote: Dear all, Actually, I had google for this error message, but I can't understand the answer clearly, and it seems the previous question didn't finish yet. I want to run a MD simulation with amber force field for a membrane protein. And the simulation box

Re: [gmx-users] question

Hi, I am not sure anyone will be able to help, because this isn't really about Gromacs. Can you please clarify who they are and what exactly you mean by perpendicular when talking about surfactants? Also, what are those surfactants? Anyway, a reference to a representative paper and some

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 133, Issue 87

Golnaz, I think you're creating a bit of a mess by replying to the digest. If you don't mind, please see my answer directly to your specific question, where I will also quote your message from below. Alex GR Thank you Alex GR First of all it is better to say that I am a beginner. I follow two

Re: [gmx-users] question

Okay, I looked at the first paper. As Abhijit said, you can manipulate any part of your input coordinates by using something like packmol. In addition, pymol and GMX itself (editconf) provides means for translation and rotation of your choosing. I think VMD has this functionality as well,

Re: [gmx-users] genion error sol not continuous

Hi Justin, Thanks for your email. I have modified it and the topology looks fine to me or at least I can't see any problem with it but still genion does not like it? Would please have a look? https://drive.google.com/file/d/0B0YMTXH1gmQsSl9KbWhXaWJKc1k/view?usp=sharing

[gmx-users] Error 'Atomtype NTL not found'

Dear all, Actually, I had google for this error message, but I can't understand the answer clearly, and it seems the previous question didn't finish yet. I want to run a MD simulation with amber force field for a membrane protein. And the simulation box contains my goal membrane protein, POPC