Re: [gmx-users] GPU+Energy Groups

Hi Mark, Thanks a lot for your help. Actually, in my case tables are defined for non-bonded LJ interactions. Anyway, I need them since all we did were on defining those tables :) Thanks again, Neda - Original Message - From: Mark Abraham To: gmx-us...@gromacs.org Sent: Fri, 06 Jul

Re: [gmx-users] Tacticity in polymer simulation

Sorry for posting the question here again. I cannot help but turn to this forum since almost all papers I have read on tacticity in atomistic simulations have used some kind of software package to build polymers with desired tacticity. My university is banned from using Gaussian, which is the most

Re: [gmx-users] Queries regarding temperature gradient

Dear Dr. Lemkul, Thank you for your answer. Can you please also advise how can I get the temperature of a system as a function of distance using gromacs 5.1.5? gmx energy plots the temperature of the centre of mass of energy groups against time. gmx traj also does the same from velocity

Re: [gmx-users] umbrella sampling tutorial

On 7/6/18 10:42 AM, hosein geraili wrote: Dear all, I have a question regarding the umbrella sampling tutorial. I am using the bash script to create the summary_distances.dat, but the problem is at first I would get the error "Unknown command-line option -o", then I used -oh instead of -o

Re: [gmx-users] Queries regarding temperature gradient

On 7/6/18 1:07 PM, Sabreen Farnaz wrote: Dear all, This is in regard to my previous queries. The warning in NVT step can possibly be ignored using -maxwarn but I am still not sure about the rest! Can someone please help? tau_t = -1 means temperature coupling is not applied. Whether that's

Re: [gmx-users] gmx convert-tpr tool is not found but tpbconv_mpi is present in gromacs 5.0.4

On 7/6/18 11:58 AM, Santanu Santra wrote: Hi all, I have installed gromacs 5.0.4 in a parallel cluster. While I was serching for gmx convert-tpr tool to extend my simulation that has been run previously upto 15 ns (I want to continue the simulation upto 100 ns). According to gromacs

Re: [gmx-users] Queries regarding temperature gradient

Dear all, This is in regard to my previous queries. The warning in NVT step can possibly be ignored using -maxwarn but I am still not sure about the rest! Can someone please help? Thanks, Neelima S. On Fri, 6 Jul 2018, 01:56 Sabreen Farnaz, wrote: > Dear all, > > I am setting up a system where

[gmx-users] gmx convert-tpr tool is not found but tpbconv_mpi is present in gromacs 5.0.4

Hi all, I have installed gromacs 5.0.4 in a parallel cluster. While I was serching for gmx convert-tpr tool to extend my simulation that has been run previously upto 15 ns (I want to continue the simulation upto 100 ns). According to gromacs documentation tpbconv_mpi tool is removed from

[gmx-users] umbrella sampling tutorial

Dear all, I have a question regarding the umbrella sampling tutorial. I am using the bash script to create the summary_distances.dat, but the problem is at first I would get the error "Unknown command-line option -o", then I used -oh instead of -o which worked, but the problem is the 

Re: [gmx-users] GPU+Energy Groups

Hi, You can't ever use a tabulated short-range interaction on a GPU in GROMACS at this time. Mark On Fri, Jul 6, 2018 at 10:55 AM Neda Rafiee wrote: > Dear GMX-Users, > I am going to use GPU acceleration for my simulations but since I have > some energy tables for LJ interactions, and I am

Re: [gmx-users] question regarding high temperature simulation in Gromacs

Hi, I don't know, sorry. This is a critical part of your study design, and I can't do it for you. Look in the literature of its use for any at high temperature that was actually validated. Or see if e.g. the density and diffusion rate of your solvent is represented accurately. Mark On Fri, Jul

Re: [gmx-users] histogram of distance between similar molecules

On 7/6/18 8:44 AM, Srinivasa Ramisetti wrote: Thanks Justin for the info. I understand that gmx distance -oh will produce the histogram for single pair of molecules. Since I want to generate histogram for several other combinations (96 in total) then I may have to call gmx distance several

Re: [gmx-users] histogram of distance between similar molecules

Thanks Justin for the info. I understand that gmx distance -oh will produce the histogram for single pair of molecules. Since I want to generate histogram for several other combinations (96 in total) then I may have to call gmx distance several times which can be done through scripting. But I

Re: [gmx-users] How to change to heavyh in an equilibrated system

On 7/6/18 4:52 AM, Ramon Crehuet wrote: Dear all, For testing reasons, I would like to compare a system that I have setup using heavy hydrogens (-heavyh option in pdb2gmx) to exactly the same system without using heavy hydrogens. I could redo all the system setup starting from the pdb2gmx,

Re: [gmx-users] histogram of distance between similar molecules

On 7/6/18 4:30 AM, Srinivasa Ramisetti wrote: Dear Gromacs users, I would like to know which tool (gmx distance or gmx pairdist) can be used to get a histogram (showing probability distribution function) of the centre of mass distance between similar molecules (14 molecules in total) for

Re: [gmx-users] ZnO Parameters

Hi, You can fınd parameters on solid state books(for example kittel) Thank you. 6 Tem 2018 Cum 13:09 tarihinde şunu yazdı: > Dear Gromacs Users > > Can anyone provide me the parameters for Zinc Oxide (ZnO)? > > Thank You > > Regards > Zaved Hazarika > PhD Scholar > Dept.of Molecular Biology

Re: [gmx-users] question regarding high temperature simulation in Gromacs

Hi Mark, I am using OPLS-AA force field for simulating my protein at high temperature under nvt condition. Does this work good for high temperature system under nvt? Can you suggest which force field I should use then? Thanks Puspita - Original Message - From: "Mark Abraham" To:

[gmx-users] ZnO Parameters

Dear Gromacs Users Can anyone provide me the parameters for Zinc Oxide (ZnO)? Thank You Regards Zaved Hazarika PhD Scholar Dept.of Molecular Biology and Biotechnology Tezpur University India * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely

[gmx-users] Coarse graining carbon nanotubes and MARTINI

Dear All, I want to run a CG simulation of carbon nanotubes (CNTs) and different proteins. I have a few questions for which I request help: 1. Several groups have used CG models of CNTs, mapping 2, 2.5 or 3 carbons per CG bead. I am a novice in CG models. Any help on creating CG models or

[gmx-users] How to change to heavyh in an equilibrated system

Dear all, For testing reasons, I would like to compare a system that I have setup using heavy hydrogens (-heavyh option in pdb2gmx) to exactly the same system without using heavy hydrogens. I could redo all the system setup starting from the pdb2gmx, but I would like to avoid that. That setup

[gmx-users] GPU+Energy Groups

Dear GMX-Users, I am going to use GPU acceleration for my simulations but since I have some energy tables for LJ interactions, and I am using cut-off scheme=group instead of Verlet, I receive these notes: "NOTE: GPU(s) found, but the current simulation can not use GPUs To use a GPU, set

[gmx-users] Thermal gradient in a system

Dear all, How can I get the temperature of a system as a function of distance using gromacs 5.1.5? gmx energy plots the temperature of the centre of mass of energy groups against time. gmx traj also does the same from velocity information. Please help! Regards, Neelima S. -- Gromacs Users

[gmx-users] histogram of distance between similar molecules

Dear Gromacs users, I would like to know which tool (gmx distance or gmx pairdist) can be used to get a histogram (showing probability distribution function) of the centre of mass distance between similar molecules (14 molecules in total) for a range of time steps. Regards, Srinivasa --

Re: [gmx-users] question regarding high temperature simulation in Gromacs

Hi, You should expect that when you heat something up under constant volume that its pressure increases. Average velocity has gone up, so the momentum transferred in collisions is also up. The more important question is what evidence you have that this force field provides a useful simulation at

Re: [gmx-users] question regarding high temperature simulation in Gromacs

Hi All, Thanks for your helpful suggestions. I'd like to share the method that I am following now for simulating my protein at high temperature. First, I carried out energy minimization run for my protein system using steepest decent method. Then I performed nvt equilibration run for 100-200