Re: [gmx-users] How to print out .gro per 100 ps?

Chih-Ying Lin wrote: Hi I want to simulate the system straight to 1ns. How to print out .gro per 100 ps? I only know Gromacs can print out the .gro file at the end of the simulation. How can I print out the .gro in the middle way of simulation? Have a look in the manual. Section 7.4 lists all

Re: [gmx-users] protein molecular weight?

Chih-Ying Lin wrote: Hi From the following website=> it lists Properties grade for molecular biology formlyophilized powder mol wt single-chain mol wt 14.7 kDa composition protein, ≥90% storage temp. -20°C How to get the molecular weight from the above protein properties? This

[gmx-users] How to print out .gro per 100 ps?

Hi I want to simulate the system straight to 1ns. How to print out .gro per 100 ps? I only know Gromacs can print out the .gro file at the end of the simulation. How can I print out the .gro in the middle way of simulation? Thank you Lin ___ gmx-users

[gmx-users] protein molecular weight?

Hi >From the following website=> it lists Properties grade for molecular biology formlyophilized powder mol wt single-chain mol wt 14.7 kDa composition protein, ≥90% storage temp. -20°C How to get the molecular weight from the above protein properties? L7651 Lysozyme from chicken eg

Re: [gmx-users] Installation Problem

farzaneh fatahi wrote: Dear gmx-users! Hi, I am trying to install an old version of Gromacs (gromacs-localp-3.0.2) for local pressure calculation. I successfully configured the gromacs with: ./configure –program-suffix=_d –prefix=/usr/local/gromacs333_double –enable-double Perhaps you should n

[gmx-users] Installation Problem

Dear gmx-users! Hi, I am trying to install an old version of Gromacs (gromacs-localp-3.0.2) for local pressure calculation. I successfully configured the gromacs with: ./configure –program-suffix=_d –prefix=/usr/local/gromacs333_double –enable-double ... ..

[gmx-users] Re: Long-range (LR) energies in gromacs v3.3.3

Shankar Prasad Kanaujia wrote: Dear justin, sorry for writing person mail. I am attaching the .mdp file. You are using a shift potential for vdwtype (and you haven't applied it correctly - read the manual.) Therefore, LJ terms are cut off at rvdw (the LJ term is zero beyond this point) an

[gmx-users] Re: Long-range (LR) energies in gromacs v3.3.3

Please keep all correspondence on the gmx-users list. I do not advertise myself as a private tutor :) Shankar Prasad Kanaujia wrote: Dear Justin, I have done simulation of protein-ligand complex using gromacs v3.3.3. The g_energy gives LJ-14, Coulomb-14, LJ-SR, Coulomb-SR energies, however,

Re: [gmx-users] Non standard amino acids.

david.lisgar...@canterbury.ac.uk wrote: Dear Users, We want to run gromacs molecular dynamics for a molecule which contains the following non standard amino acids: D-MeVal and L-Nva (norvaline) How may we proceed to parameterise these residues to include in the appropriate force field. (ffG43a2.

Re: [gmx-users] protein molecular weight?

Chih-Ying Lin wrote: Hi : Would anyone explain how to get the protein molecular weight from the following note from the catalog? mol wt single-chain mol wt 14.7 kDa Where did this come from? Is this in the manual somewhere? In any case it's probably just an example of expected output fro

[gmx-users] protein molecular weight?

Hi : Would anyone explain how to get the protein molecular weight from the following note from the catalog? mol wt single-chain mol wt 14.7 kDa What does it mean single-chain? Is it correct => 1 kDa = 1000 Da = MW 1000. So MW 240 = 0.24 kDa. Thank you Lin _

Re: [gmx-users] Installing topolbuild

On Friday, May 29, 2009 9:38:00 AM, vivek sharma wrote: > Thanks a lot for your quick response. It is really encouraging to get > response from developers like you. > > I tried generating topology again with the same command line and corrected > input file.This time I am > getting error a

[gmx-users] Non standard amino acids.

Dear Users, We want to run gromacs molecular dynamics for a molecule which contains the following non standard amino acids: D-MeVal and L-Nva (norvaline) How may we proceed to parameterise these residues to include in the appropriate force field. (ffG43a2.rtp). We would be grateful for any informa

Re: [gmx-users] Nanoparticles does not interact

osmair oliveira wrote: Hi Mark, My *.mdp file: cpp = /lib/cpp integrator = md ;constraints = h-bonds dt = 0.001 nsteps = 500 nstcomm = 1 nstxout = 1000 nstvout = 1000 nstxtcout

RE: [gmx-users] Nanoparticles does not interact

Hi Mark, My *.mdp file: cpp = /lib/cpp integrator = md ;constraints = h-bonds dt = 0.001 nsteps = 500 nstcomm = 1 nstxout = 1000 nstvout = 1000 nstxtcout = 100 nstlog

Re: [gmx-users] membrane protein simulation

Thanx Justin...i must go throuh that tutorial. thanx for the help. --- On Fri, 29/5/09, Justin A. Lemkul wrote: From: Justin A. Lemkul Subject: Re: [gmx-users] membrane protein simulation To: "Discussion list for GROMACS users" Date: Friday, 29 May, 2009, 4:49 PM Samik Bhattacharya wrote:

Re: [gmx-users] membrane protein simulation

Samik Bhattacharya wrote: hi i'm new to gromacs and want to simulate a protein inside a phospholipid envelop (may be box or dodecahedron). for this i got the pdb files of both the proteins and the lipids(e.g.POPC, POPE etc). but i'm facing a lot of problems in generating the topology files a

[gmx-users] membrane protein simulation

hi  i'm new to gromacs and want to simulate a protein inside a phospholipid envelop (may be box or dodecahedron). for this i got the pdb files of both the proteins and the lipids(e.g.POPC, POPE etc). but i'm facing a lot of problems in generating the topology files as well as in running grompp a

Re: [gmx-users] missing atoms

swa...@ncbs.res.in wrote: Hi All, I am running Gromacs for drug enzyme complex using AMBER as forcefield.While running pdb2gmx command I am getting error and warning of 790 missing atoms. Can anybody suggest me how to correct this error. Either supply a structure file that has suitable hydroge

RE: [gmx-users] missing atoms

It is not straightforward to use the AMBER forcefield with Gromacs. You need to edit your pdb-file to account for different atom/residue names used by AMBER as opposed to GROMOS forcefields. Detailed info is here: http://chemistry.csulb.edu/ffamber/ If this is your first MD simulation, try thing

Re: [gmx-users] how to do MD simulation of protein with Fe-S cluster

amri ta wrote: Dear Gromacs users, I am currently working on Dynamic simulation studies using GROMACS software. In my current work I want to do simulation of a protein containing Fe-S cluster. If i directly do through pdb2gmx then it is giving a error massage like "FES in not included in .

[gmx-users] missing atoms

Hi All, I am running Gromacs for drug enzyme complex using AMBER as forcefield.While running pdb2gmx command I am getting error and warning of 790 missing atoms. Can anybody suggest me how to correct this error. error : --- WARNING: atom H i

[gmx-users] how to do MD simulation of protein with Fe-S cluster

Dear Gromacs users,   I am currently working on Dynamic simulation studies using GROMACS software. In my current work I want to do simulation of a protein containing Fe-S cluster. If i directly do through pdb2gmx then it is giving a error massage like "FES in not included in .rtp file". Regardin

Re: [gmx-users] grompp warning

sarbani chattopadhyay wrote: Hi, I have a 13 residue peptide which I have kept in a box using the following command editconf -f conf.gro -bt cubic -o box.gro -d 0.75 the flag "-d 0.75" is given as per the ' minimum image convention'. When I solvate the box, 6772 water molecules get added. Wi

[gmx-users] grompp warning

Hi, I have a 13 residue peptide which I have kept in a box using the following command editconf -f conf.gro -bt cubic -o box.gro -d 0.75 the flag "-d 0.75" is given as per the ' minimum image convention'. When I solvate the box, 6772 water molecules get adde

Re: [gmx-users] constant term in dihedral potential function

Berk Hess wrote: But this is a different issue. These changes are to enable automatic parameter settings based on atomtypes for multiple dihedrals over the same bonds. Andreas specifies the parameters on the same line in the [ dihedrals ] section. In that case every works (and has alwats worke

RE: [gmx-users] constant term in dihedral potential function

> Date: Fri, 29 May 2009 16:52:50 +1000 > From: mark.abra...@anu.edu.au > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] constant term in dihedral potential function > > Kukol, Andreas wrote: > > Many thanks for your help. > > > > As for the 1-4 interactions, I am using the Gromos53a6 fo