[gmx-users] RMSD sudden jump

Dear gromacs users, I have performed ~30ns MD on a protein in TIP4P water using the OPLS forcefield. I have concatenated the trajectories for each step using trjcat and removed pbc effects using pbc nojump. All the particles of the system now don't jump anymore and the molecule doesn't appear as

Re: [gmx-users] Ques

Hi Xianwei Wang, According to the information in your mail (the comments from the mdp file), it's just the other way around: phi is the amplitude and a is the phase. Cheers, Tsjerk On Mar 13, 2012 3:11 AM, "Xianwei Wang" wrote: *Dear gmx users: **I would like to apply electric fie

Re: [gmx-users] help on replica exchange dynamics with gromacs

On 13/03/2012 3:17 PM, Raghuvir Pissurlenkar wrote: Dear friends Can someone help me with tutorial on replica exchange dynamics Thanks in advance Raghuvir Search the GROMACS webpage, please. You will want to do some normal tutorials to understand normal workflows first. Mark -- gmx-us

[gmx-users] help on replica exchange dynamics with gromacs

Dear friends Can someone help me with tutorial on replica exchange dynamics Thanks in advance Raghuvir -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

[gmx-users] Ques

Dear gmx users: I would like to apply electric field to my simulation box. I have already read the manual and I added this into mpd file as manual told: ; Electric fields = 7.1e-10V/nm ; Format is number of terms (int) and for all terms an amplitude (real) = ; and a phase angle (

Re: [gmx-users] There was 1 error in input file(s)

On 2012-03-12 22:56, saly jackson wrote: Hi everybody I want to build a simulation box fill of water and some SDS molecules. To do this at first I fill the box with SDS molecules without their Na+ ions. Then I filled the simulation box with water molecules. After that, I want to replace some wat

[gmx-users] There was 1 error in input file(s)

Hi everybody I want to build a simulation box fill of water and some SDS molecules. To do this at first I fill the box with SDS molecules without their Na+ ions. Then I filled the simulation box with water molecules. After that, I want to replace some water molecules with Na+ ions. I ran the follo

Re: [gmx-users] pdb file

A neat way to get generic coordinates of organic molecules like this is using Jmol: 1) go to http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm?USESIGNED This requires Sun/Oracle Java plugin activated in the browser and asks for permission to trust the signed applet. Alternatively on

[gmx-users] pdb file

Thank you very much from your response. Best Regards Dina From: Justin A. Lemkul To: dina dusti ; Discussion list for GROMACS users Sent: Monday, March 12, 2012 10:02 PM Subject: Re: [gmx-users] pdb file dina dusti wrote: > Dear Gromacs Specialists, >

Re: [gmx-users] pdb file

dina dusti wrote: Dear Gromacs Specialists, I need pdb file of tiofen, but I didn't find it!!! Can I change pdb file of one compound that is as same as tiofen (for example pyrrole) and give it to PRODRG for obtain gro file and topology file of tiofen? There are numerous methods for produ

[gmx-users] pdb file

Dear Gromacs Specialists, I need pdb file of tiofen, but I didn't find it!!! Can I change pdb file of one compound that is as same as tiofen (for example pyrrole) and give it to PRODRG for obtain gro file and topology file of tiofen? Please help me. Thanks in advance. Best Regards Dina -- gmx-

Re: [gmx-users] Literature reading on DispCorr for energy and pressure

Hi, This paper comes to mind: Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations Shirts, Mobley, Chodera and Pande J. Phys. Chem. B 2007, 111, 13052-13063 Cheers Tom Andrew DeYoung wrote: Hi, Only if you have time, can you please recommend lite

[gmx-users] pull code - i-motif constant velocity pull

Hello All, I am trying to apply pull code on DNA I-motif structure which is 4 stranded DNA with the pair of 2 parallel duplexes arranged in anti-parallel manner. I have followed the tutorial by Justin Lemkul it works well but I have to select the fixed and pull group on different chains together

[gmx-users] Literature reading on DispCorr for energy and pressure

Hi, Only if you have time, can you please recommend literature reading on how long-range dispersion corrections are computed? I have been using DispCorr = EnerPres for my simulations, which are in the NPT ensemble. When I search through this user's list, I find frequent mention of the fact that

Re: [gmx-users] Umbrella Sampling - Ligand Protein

Steven Neumann wrote: On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul mailto:jalem...@vt.edu> >> wrot

Re: [gmx-users] Umbrella Sampling - Ligand Protein

On Mon, Mar 12, 2012 at 11:06 AM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >>Hi Justin, >> As you advised I reduced number of my windows and

Re: [gmx-users] Umbrella Sampling - Ligand Protein

On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Hi Justin, >> As you advised I reduced number of my windows and I obtined histogram: >> http://speedy.sh/2b9dT/histo.**JPG >> Which looks really good. >> The correspond

Re: [gmx-users] Generation of the Distance Restraints

James Starlight wrote: Francesca, Yes I suppose this is good aproach for the generation of position restricktions on the desired atoms. But I want to restrain the distance between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two different residues). How many restraint

Re: [gmx-users] Generation of the Distance Restraints

On 13/03/2012 12:54 AM, James Starlight wrote: Dear Gromacs users! I want to perform constrained MD simulation of my protein with inclusion of some experimental restraints. 1) I found that genrest cpmmand could be usefull for the generation of the distance restrictions wich I could use in

Re: [gmx-users] Generation of the Distance Restraints

On 13/03/2012 1:13 AM, James Starlight wrote: Francesca, Yes I suppose this is good aproach for the generation of position restricktions on the desired atoms. But I want to restrain the distance between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two different residues).

Re: [gmx-users] Generation of the Distance Restraints

Francesca, Yes I suppose this is good aproach for the generation of position restricktions on the desired atoms. But I want to restrain the distance between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two different residues). Also I want to restrain some dihedral angles in the

Re: [gmx-users] Generation of the Distance Restraints

I think you can make an index file using make_ndx where you specify the atoms you want to restraint. Hope this can help. Francesca 2012/3/12 James Starlight : > Dear Gromacs users! > > > I want to perform constrained MD simulation of my protein with inclusion of > some experimental restraints. > >

[gmx-users] Generation of the Distance Restraints

Dear Gromacs users! I want to perform constrained MD simulation of my protein with inclusion of some experimental restraints. 1) I found that genrest cpmmand could be usefull for the generation of the distance restrictions wich I could use in my constrined simulation. Also in manual I've found

Re: [gmx-users] Re: questions about Principal Component Analysis

Hi Thomas, Whether or not it makes sense to do PCA on the domain only depends on the question you ask. It may well make sense if you aim at characterizing the intra-domain motions. But be aware that you will view those motions within the context of the rest of the protein. It is quite likely that

Re: [gmx-users] Umbrella Sampling - Ligand Protein

Steven Neumann wrote: On Sun, Mar 11, 2012 at 10:13 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: Hi Justin, As you advised I reduced number of my windows and I obtined histogram: http://speedy.sh/2b9dT/histo.__JPG

[gmx-users] Re: gmx-users Digest, Vol 95, Issue 60

Hi, so further to my last email, I have run a quick test on my desktop machine (4 cores, 12Gb RAM). It seems that when running the parrinello-rahman barostat with domain decomposition (-dd 2 2 1) that I'm still getting memory leak (this time with GNU compilers). I followed proper equilibration wit

[gmx-users] Re:g_enemat

Dear All, I was going to use g_enemat to make my life easier than splitting things up into individual files for a break down of multiple components in a trajectory (multiple protein domains and atooms, etc...I indexed before the run rather complex or long depending on your point of view). Whe

[gmx-users] gromacs 4.5.5 cygwin installation error message

Dear All,   For the fftw3 I use the following configuration: ./configure --disable-threads --enable-float --enable-sse   For the gromacs I use the following configuration: ./configure --disable-threads   But in the gromacs I get the following new error message.   I am looking forward to getting yo

[gmx-users] Gromacs 4.5.5 GPU Error

Hi all, I am trying to get the GPU version of gromacs running. I manage to install OpenMM, compile and install mdrun-gpu. However when I ran mdrun-gpu on any of the benchmark files, I got this: ./run.sh: line 2: 14224 Floating point exception/usr/local/gromacs-4.5.5-cuda/bin/mdrun-gpu -v Any ide