Re: [gmx-users] Regarding masses in Martini force field

On Nov 11, 2010, at 6:35 PM, George Khelashvili wrote: > I am relatively new to Martini force fields and the fact that masses of all > the coarse grained beads are set to a same value (72amu) somewhat bothers me. > I was wondering what influence may this have on the process of spontaneous > lipi

[gmx-users] Regarding masses in Martini force field

Dear users, I am relatively new to Martini force fields and the fact that masses of all the coarse grained beads are set to a same value (72amu) somewhat bothers me. I was wondering what influence may this have on the process of spontaneous lipid aggregation into different phases? I read that

RE: [gmx-users] ./mdrun

yeah，Thanks a lot :) YY > Date: Thu, 11 Nov 2010 20:32:55 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] ./mdrun > > > > lin hen wrote: > > It doesn't work, even I deleted this line > > it stills shows the same error... > > > > Did you re-gene

Re: [gmx-users] ./mdrun

lin hen wrote: It doesn't work, even I deleted this line it stills shows the same error... Did you re-generate the .tpr file? I see no reason that a suitable setting for nsteps would be magically substituted by either grompp or mdrun. I use ./mdrun-gpu without any flags. Did I miss

RE: [gmx-users] ./mdrun

It doesn't work, even I deleted this line it stills shows the same error... I use ./mdrun-gpu without any flags. Did I miss something? YY > Date: Thu, 11 Nov 2010 20:25:45 -0500 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] ./mdrun > > > > lin hen wrote

Re: [gmx-users] ./mdrun

lin hen wrote: constraints = all-bonds integrator = md dt = 0.002; ps ! #nsteps = -1 nsteps = 100 nstlist = 0 ns_type = grid rlist = 0 coulombtype = cut-off vdwtype

RE: [gmx-users] ./mdrun

constraints = all-bonds integrator = md dt = 0.002; ps ! #nsteps = -1 nsteps = 100 nstlist = 0 ns_type = grid rlist = 0 coulombtype = cut-off vdwtype = cut-off rcou

Re: [gmx-users] What can we do with gromacs?

mustafa bilsel wrote: Hi, I would like to ask questions about what we can do with Gromacs. 3. For example I have some different molecules and I would like to see their binding affinity to carbon nanotubes. Is it possible to do this simulation with Gromacs? If possible, I should have attractiv

[gmx-users] What can we do with gromacs?

Hi, I would like to ask questions about what we can do with Gromacs. 3. For example I have some different molecules and I would like to see their binding affinity to carbon nanotubes. Is it possible to do this simulation with Gromacs? If possible, I should have attractive and repulsive potentials.

[gmx-users] virtual site error

Hi, when I run pdb2gmx -v -f 2KO3.pdb -o initial-vacuum.gro -ff oplsaa -water tip4p -vsite hydrogens -ignh , I got Fatal error: Invalid directive HISD in vsite database /home/XXX/gromacs/g/share/gromacs/top/oplsaa.ff/aminoacids.vsd . What is the problem? 2KO3.pdb was downloaded from PDB. Best reg

Re: [gmx-users] mdrun -rerun: bonded interactions of protein

On 11/11/2010 7:46 PM, NG HUI WEN wrote: Thanks a lot Justin and Mark for your useful input. Indeed Justin was right, the quest to dissect the total energy of the system to get that contributed by the protein alone was not trivial at all! Indeed. If I'd observed you were doing PME, I'd ha

Re: [gmx-users] Translation motion during MD

nahren manuel wrote: Dear Gromacs Users, Yes Justin I totally agree with you and your point is well taken. But given the fact that if i dont restrain the protein, they rotate and I dont get the formation of clusters. If you know the manner in which the clusters should form, then isn't t

Re: [gmx-users] g_hbond

Hi, I have looked at the files to sent me, and I can't spot any errors. There *is* a hydrogen bond at y=1. It only occurs in 5 frames though, so they're really hard to find when isnpecting the xpm in e.g. Gimp, since the image is 6 pixels wide. So, I got tired of sqinting in front of Gimp

Re: [gmx-users] g_hbond

Hi everyone, actually Erik is right. My problem is that I wasn't using the "-nomerge" option. So g-hbond was printing the wrong number of hydrogen atom and so all my results were not matching. Now that I used "-nomerge", all my H-bonds match even in my concatenated trajectory. Thanks to all, It t

Re: [gmx-users] Translation motion during MD

Dear Gromacs Users, Yes Justin I totally agree with you and your point is well taken.  But given the fact that if i dont restrain the protein, they rotate and I dont get the formation of clusters. Yes, i do want to protein to rotate in the plane of the membrane, but not the rotation that membr

[gmx-users] When will FEP be on GPU?

Hi all,   Our group is doing FEP calculations and finding that we need to run alot of simulations for a long time to get accurate results. We would love to see FEP on GPU as this would help us increase our computational power without buying a new expensive cluster. I would b

Re: [gmx-users] g_hbond

Hi, I'm thinking it *may* have something to do with how search_donors() and the -merge flag work. The hydrogen must be part of the index group you provide. Nothing strange there. But the hydrogen that is printed to the index file may in fact *not* be the hydrogen bonding one if the -merge fla

Re: [gmx-users] Translation motion during MD

nahren manuel wrote: Dear Gromacs Users, I am simulating a Membrane protein, the extracellular domain alone (since the structure of only extracellular domain is solved). So I will have to simulate the protein in such a way that only the translational motion is allowed but the rotational mot

Re: [gmx-users] g_hbond

Oliver Grant skrev 2010-11-11 11.45: Hi Carla, I've seen this behavior too but I didn't look at the code. I figured with the hydrogen included it checks the angle too or if the hydrogen is between the two heavy atoms. So the first pass just looks at distances between donor and acceptor atoms

[gmx-users] Translation motion during MD

Dear Gromacs Users, I am simulating a Membrane protein, the extracellular domain alone (since the structure of only extracellular domain is solved). So I will have to simulate the protein in such a way that only the translational motion is allowed but the rotational motions are prevented (which

[gmx-users] New release of Wordom, molecular analysis program

Hi all, a new version of Wordom, a program for the analysis of molecular structures, trajectories, and free energy surfaces, has been released. You can find all about it at: http://wordom.sf.net Wordom can deal with Gromacs and Charmm trajectories and, besides analysis modules, has many features t

Re: [gmx-users] Re: which force file has parameters for creatine md simulations?

Olga Ivchenko wrote: Dear All, I just want to know if the programm PRODRG is able to generate for my ligand files with .top extension. No, but it is trivial to interconvert .itp and .top manually: http://www.gromacs.org/Documentation/File_Formats/.itp_File -Justin I have two files one

[gmx-users] hydration maps

Dear all I would like to analysis the hydration site near the proteins the one done by the following paper "Biophysical Journal Volume 79 December 2000 2966–2974" is there any tool available in gromacs to do this kind of analysis could anyone help me in this regard. what tool will be useful to

Re: [gmx-users] Re: which force file has parameters for creatine md simulations?

Dear All, I just want to know if the programm PRODRG is able to generate for my ligand files with .top extension. I have two files one is itp format and other is gro using PRODRG. If it is possible what is the name here : http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta#DRGFIN.GRO Yours sin

Re: [gmx-users] g_hbond

Hi Carla, I've seen this behavior too but I didn't look at the code. I figured with the hydrogen included it checks the angle too or if the hydrogen is between the two heavy atoms. So the first pass just looks at distances between donor and acceptor atoms and doesn't consider that the hydrogen may

[gmx-users] hblife.xvg and hbac.xvg files

Dear gromacs users I used g_hbond -f .trr -s .tpr -n .ndx -ac -life can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg files by details. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht

[gmx-users] difference between p(t) and c(t)

Dear all I want to know what is difference between p(t) in hblife.xvg and c(t) in hbac.xvg file? which of them is more suitable for HB lifetime? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs

Re: [gmx-users] on calculation of the atomic covariance

Hi Vignesh, If your covariances show different ranges, isn't that a difference between your systems, wild-type and mutated? Then again, there's also noise in the covariances (noise in the fluctuations, ergo noise in the noise ;)). The rest might be comparable, making scaling based on the extremes

RE: [gmx-users] mdrun -rerun: bonded interactions of protein

Thanks a lot Justin and Mark for your useful input. Indeed Justin was right, the quest to dissect the total energy of the system to get that contributed by the protein alone was not trivial at all! I missed out this thread yesterday http://www.mail-archive.com/gmx-users@gromacs.org/msg3461