Re: [gmx-users] where can I download POPC membrane file?

Hi, I just checked with Gromacs 4.5.4 and VMD 1.9: 1. Download charmm36.ff.tgz from Gromacs downloads and unpack to appropriate Gromacs installation folder {root}/share/gromacs/top or your working directory. 2. Open VMD, go to Extensions->Modeling->Membrane builder, choose POPC, fo

[gmx-users] Parameters for DMPG and G53a6 force field

Hello, I need parameters for DMPG membrane (G53a6 force field). Does anybody know where I could find a tested parameter set and pdb file? If not, I believe I could construct my own from e.g. Kukol A, Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins, DOI: 10.1021/ct8003468 by

Re: [gmx-users] Using mdrun -rerun to get energy values

Hi, You need to use md integrator for -rerun to work. Good luck, Chris 2010/11/6 Martin Kamp Jensen > Hello, > > Hopefully someone can help me understand how to use the mdrun -rerun > functionality, because currently I am confused. I would like to be able to > look up potential energy values f

Re: [gmx-users] Using mdrun -rerun to get energy values

good to add a check in the future releases so that gmx_fatal() is called in case someone combines -rerun with integrators from minimize.c. I'm happy that I was helpful. Chris 2010/11/6 Martin Kamp Jensen > Hi Chris, > > On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk &g

Re: [gmx-users] Installing gromacs in Red hat E5

I'd also suggest to install the newest version 4.5.2. Chris 2010/11/9 Kamalesh Roy > Dear all, > > Can anybody tell me the the specification of installation of gromacs 4.5.1 > in Red Hat E5 platform. > GCC package works good here or any other option I have to think of. > > Thank you > > kamales

Re: [gmx-users] transmembrane protein simulation

Hi, Yes, g_membed is the right tool for you. Please read the paper Wolf et al, J Comp Chem, 31 (2010) 2169-2174. You will find a detailed description of the insertion method and a quick manual. It will save you a lot of headache. Regards, Christopher 2011/1/24 Mohana lakshmi > Dear all > >

Re: [gmx-users] Angle between normal of rings at same molecule

I'm not sure if this can be done with any of the gromacs tools, but using the linalg module from numpy library will help you. But be aware that a flip by 180 degrees is meaningful for you, but undistinguishable for the mathematical procedure. This issue can be more or less easily solved depending o

[gmx-users] Lipid parameters for GROMOS96 force fields

Hello, On Peter Tieleman's website we can find topologies for various popular lipids. However those seem to be valid for the deprecated GROMOS87 force field. The g96_lipids.itp file is still unavailable. I'd like to run a simulation of 7TM protein embedded into POPC membrane. G43a2x seems to be a

Re: [gmx-users] Lipid parameters for GROMOS96 force fields

lto: > gmx-users-boun...@gromacs.org] > > On Behalf Of Justin A. Lemkul > > Sent: 21 January 2010 01:36 > > To: Discussion list for GROMACS users > > Subject: Re: [gmx-users] Lipid parameters for GROMOS96 force fields > > > > > > > > Justin A. Le

Re: [gmx-users] Lipid parameters for GROMOS96 force fields

2010/1/21 Justin A. Lemkul > > > Krzysztof Mlynarczyk wrote: > > 2. If not, is there any way to derive the proper parameters for the force >> field of my choice using the lipid parameters from Peter Tieleman's website >> or e.g. the parameters published by An

Re: [gmx-users] Lipid parameters for GROMOS96 force fields

people are working on it ... > > > > I would advise to be very carefull in interpreting results with this FF. > > > > XAvier. > > > > On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote: > > > >> > >> > >> Krzysztof Mlynarczyk wro

Re: [gmx-users] Lipid parameters for GROMOS96 force fields

is definitely real >> and unfortunately not documented. Some people are working on it ... >> >> I would advise to be very carefull in interpreting results with this FF. >> >> XAvier. >> >> On Jan 21, 2010, at 2:13 PM, Justin A. Lemkul wrote: >>

Re: [gmx-users] MARTINI-CG updated web site

I wish G96 force fields had a similar website with so much useful information. It would be good if authors posted anything on the forum cause it's completely empty right now. 2010/1/26 XAvier Periole > > Dears, > > the MARTINI CG force field web site has been remodeled. > > It now includes FAQs,

Re: [gmx-users] Help for running gromacs

Please post more details including the following: - What is the exact command line? - What group do you select as a "continuous solvent"? I know it might sound weird to ask this but what I learned while teaching students is that these questions really should be asked when there are pro

Re: [gmx-users] The grompp problem!! (Urgently)

If this is the tutorial I have in front of my eyes, then the problem is that order of force fields changed and "gromacs force field" you are told to choose is no longer under "0" as it is deprecated. "0" is ffG43a1, where this atom type is not present anymore. Good luck, Chris 2010/7/22 Yuranat S