Re: [gmx-users] How to construct mixed lipid bilayer

Let me correct myself :). Its pre-equilibrated. Not pretty equilibrated. :) On Nov 13, 2013 7:23 PM, "Arun kumar V" wrote: > Start with packmol if you want to start from scratch. Or else get a pretty > equilibrated mixed lipid bilayer if available somewhere on web. > On N

Re: [gmx-users] How to construct mixed lipid bilayer

Start with packmol if you want to start from scratch. Or else get a pretty equilibrated mixed lipid bilayer if available somewhere on web. On Nov 13, 2013 6:45 PM, "Nikhil Agrawal" wrote: > Dear All, > > can anyone tell me how to construct mixed lipid bilayer in gromacs > > id possible also provi

[gmx-users] Restarting a simulation after replacing an empty md.trr file

exact, but is not guaranteed to be binary identical. ... Source code file: checkpoint.c, line: 1767 Fatal error: Can't read 1048576 bytes of 'md.trr' to compute checksum. The file has been replaced or its contents has been modified. please help me in overcoming this problem. Thanking

[gmx-users] do_dssp segmentation fault

an anybody please say what it means and how to solve it Regards, -- Arun Kumar Somavarapu Project-JRF Dr. Prasanna's lab TMC, ACTREC Navi Mumbai-410210 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://

[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION

GAND COMPLEX SIMULATION > To: Discussion list for GROMACS users > Message-ID: <4ec24faf.5050...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > arun kumar wrote: > > Dear friends, > > > > i had a problem while running the of

[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION

-- Arun Kumar Somavarapu Project-JRF Dr. Prasanna's lab TMC, ACTREC Navi Mumbai-410210 -- 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 posting! Please

[gmx-users] simulation at higher temperatures gmx-users Digest, Vol 88, Issue 167

y minimization (ITHAYARAJA) > 3. Re: Error found on grompp - energy minimization (Mark Abraham) > 4. Re: gromacs question topologie (Justin A. Lemkul) > 5. Re: Difficulty building a topology for a synthetic, branched > PEG-peptide molecule [SOLVED] (Pablo Englebienne) >

[gmx-users] simulation at higher temperatures

calculated at room temperature, so in that case what are the parameters and forcefield that we need to fallow for higher temperature simulations. so can any one please takes time to explain this, it would be helpful for me to study further. Thanking you. with regards -- Arun Kumar Somavarapu

Re: [gmx-users] Simulation of only Lipid Bilayer

On Tue, Apr 6, 2010 at 5:05 PM, Justin A. Lemkul wrote: > > > Arun kumar V wrote: > >> Try PRODRG server to build the molecule as well as to get topology file. >> Though you might have to be careful in using this topology file. >> >> > If by "be caref

Re: [gmx-users] Simulation of only Lipid Bilayer

Try PRODRG server to build the molecule as well as to get topology file. Though you might have to be careful in using this topology file. Arun Saumya wrote: Hi all, Well, I have been trying to make lipid bilayers using genconf of gromacs from a single lipid molecule. Can anyone tell me how t

[gmx-users] Re: Forming a micelles

simulations of mixture of cationic > surfactants, fatty alcohols and water with various ratios of > surfactant/alcohol. Usually for a system of 100 surfactants +100 > co-surfactants + 4000 water molecules, it took 3 x 600 ps to see the > micelles and other structures forming from rand

Re: [gmx-users] Forming a micelles

55 > [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gr

Re: [gmx-users] Relationship between the spetide.gro file and the #spetide.gro.1#?

Hai. If your working directory contains a file named already speptide.gro, when u run another simulation for which the output (final coordinates) is also speptide.gro, then the previous file will be backed up as #speptide.gro.1# . Similarly if u run another simulation then the speptide.gro fi

Re: [gmx-users] CVS code needed

Dear Erik, Thank you for the link Kumar On 7/22/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: I put a recent copy (friday) at http://lindahl.sbc.su.se/outgoing/aatto/ Cheers, Erik And yes... we should get a nightly-snapshot system running... :-) On Jul 22, 2007, at 4

Re: [gmx-users] Continuing runs that stopped

There are two ways of doing this 1) using grompp (check man page) 2) using tpbconv(easier) check man pages for tpbconv.. On 6/13/07, michelle yap <[EMAIL PROTECTED]> wrote: Hello, I was doing an MD simulation and I need to restart my PC because of some technical problems that occurred in the p

Re: [gmx-users] glibc error with g_density (only for some cases)

Dear David, I will check the reproducibility of the result once again. And then I will submit the bugzilla with all inputs I used for these simulations. Regards, Arun On 5/19/07, David van der Spoel <[EMAIL PROTECTED]> wrote: Arun kumar wrote: > Dear David, > My

Re: [gmx-users] glibc error with g_density (only for some cases)

Dear David, My gcc compiler version is 4.0.1. Is there any problem with this version?? On 5/18/07, David van der Spoel <[EMAIL PROTECTED]> wrote: Arun kumar wrote: > Hai Mark.. > Thanks for your suggestions. I will think about my > problem clearly

Re: [gmx-users] glibc error with g_density (only for some cases)

there is nothing went wrong in my simulations in between 500 and 1500 time steps. I am able to evaluate all properties for those frames also. Anyway I will check once again. Thanks and regards Arun Kumar On 5/18/07, Mark Abraham <[EMAIL PROTECTED]> wrote: Arun kumar wrote: > Dear

[gmx-users] glibc error with g_density (only for some cases)

Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I

Re: [gmx-users] initial configuration problems and energy minimization

Hi Mark. Thanks for your suggestions I will use your suggestions to solve the problem. And then I will reply here about the outcomes. Regards Arun On 5/18/07, Mark Abraham <[EMAIL PROTECTED]> wrote: Arun kumar wrote: > Dear gmx-users, >

[gmx-users] initial configuration problems and energy minimization

Dear gmx-users, Here I have a some problem regarding initial configuration My system is composed of cationic surfactants, co-surfactants, water. I am able to minimize the energy of my system(random), if it contains 15(surfactants)+ 15(co-surf)+ 1000(water)+ 15 (counter

Re: [gmx-users] Re: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

doing that. Thanks and Regards Arun Kumar On 5/6/07, Mark Abraham <[EMAIL PROTECTED]> wrote: Arun kumar wrote: > Hi Tsjerk and others, > I tried to simulate one surfactant and one > chloride ion in 500 waters and got similar type of errors. I mean my > system g

[gmx-users] Re: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

seems the problem is with topology. Earlier I asked about what is meant by broken topology?? Can anyone tell what may ne the problem and also about what is meant by broken topology?? Thanks and Regards Arun Kumar M.E chem engg Hi Tsjerk and gmx-users, Thank you for the

[gmx-users] Re: gmx-users Digest, Vol 37, Issue 18

broken topologies in some of the posts I observed, with my problem. Can anyone explain what is meant by a broken topology file. Try to help me to understand these thing well??? I can give any more details if it is needed. Thanks and regards Arun Kumar M.E chem engg Hi Arun, You have to get your

[gmx-users] Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

Dear gmx-users: I am trying to simulate a surfactant-water system(also contains some co-surfactants). Surfactant is a cationic surfactant with chloride as counterion. And the cosurfactant is fatty alcohol. water is of spc model. I got topologies from Prodrg for my surfactan

[gmx-users] problem regarding editconf - atommass

Hai all I am trying to simulate the bulk phase decane system using GROMACS... I used decane pdb file which I goT from HIC UP I changed the residue name to C10 from D10 to match the residue name in ffgmx.rtp(GROMACS force field) I ran pdb2gmx , selected forcefield "4

[gmx-users] Regarding preparation of .itp file for a new molecule

Hai all...    I am a newbie to gromacs simulation software and its file formats. I want to develop coarse grain models for surfactant systems by using atomistic simulations. I got a .pdb file for BTMAC surfactant.   But to run simuations on gromacs,I need to include .itp file in s