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
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
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
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
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GAND COMPLEX SIMULATION
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>
>
>
> arun kumar wrote:
> > Dear friends,
> >
> > i had a problem while running the of
--
Arun Kumar Somavarapu
Project-JRF
Dr. Prasanna's lab
TMC, ACTREC
Navi Mumbai-410210
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Please
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)
>
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
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
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
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
55
> [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gr
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
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
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
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
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
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
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
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,
>
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
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
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
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
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
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
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
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