Have you tried swissparam.ch server (charmm ff) or vienna.ptm.univie.ac.at
server ( gromos ffg45a3, ffg45a7 and ffg54a8 ff) for beta alanine
On Oct 12, 2017 7:16 PM, "Justin Lemkul" wrote:
On 10/12/17 5:03 AM, Dilip H N wrote:
> Hello,
> 1] I wanted to simulate beta-alanine amino acid. Since
On 10/9/17 10:50 AM, Bradley Treece wrote:
Hi All,
I have a question about the handling of coordinates in local arrays with
domain decomposition. It may take a moment to get to my actual question,
but I want to make sure to be thorough with my explanation. Also, if I need
to point this questio
On 10/12/17 5:03 AM, Dilip H N wrote:
Hello,
1] I wanted to simulate beta-alanine amino acid. Since i am using charmm 36
FF for simulation of other molecules too, so prefer using the same
Forcefield.
But i tried searching in the .rtp file, but only alanine [ALA] amino-acid
is there...but not b
Use packmol software for system generation, save it in PDB file and then
use appropriate force field .
On Thu, Oct 12, 2017 at 8:01 AM, Amali Guruge wrote:
> -- Forwarded message --
> From:
> Date: Thu, Oct 12, 2017 at 10:11 PM
> Subject: Simulation of surfactant and water compo
As you already run 1ns molecular dynamics now you have md.tpr, md.cpt files
in your working directory
You need to creat a new tpr file (newmd.tpr) from previous md.tpr file
tpbconv -s md.tpr -extend 149000 -o newmd.tpr
149000 is ps
then use
mdrun -s newmd.tpr -cpi previous.cpt
On Thu, Oct 12
Hi,
i am a beginner with Gromacs and i have run the simulation using Gromacs
forcefield for 1000 ps* (1ns)* . Now I want to extend it to *150 ns*. How
should I proceed?
should i change the md.mdp file ?? actually i am using the defaul mdp file
in gromacs tutorial :
integrator = md;
Dear Gromacs Users,
I have found that 2 ps is a standard value for the tau_t for SD integrator.
Since it is a reverse friction constant, does it means that the values
below 2 ps will provide stronger coupling with thermostat (more virtual
collisions => more viscosity) and the values above 2 ps sho
-- Forwarded message --
From:
Date: Thu, Oct 12, 2017 at 10:11 PM
Subject: Simulation of surfactant and water composition
To: amaligg2...@gmail.com
You are not allowed to post to this mailing list, and your message has
been automatically rejected. If you think that your messages
Thanks Mark. I added my files and description to
https://redmine.gromacs.org/issues/2187.
Peter
On 12-10-17 12:02, Mark Abraham wrote:
> Hi,
>
> On Thu, Oct 12, 2017 at 11:26 AM Peter Kroon wrote:
>
>> Hi all,
>>
>> I'm trying to produce a tng file from my trajectory (can mdrun write
>> those
Hi,
There are many bilayer building webservers on the net, Google around and
pick what fits your needs.
Mark
On Thu, Oct 12, 2017 at 10:45 AM Du, Yu wrote:
> Dear GMX Users,
>
>
> My question is 512-lipid bilayer is too big. How can I resize it and the
> cooresponding box size?
>
>
> I duplica
Hi,
On Thu, Oct 12, 2017 at 11:26 AM Peter Kroon wrote:
> Hi all,
>
> I'm trying to produce a tng file from my trajectory (can mdrun write
> those directly yet?)
gmx mdrun -x file.tng has always worked, but we can't make that the default
until we've got more things working well in the broader
Hi all,
I'm trying to produce a tng file from my trajectory (can mdrun write
those directly yet?) since VMD likes those better for coarse grained
systems. I'm not interested in my solvent, so I select a smaller group
for my output.
When I run the following commands it produces a segfault. If I te
Dear Experts, We know that gmx wham cannot be used for more than
one penetrant for calculating PMF from umbrella sampling.Have you come across
any publication or script to do umbrella sampling for multiple penetrants
through the Bilayer.Please shareThanks YogiSent
Hi,
the problem is that I am not able to compile MOPAC7 correctly. Some routines
work, but not all and lead to erroneous results.
If you need to run MD with semi empirical methods, I recommend using gaussian
instead.
best,
Gerrit
Message: 3
Date: Thu, 12 Oct 2017 10:24:33 +0900
From: minky
Hello,
1] I wanted to simulate beta-alanine amino acid. Since i am using charmm 36
FF for simulation of other molecules too, so prefer using the same
Forcefield.
But i tried searching in the .rtp file, but only alanine [ALA] amino-acid
is there...but not beta-alanine. So i am not able to find it i
Dear GMX Users,
My question is 512-lipid bilayer is too big. How can I resize it and the
cooresponding box size?
I duplicated the 128-lipid bilayer using
$gmx_mpi genconf -f lipid128.gro -o lipid_new.gro -nbox 2 2 1
But the new 512-lipid bilayer is so large, I want to remove the some lipid
I suggest ignoring/deleting TL and then replacing waters with K randomly
with:gmx genion.Ofc. it depends what you try to do.
On Wednesday, October 11, 2017, 5:01:52 PM GMT+3, Du, Yu
wrote:
Dear GMX Users,
Keyword: metal, energy minimization, segmentation fault
I have pinpointed
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