On 16/11/2010 3:24 PM, S. Mohamadi wrote:
Dear All
I want to simulate a protein in Electric Field how can I do that?
where should I start from!
It's very Important for me! Please help me!
Thanks
Start by looking in the manual.
Mark
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Message: 2
Date: Tue, 16 Nov 2010 03:47:54 -0300
From: Esteban Gabriel Vega Hissi egv...@gmail.com
Subject: Re: [gmx-users] Re: still can not run md for creatine
Dear all,
What is the difference between the option Distance and Direction in
Umbrella Sampling?
In my opinion, the option Direction means that pulling the pull_group1
through the direction related to the reference group. Right? But how about
the option Distance?
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gmx-users mailing
Dear all
I am using gromacs 4.5.1. I am running gromacs examples
(methanol). when I use grompp -v, I encounter a fatal error: Atomtype
CMET not found. I understand gromacs use ffG43a1. In rtp file of this
forcefield there is:
[ CH3OH ]
[ atoms ]
Omet OMet -0.57400 0
HMet H
Esteban Gabriel Vega Hissi wrote:
Justin,
Regarding the charges you mention, what do you think about RESP charges
for this kind of compounds (drugs) parameterization?
We have not found any single charge calculation method that correctly reproduces
the charges on Gromos96 charge groups,
Two notes before the comments below:
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ITHAYARAJA wrote:
Dear Sir,
Greetings!
It may
Dear Gmx-users,
I am simulating a carbon nanotube in vaccum (NVE ensemble). I have taken
parameters of carbon nanotube from Strong correlations and Fickian
water water
diffusion in narrow carbon nanotube, Biswaroop Mukherjee, Prabal K.
Maiti Chandan
Dasgupta and A. K. Sood, JCP, 126
DeChang Li wrote:
Dear all,
What is the difference between the option Distance and Direction in
Umbrella Sampling?
In my opinion, the option Direction means that pulling the
pull_group1 through the direction related to the reference group. Right?
But how about the option Distance?
Mina Madah wrote:
Dear all
I am using gromacs 4.5.1. I am running gromacs examples (methanol). when
I use grompp -v, I encounter a fatal error: Atomtype CMET not found. I
understand gromacs use ffG43a1. In rtp file of this forcefield there is:
[ CH3OH ]
[ atoms ]
Omet OMet-0.57400
Hello,
It doesn't contribute as such. I was using a different force
field before OPLSAA and it was all atom so I could make the charges
zero in the topology file, I wanted to do the same.
Quoting Justin A. Lemkul jalem...@vt.edu:
Mark Abraham wrote:
On 16/11/2010 7:14 AM,
- Original Message -
From: Fabio Affinito f.affin...@cineca.it
Date: Wednesday, November 17, 2010 1:58
Subject: [gmx-users] problem linking fftw2 with gromacs 4.5.3
To: gmx-users@gromacs.org
Hi folks,
I'm experiencing some problem when I try to compile gromacs 4.5.3
linking fftw.
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Message: 2
Date: Tue, 16 Nov 2010 08:01:42 -0500
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] distance VS. direction option in Umbrella
sampling, in Gromacs 4.0
To: Discussion list for GROMACS users gmx-users@gromacs.org
DeChang Li wrote:
--
Message: 2
Date: Tue, 16 Nov 2010 08:01:42 -0500
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Subject: Re: [gmx-users] distance VS. direction option in Umbrella
sampling, in Gromacs 4.0
Dear Gmx-users,
I am simulating a carbon nanotube in vaccum (NVE ensemble). I have taken
parameters of carbon nanotube from Strong correlations and Fickian
water water
diffusion in narrow carbon nanotube, Biswaroop Mukherjee, Prabal K.
Maiti Chandan
Dasgupta and A. K. Sood, JCP, 126
Dear Gmx-users,
I am simulating a carbon nanotube in vaccum (NVE ensemble). I have taken
parameters of carbon nanotube from Strong correlations and Fickian
water water
diffusion in narrow carbon nanotube, Biswaroop Mukherjee, Prabal K.
Maiti Chandan
Dasgupta and A. K. Sood, JCP, 126
Vitaly Chaban wrote:
Dear Gmx-users,
I am simulating a carbon nanotube in vaccum (NVE ensemble). I have taken
parameters of carbon nanotube from Strong correlations and Fickian
water water
diffusion in narrow carbon nanotube, Biswaroop Mukherjee, Prabal K.
Maiti Chandan
Dasgupta and A. K.
Sorry, Mark,
the problem was in fact in the compilation of fftw.
I solved everything by compiling them in the most simple way:
./configure --prefix=whatelse
and now everything works fine.
Thank you
On 11/16/2010 04:18 PM, Mark Abraham wrote:
- Original Message -
From: Fabio
¿Did you change also the name of the “residue” (from 1MeOH to 1CH3OH (that is
the “residue” name appearing in the RTP file))?
Best regards
Lucio
From: Mina Madah
Sent: Tuesday, November 16, 2010 6:00 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Atomtype CMET not found
Dear all
Oh! Thanks a lot.
Samrat
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Mon, November 15, 2010 6:16:51 PM
Subject: Re: [gmx-users] compressing two selections or just the reverse of
pulling simulation
Quoting Vitaly Chaban vvcha...@gmail.com:
Dear Gmx-users,
I am simulating a carbon nanotube in vaccum (NVE ensemble). I have taken
parameters of carbon nanotube from Strong correlations and Fickian
water water
diffusion in narrow carbon nanotube, Biswaroop Mukherjee, Prabal K.
Maiti Chandan
On 15/11/2010 11:18 PM, Yudong Sun wrote:
Hi,
I want to build an all static library because a job running on
background nodes may not be able to find the dynamic libraries
installed on the front node in my system.
My configure line for GCC is:
./configure --prefix=/path-to/gromacs_4.5.3
On 15/11/2010 5:56 AM, Silvia Crivelli wrote:
We have a visualization tool that allows us to visualize the changes
in the energy during energy minimization.
The areas with more intense color are those where the atoms contribute
the most to the total energy value.
I just wrote a plug-in to use
On 17/11/2010 12:24 AM, nishap.pa...@utoronto.ca wrote:
Hello,
It doesn't contribute as such. I was using a different force field
before OPLSAA and it was all atom so I could make the charges zero in
the topology file, I wanted to do the same.
Being all-atom or not has nothing to do
On 16/11/2010 9:04 PM, hengame fallah wrote:
Thank you very much, Mark!
Now i have errors from my .top file after grompp command.
The question is that why in pdb2gmx, editconf ,genbox and make_ndx
steps i don't see these errors:
...
processing topology...
Opening library file
I would not say that you tube rotates so vigorously to be
suspicious... The tube is also very small. What about trying a bigger
one, e.g. with about 1 000 atoms? It should be more inert, if you'd
like it to be such.
hope this might be useful:
they are top and sideviews
Why my rdf is larger than 1 in the long range
2010-11-17
Raymond
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