Hi,
This is an interesting issue.
The chance is quite small that this happens, but maybe not negligible.
In single precision the maximum a float can store is 2^127.
This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm.
The chance of inserting a particle within this radius is dens*3e-10,
whe
- Original Message -
From: Navjeet Ahalawat
Date: Thursday, September 9, 2010 16:56
Subject: [gmx-users] Re: multiplication of lambda constant with LJ potential
affecting only solvent.
To: gmx-users@gromacs.org
> Hi all
>
> I want to change LJ potential for water only by multiplying a
Hmm. I am getting the desired output now, at least as far as the pulled
atoms are concerned, they are all close to the bilayer center (was not so in
a free simulation), and therefore my suspicion is that the code is working.
Just to re-iterate, the atoms to be pulled to the bilayer center were
pre
Dear Elton, Of course, I happy to discuss some questions about CNT in
GROMACS. My Email is zhongjin1...@yahoo.com.cn
Zhongjin He
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.
Dear users,
I got a question concerning simulations with implicit solvent. So far it
is only possible to use this model when applying a cut-off for the long
range electrostatic and vdW interactions which leads to bad energy
conservation etc.
Will there be an update allowing to use reaction-
Hi!
This is not something that is planned for the immediate future, as useful as it
might be.
However, for small to medium sized systems one can get good performance by
using the all-vs-all kernels. Then the problem of poor energy conservation
disappears.
Cheers
/Per
Skickat från min iPhon
Hi,
I realized now that this is an SSE issue.
Normally you would get NAN (or is it INF?). That is treated correctly in the
GROMACS TPI code.
But in SSE a float "wraps around" when it overflows, which could, in very few
cases, lead to a reasonably
looking energy value (I check for very high and
Dear Gromacs Users,
I've read through various posts on a related issue but am hoping that
someone will have some ideas on this or at least point me in the right
direction. I am also hoping that some discussion on this will help develop
some routines that would allow users to approach this prob
Hi there,
when using for example:
pdb2gmx -f aQQQ.pdb -o agQQQ.pdb -p agQQQ.top -ff amber99sb -water none
I got in the agQQQ.pdb, things like:
ATOM 15 NE2 NGL 1 4.309 7.159 2.648 1.00 0.00
N
ATOM 16 1HE2 NGL 1 4.030 7.698 3.448 1.00 0.00
HE
ATOM 17
Hello, vidhya sankar -
If the env. var's are really set and operate correctly, one should look for
the problem in the MOPAC library itself. Do you use precompiled libmopac.a
or compile it by hand?
BTW, did you try to exactly follow the procedure described on my website,
from the very beginning??
Hello,
I want to convert force constant from mdyn/A to kJ/mol rad2.
How to convert mdyn/A to kJ/mol rad2
Thanks
NIlesh
--
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_Li
Hi. I am running simulations with DPPC and water molecules. I made groups
from a set of atoms from each DPPC molecule (example: Group 1 = C1, C2, C3
Group 2 = C4, C5, C6). I want to calculate the rdf for the center of mass
of each group from each DPPC molecule while excluding groups located o
On 2010-09-09 18.37, Alan wrote:
Hi there,
when using for example:
pdb2gmx -f aQQQ.pdb -o agQQQ.pdb -p agQQQ.top -ff amber99sb -water none
I got in the agQQQ.pdb, things like:
ATOM 15 NE2 NGL 1 4.309 7.159 2.648 1.00 0.00
N
ATOM 16 1HE2 NGL 1 4.030 7.
First off I am using gromacs 4.5. I will also post all of my files and errors if they help.
If I run a protein in GROMOS96 all my md runs complete succesfully. But if I change to any of the AMBER force fields I get LINCS errors in my positional restraint md run
Hi,
I am running charmmm force field (ff) in gmx 4.5 version and just trying on
tip5p water model in it. Unfortunately I only find tip5p.gro is in the ff, not
tip5p.itp file. Can anyone help me with hints on constructing it?
Many thanks,
Yao
--
gmx-users mailing listgmx-users
TJ Mustard wrote:
First off I am using gromacs 4.5. I will also post all of my files and
errors if they help.
If I run a protein in GROMOS96 all my md runs complete succesfully. But
if I change to any of the AMBER force fields I get LINCS errors in my
positional restraint md run. I hav
Of course.
I am trying to run the ribosome 30s subunit on gromax 4.5. I chose the AMBER force field since it had the least issues with RNA and that made running pdb2gmx much easier. Everything is fine till I run a md. Below I have attached everything I think is informativ
My one thought is that it is to large of a system for GROMACS to run it, yet I have run a small protein in GROMOS96-43a1 and it works but not in any of the AMBER force fields.
On September 9, 2010 at 9:35 PM TJ Mustard wrote:
Of course
Hello.
Probably that will not be related with the original problem but that's
something that came to me when reviewing the tpi.c code:
In line 583 (and follow), it is stated:
if (epot != epot || epot*beta < bU_neg_limit)
{
if (debug)
TJ Mustard wrote:
*Positional restraint mdp file:*
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.004 ; ps
Unless you're using virtual sites (which, per your commands below, you are not)
this time step i
- Original Message -
From: Nilesh Dhumal
Date: Friday, September 10, 2010 4:41
Subject: [gmx-users] mdyn/A to kJ/mol rad2
To: gmx-users@gromacs.org
> Hello,
> I want to convert force constant from mdyn/A to kJ/mol rad2.
> How to convert mdyn/A to kJ/mol rad2
So what's the definition of
On September 9, 2010 at 10:04 PM "Justin A. Lemkul" wrote:
>
>
> TJ Mustard wrote:
>
>
>
> > *Positional restraint mdp file:*
> >
> >
> >
> > define = -DPOSRES
> > constrain
> Dear Gmxers,
>
> I am working on a new project and I plan to do some molecular dynamic
> simulation on an engineered GFP molecule. I have been searching for the
> parameters for the GFP chromophore without success. Could some one help
> me? Any
> reference or parameters will be appreciated.
Nath
Hi,
Thank you for taking the time to fix the issue. I would be very interested
in testing out the modified code, but unfortunately I have had some
difficulties compiling the Gromacs code obtained straight from GIT. In
particular, I encounter the following error:
~/gromacs/src/tools/gmx_membed.c:1
- Original Message -
From: Yao Yao
Date: Friday, September 10, 2010 6:05
Subject: [gmx-users] tip5p.itp in Charmm
To: gmx-users@gromacs.org
> Hi,
>
> I am running charmmm force field (ff) in gmx 4.5 version and
> just trying on tip5p water model in it. Unfortunately I only
> find tip
- Original Message -
From: Mark Abraham
Date: Friday, September 10, 2010 8:59
Subject: Re: [gmx-users] tip5p.itp in Charmm
To: Discussion list for GROMACS users
>
>
> - Original Message -
> From: Yao Yao
> Date: Friday, September 10, 2010 6:05
> Subject: [gmx-users] tip5p.it
Hi,
Thank you for taking the time to fix the issue. I would be very interested
in testing out the modified code, but unfortunately I have had some
difficulties compiling the Gromacs code obtained straight from GIT. In
particular, I encounter the following error:
~/gromacs/src/tools/gmx_
membed.c:
Hi,
Thank you for taking the time to fix the issue. I would be very
interested in testing out the modified code, but unfortunately I have
had some difficulties compiling the Gromacs code obtained straight
from GIT. In particular, I encounter the following error:
~/gromacs/src/tools/gmx_membed.c:1
- Original Message -
From: Ali Hassanali
Date: Friday, September 10, 2010 2:21
Subject: [gmx-users] selected forces
To: gmx-users@gromacs.org
> Dear Gromacs Users,
>
> I've read through various posts on a related issue but am hoping
> that someone will have some ideas on this or at le
Dear Sir,
I am using nwall to run my system. My version is Gromacs 4.0.7.
Interestingly, I could parallel run my system on 1 node with 4 or 8 cpus,
but when I run it on multi-node PC-cluster, it always fails and gives no
message at all. I wonder if you could help me to resolve this problem?
Thanks
- Original Message -
From: Yi Gao
Date: Friday, September 10, 2010 12:23
Subject: [gmx-users] parallel run problem for nwall
To: gmx-users@gromacs.org
> Dear Sir, > > I am using nwall to run my system. My version is Gromacs
> 4.0.7. Interestingly, I could parallel run my system on 1
Gromacs is running well on multi-nodes without nwall. But with nwall, it
doesn't work.
Yi
On Thu, Sep 9, 2010 at 9:28 PM, Mark Abraham wrote:
>
>
> - Original Message -
> From: Yi Gao
> Date: Friday, September 10, 2010 12:23
> Subject: [gmx-users] parallel run problem for nwall
> To: gmx-
32 matches
Mail list logo
