Dear David sir,
Is it feasible to evaluate Gibbs free energy landscape of only the
concerned loops from cartesian coordinates?
I mean to say is it feasible to extract covariance matrix of my concerned
loops from the entire trajectory and then evaluating Gibbs free energy
landscape?
OR, should I ex
org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Gromacs says that may GeForce 9800gt is
incompatibleany help?
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Message: 2
Date: Fri, 25 Sep 2015 19:15:43 +
From: Repic Matej
To: "gmx-users@gromacs.org"
Subject
I will answer my own question: I found in another post that indeed in GROMACS
its Rmin.
Thanks
> On Sep 25, 2015, at 5:25 PM, Ebert Maximilian wrote:
>
> Yeah that is what I thought but that’s life.
>
> One more question.In the [ atomtypes ] section I need the sigma and epsilon
> value. In
Yeah that is what I thought but that’s life.
One more question.In the [ atomtypes ] section I need the sigma and epsilon
value. In found them in the GAFF FF in the MOD4 section. In GROMACS sigma is in
nm and epsilon in KJ/mol. In GAFF epsilon is in Kcal/mol and sigma is in
angstroem and define
On 9/25/15 4:40 PM, Ebert Maximilian wrote:
I read that and this is the way I added the cysteine to AMBER which connects to
the heme. Now I am adding the heme but the FF definition for bonds, angles, etc
are all in lower case for the GAFF FF. From you answer I guess I need to add
these lower
I read that and this is the way I added the cysteine to AMBER which connects to
the heme. Now I am adding the heme but the FF definition for bonds, angles, etc
are all in lower case for the GAFF FF. From you answer I guess I need to add
these lower case atom types and the bonds, angles, etc defi
On 9/25/15 4:22 PM, Ebert Maximilian wrote:
Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF
FF to work in GROMACS? I would need all the bonded and non bonded definitions
of GAFF for the heme in der AMBER FF port in GROMACS right?
http://www.gromacs.org/Documen
Since the heme definition in AMBER uses GAFF atom types how do I get the GAFF
FF to work in GROMACS? I would need all the bonded and non bonded definitions
of GAFF for the heme in der AMBER FF port in GROMACS right?
Max
> On Sep 25, 2015, at 1:36 PM, Justin Lemkul wrote:
>
>
>
> On 9/25/15
Unfortunately, it is incompatible. 9800GT has compute capability 1.1, but
gromacs needs 2.0 or higher. The oldest compatible cards are GTX 4xx series
from 2010, but 9800GT is from 2008.
Best,
--
Dr. Matej Repic
Ecole Polytechnique Fédérale de L
Gromacs 5 says that may GeForce 9800gt is incompatible any help?
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Hi Tsjerk,
Thank you for the quick reply. Yes I can access it with other versions,
like 4.5.5, 5.0.4.
On Fri, Sep 25, 2015 at 11:33 PM, Tsjerk Wassenaar
wrote:
> Hi Venkat,
>
> Does it exist? Is it accessible? The XTC format did not change since the
> early years of Gromacs. Can you access it wi
Hi Venkat,
Does it exist? Is it accessible? The XTC format did not change since the
early years of Gromacs. Can you access it with a different version?
Cheers,
Tsjerk
On Sep 25, 2015 19:52, "Venkat Reddy" wrote:
> Dear all,
> I have a trajectory file generated by gromacs-4.5.5. Recently I trie
Dear all,
I have a trajectory file generated by gromacs-4.5.5. Recently I tried to
plot radial distribution function using 'gmx rdf' tool available in
gromacs-5.1. But I am getting the following error.
Error in user input:
Invalid command-line options
In command-line option -f
File 'system.xt
On 9/25/15 1:32 PM, Ebert Maximilian wrote:
Hi there,
I am trying to simulate a heme containing protein. I found AMBER heme
parameters in the mol2 and frcmod file format. I know that I can generate
.itp files containing the parameters, which I can later add to my .top file.
However, it would b
Hi there,
I am trying to simulate a heme containing protein. I found AMBER heme
parameters in the mol2 and frcmod file format. I know that I can generate .itp
files containing the parameters, which I can later add to my .top file.
However, it would be much easier to use pdb2gmx directly without
Thanks a lot for such in-depth insight! Will look into all of this and get
started asap!
On Wed, Sep 23, 2015 at 1:29 AM, Mark Abraham
wrote:
> Hi,
>
> On Mon, Sep 21, 2015 at 7:10 PM Sabyasachi Sahoo
> wrote:
>
> > Dear Gromacs users and developers,
> >
> > I am a parallel programming research
Hi,
mdrun uses -tunepme by default, which does this. You can learn more about
the theory behind the implementation in the PDF reference manual. There is
also gmx tune_pme to scan a larger range of parameters than mdrun can.
Mark
On Fri, Sep 25, 2015 at 4:12 AM Vy Phan wrote:
> Dear All gromacs
Hi,
That kind of error usually means you're trying to install into the build
tree, or something like that. Source, build and install locations should be
different.
Mark
On Fri, Sep 25, 2015 at 10:42 AM 신은혜 wrote:
> I installed gromacs 5.0.5, but during installation, i got error massages
>
> CM
On 9/25/15 10:50 AM, Amali Guruge wrote:
Dear all,
My enzyme contains PTR (phosphotyrosine) molecule which connect to the DNA.
When I run the command pdb2gmx, it gives an error stating that PTR is not
found in residue topology database.
How can I fix this problem?
Can anyone help me?
http:
Dear all,
My enzyme contains PTR (phosphotyrosine) molecule which connect to the DNA.
When I run the command pdb2gmx, it gives an error stating that PTR is not
found in residue topology database.
How can I fix this problem?
Can anyone help me?
Thank you.
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* Please
Thanks with selections syntax it works!
--
Karozis Stelios
Chemical Engineer, MSc
Research Associate at EREL
NCSR D- INRASTES
tel:0030 210 650 3403
e-mail: skaro...@ipta.demokritos.gr
On Fri, 25 Sep 2015 12:05:41 +0300, "Teemu Murtola"
wrote :
> Hi,
>
> indeed, this appears to be a bug
Hi,
indeed, this appears to be a bug, likely originating already from 5.0
times. I'll try to fix that soon. But it is just a convenience option,
anyways: you can always write each of your selections as "mol_com of ...",
and it should work the same.
Best regards,
Teemu
On Fri, Sep 25, 2015 at 11:
Hi Teemu
Thanks for your response, but -seltype is not available as a flag for
gmx rdf in gromacs 5.1 documentation, nor recognizable from cmd (I gave
it a try...)
--
Karozis Stelios
Chemical Engineer, MSc
Research Associate at EREL
NCSR D- INRASTES
tel:0030 210 650 3403
e-mail: skaro...@ipta
I installed gromacs 5.0.5, but during installation, i got error massages
CMake Error at src/programs/cmake_install.cmake:42 (FILE):
file INSTALL cannot find
"//phome01/p580seh/gromacs-5.0.5/build/bin/gmx_mpi_d".
Call Stack (most recent call first):
src/cmake_install.cmake:40 (INCLUDE)
cma
Hi,
You should use -seltype instead of -selrpos in this case.
Best regards,
Teemu
On Fri, Sep 25, 2015, 11:12 Stelios Karozis
wrote:
> Greeting everyone,
> I strated using gromacs 5.1 and I have difficulties with gmx rdf
> command. With older version of gromacs I used -xy -rdf mol_com
> flags
Greeting everyone,
I strated using gromacs 5.1 and I have difficulties with gmx rdf
command. With older version of gromacs I used -xy -rdf mol_com
flags. As far as I can understand, the equivalent flags for gromacs 5.1
are -xy -selrpos mol_com but the result is not correct. For instance
the firs
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