Hi Shahab,
What did you do exactly? Can you state your complete protocol (1. fetched
this structure file there, 2. got the topology from there, 3. did
something, 4. ran grompp like this, etc)? Use brief, clear explanations and
the command lines as you issued them.
Cheers,
Tsjerk
On Tue, Sep 17
Hi Neha,
Yes. The MN* particles are the virtual sites.
Cheers,
Tsjerk
On Wed, Sep 18, 2013 at 7:13 AM, Neha Gandhi wrote:
> Dear Users,
>
> I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am
> using following command.
> pdb2gmx -f input.gro -o input1.gro -vsite hydrogens -i
Dear Users,
I am trying to prepare file using pdb2gmx using Gomos 43a1 ff. I am
using following command.
pdb2gmx -f input.gro -o input1.gro -vsite hydrogens -ignh
Upon visualisation I could see triangle like sites. Does the output seem right?
75
1VALMN11 2.913 3.551 3.288
On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote:
Can you give some examples of how these verifications are different for
different force fields? It doesnt seem like verifying takes that much time,
but a theorist prof in my department told me not to worry as long as my
system doesnt
Can you give some examples of how these verifications are different for
different force fields? It doesnt seem like verifying takes that much time,
but a theorist prof in my department told me not to worry as long as my
system doesnt blow up...
And what do you mean "thourough parametrization?
I pa
Indeed, it works just fine when I compile with mpi. I never thought to check
that. My usual procedure is
to compile the whole package without mpi and then to compile mdrun with mpi.
Thanks for the help Mark.
Here is the compilation script that worked for me.
module purge
module load vacpp/12.1
Does anyone have proper parameters for CNTs ? I have been trying to perform
Simulations with finite CNTs. However, none of the parameters so far
(obtained from literature) seem to give the output temperatures equal to
set temperatures.
I have been looked into my input files time and again, but I c
No. Theoretically useful, but not implemented.
Mark
On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui
wrote:
> Thanks. Is it possible to dump the parameters in the tpr file to a mdp file?
>
>
> On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham wrote:
>
>> mdrun -nsteps in 4.6 overrides the number of ste
On Tue, Sep 17, 2013 at 5:31 PM, Christopher Neale
wrote:
> Dear Users:
>
> I am attempting to use the new BGQ kernels with the version of gromacs at
> https://gerrit.gromacs.org/#/c/2572/ , which I obtained by:
>
> git init
> git fetch https://gerrit.gromacs.org/gromacs refs/changes/72/2572/1 &&
the smart way is to constrain everything at once in MDP...
Dr. Vitaly V. Chaban
On Tue, Sep 17, 2013 at 10:50 PM, HANNIBAL LECTER
wrote:
> Is there a smart way of writing the constraint sections in the topology
> file other than entering the values manually ?
>
>
> On Tue, Sep 17, 2013 at 10:10
Dear Users:
I am attempting to use the new BGQ kernels with the version of gromacs at
https://gerrit.gromacs.org/#/c/2572/ , which I obtained by:
git init
git fetch https://gerrit.gromacs.org/gromacs refs/changes/72/2572/1 && git
checkout FETCH_HEAD
I then attempted to compile like this:
modu
Is there a smart way of writing the constraint sections in the topology
file other than entering the values manually ?
On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
wrote:
> Thanks
>
>
> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul wrote:
>
> >
> >
> > On 9/17/13 10:00 AM, HANNIBAL LECTER wro
Thanks. Is it possible to dump the parameters in the tpr file to a mdp file?
On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham wrote:
> mdrun -nsteps in 4.6 overrides the number of steps in the .tpr
>
> Mark
>
> On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui
> wrote:
> > Dear GMX users,
> >
> > I'm
Yes. That is the way to go about it. I was hoping for a more lazy
approach... Thanks anyways.
On Tue, Sep 17, 2013 at 5:07 PM, Justin Lemkul wrote:
>
>
> On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:
>
>> Is there a smart way of writing the constraint sections in the topology
>> file other than en
@Vitaly. Yes you are right. However, I noticed that if I do not constraint
the bonds in my CNT my simulations run fine. It is indeed surprising to me
but I do not have much experience with simulating CNTs and if not
constraining the bonds seem to get things done, I think it is a viable
option. But
On 9/17/13 4:50 PM, HANNIBAL LECTER wrote:
Is there a smart way of writing the constraint sections in the topology
file other than entering the values manually ?
Write a script that parses the [bonds] directive of the post-processed topology
(output by grompp -pp) and write the relevant fie
mdrun -nsteps in 4.6 overrides the number of steps in the .tpr
Mark
On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui
wrote:
> Dear GMX users,
>
> I'm new to Gromacs. So apologies if this question is too simple.
>
> I downloaded top/tpr files from the supplementary material of a published
> paper. T
Dear GMX users,
I'm new to Gromacs. So apologies if this question is too simple.
I downloaded top/tpr files from the supplementary material of a published
paper. The nsteps set in the tpr file is 100ns. I wish to do a small test
run. Is there any way I can modify that? I've tried to create a mdp
Dear Justin
I did minimization with the newest version of gromacs (4.6.3).
But, unfortunately, problem was not solved.
Best wishes for you.
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* Please search the archive at
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Hello,
Please keep correspondence on the list so that others may benefit from it,
and you don't need to wait for some particular person to respond.
On Tue, Sep 17, 2013 at 1:24 PM, Venkat Reddy wrote:
>
> On Tue, Sep 17, 2013 at 12:38 AM, Teemu Murtola
>> wrote:
>>
>>> version (from the git ma
Hi Nilesh,
I looked at the code and was not able to find a reasonable condition, where
the last column of the mc output can contain -inf.
The only thing where the normalization would produce something like this is,
when the number of frames (nfr) equals the counter in the loop i for the
integral
On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
Is there a way to constraint bonds of a part of the system while keeping
the other part flexible? For example for a simulation with two proteins, I
would like to constraint the bonds of one and would like to keep the other
flexible.
I would prefer to
Is there a way to constraint bonds of a part of the system while keeping
the other part flexible? For example for a simulation with two proteins, I
would like to constraint the bonds of one and would like to keep the other
flexible.
I would prefer to use LINCS to constraint the system
--
gmx-user
Thanks
On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul wrote:
>
>
> On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
>
>> Is there a way to constraint bonds of a part of the system while keeping
>> the other part flexible? For example for a simulation with two proteins, I
>> would like to constraint
On 9/17/13 8:47 AM, shahab shariati wrote:
Dear Justin
Very very thanks for your quick reply.
I am very confused and amazed.
After visualization of atom 618 ( where the maximum force is),
what should I do to resolve me problem.
Any help will highly appreciated.
I honestly have no idea.
Dear Justin
Very very thanks for your quick reply.
I am very confused and amazed.
After visualization of atom 618 ( where the maximum force is),
what should I do to resolve me problem.
Any help will highly appreciated.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org
On 9/17/13 8:17 AM, shahab shariati wrote:
Dear Justin
Thanks for your time and consideration.
As I suggested before, visualize the output file and figure out what is
around atom 618 to cause such forces.
I visualized output file (em.gro) by VMD. Atom 618 is belonged to a dopc
molecule (t
Dear Justin
Thanks for your time and consideration.
> As I suggested before, visualize the output file and figure out what is
> around atom 618 to cause such forces.
I visualized output file (em.gro) by VMD. Atom 618 is belonged to a dopc
molecule (this dopc molecule is intact and is not broken
On 9/17/13 7:26 AM, mabbasi wrote:
Dear All users
used OPLS ff for my system
After md production i get this error:
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
How to solve the problem ??
St
On 9/17/13 7:02 AM, shahab shariati wrote:
Dear Justin
Thanks for your reply
You're still working with outdated software. Please follow my
suggestion of trying 4.6.3.
I try to install 4.6.3.
The larger issue, in the end, is the unphysical configuration of the drug
in the membrane. Ind
Dear All users
used OPLS ff for my system
After md production i get this error:
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
How to solve the problem ??
Thank you
maryam abbasi, PhD student of
Dear Justin
Thanks for your reply
> You're still working with outdated software. Please follow my
> suggestion of trying 4.6.3.
I try to install 4.6.3.
> The larger issue, in the end, is the unphysical configuration of the drug
> in the membrane. Independent of Gromacs version, that setup wi
Dear all
When I use the following command:
g_analyze -ffree_bi_0.9.xvg -av average_0.9
I got
set average standard deviation *std. dev. /
sqrt(n-1)*…
SS16.053822e+01 3.062230e+01 1.936724e-02…
What is “*std. dev. / sqrt(n-1)”
On 9/17/13 5:58 AM, Mahboobeh Eslami wrote:
dear mark
will all my output write well after restart and are their names md?
will old my output reconstruct or will generate new output?
The default behavior of mdrun is to append to existing files. Otherwise, you
can use -noappend to get a new
dear mark
will all my output write well after restart and are their names md?
will old my output reconstruct or will generate new output?
thank
- Forwarded Message -
From: Mahboobeh Eslami
To: "gmx-users@gromacs.org"
Sent: Tuesday, September 17, 2013 2:00 PM
Subject: Fw: Fw: [gmx-use
On 9/17/13 5:03 AM, shahab shariati wrote:
Dear Justin
I used newer version of gromacs (4.6.1), but my problem was not solved.
You're still working with outdated software. Please follow my suggestion of
trying 4.6.3. The larger issue, in the end, is the unphysical configuration of
the d
dear mark
thank you so much
Good luck
- Forwarded Message -
From: Mark Abraham
To: Mahboobeh Eslami ; Discussion list for GROMACS
users
Sent: Tuesday, September 17, 2013 1:21 PM
Subject: Re: Fw: [gmx-users] How to restart the crashed run
mdrun -v -deffnm md -cpi md
IIRC the -cp
Dear Justin
I used newer version of gromacs (4.6.1), but my problem was not solved.
Any help will highly appreciated.
--
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* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lis
mdrun -v -deffnm md -cpi md
IIRC the -cpi file is immune from -deffnm
Mark
On Tue, Sep 17, 2013 at 4:48 AM, Mahboobeh Eslami
wrote:
> dear mark
>
> yes i do
> my comment for md run was following
>
>
> mdrun -v -deffnm md >& md.job &
>
> now what comment is true for restart?
> I've recently star
dear mark
yes i do
my comment for md run was following
mdrun -v -deffnm md >& md.job &
now what comment is true for restart?
I've recently started working with the gromacs and i am not professional
thank you and best wishes for you
- Forwarded Message -
From: Mark Abraham
To: Mahboo
You named them last time you ran mdrun, either explicitly or with
-deffnm. Do the same.
Mark
On Tue, Sep 17, 2013 at 3:19 AM, Mahboobeh Eslami
wrote:
> when i use following omment for restart
>
> mdrun -s md.tpr -cpi md.cpt
> i get following error
>
> Output file appending has been requested,
>
when i use following omment for restart
mdrun -s md.tpr -cpi md.cpt
i get following error
Output file appending has been requested,
but some output files listed in the checkpoint file md.cpt
are not present or are named differently by the current program:
output files present: md.log
output file
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