Hi all,
I am facing the problem while calculating backbone RMSD over 30 ns. upto
~6-7 ns g_rms gives correct RMSDs and later all RMSD values are unexpectedly
and unusually high (within 20 ps RMSD value shoots up by ~8A). But when i
calculate RMSD using g_confrms programme, it gives me expe
Dear GMX-users,
Is it possible to exclude a group of atoms or molecules from having
their bonds converted to constraints when using the all-bonds
mdp-option?
Best regards,
Soren
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Aditi Borkar wrote:
Dear Mark,
Thank you. I was indeed using pressure coupling.
My protein is crescent shaped so if I use a regular simulation box, I
get one with a large volume. I hoped that using a shell will reduce
the number of atoms in the system and will facilitate computation.
So should
Have you tried loading the .gro into VMD first? VMD requires it to
understand the contents of your trr/xtc files. I believe that VMD can
sometimes find it automatically, but sometimes it can't, and you have to
first load it and then load the trajectory.
Otherwise, you can trjconv your trajectory to
malve...@iq.usp.br wrote:
Hello,
Is there a visualization tool to see .trr files on a windows machine?
I already have VMD, but the windows version does not seem to play
trajectory files.
Then it sounds like a bug the VMD folks should be aware of, but it works fine
for colleagues of mine who
Hello,
Is there a visualization tool to see .trr files on a windows machine?
I already have VMD, but the windows version does not seem to play
trajectory files.
Thanks
Alberto
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Justin A. Lemkul wrote:
darre...@ece.ubc.ca wrote:
Hi Justin,
I am using version 3.3.3 and read through the version 3.3 manual but do
not see an option to set "pbc = full" in this manual. I only see
options to set pbc to "xyz" or "no". Will setting pbc=full be
recognized in GROAMCS version 3
darre...@ece.ubc.ca wrote:
Hi Justin,
I am using version 3.3.3 and read through the version 3.3 manual but do
not see an option to set "pbc = full" in this manual. I only see
options to set pbc to "xyz" or "no". Will setting pbc=full be
recognized in GROAMCS version 3.3.3 and will this solve my
Hi Justin,
I am using version 3.3.3 and read through the version 3.3 manual but do
not see an option to set "pbc = full" in this manual. I only see
options to set pbc to "xyz" or "no". Will setting pbc=full be
recognized in GROAMCS version 3.3.3 and will this solve my problem?
Thanks.
Darrell
>
Vitaly V. Chaban wrote:
Hi,
I which file should one look for the value of shear viscosity as using
"g_energy -vis" to calculate it?
A variety of output files are generated with this command. Either visco.xvg or
evisco.xvg should have what you're looking for, according to the headers of the
Hi,
you can send mdrun the TERM or the USR1 signals which will
stop the simulation without data loss. See also the Gromacs
manual on page 281 ("mdrun").
On Unix/Linux this would be kill -USR1
Carsten
On Sep 22, 2009, at 6:39 PM, Miguel Quiliano Meza wrote:
Dear gromacs users
I am running
Dear gromacs users
I am running a molecular dynamics calculation, all is fine but the time of
calculation is big, I would like to know if I can stop the calculation
without lose the information generated until that point.
thanks in advance.
Miguel Quiliano.
__
Hi,
I which file should one look for the value of shear viscosity as using
"g_energy -vis" to calculate it?
Thanks,
Vitaly
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Please search the archive
Nilesh Dhumal wrote:
Hello
How to convert gaussian force constant (mdyne/A) to kJ/mole.nm2
Nilesh
google
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Hello
How to convert gaussian force constant (mdyne/A) to kJ/mole.nm2
Nilesh
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Dear Justin,
Thanks for the suggestion, will try to apply position restraints on lipid as
mentioned in the advanced trouble shooting section.
Ram
On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul wrote:
>
>
> ram bio wrote:
>
>> Dear Gromacs Users,
>>
>> I am following the justin tutorial on K
ram bio wrote:
Dear Gromacs Users,
I am following the justin tutorial on KALP-15 in lipid bilayer, I have a
query regarding the nvt.gro that is after the NVT equillibration phase.
The mdrun was proper without any warnings or errors, but when i
visuallized the nvt.gro in VMD, i found that th
Dear Gromacs Users,
I am following the justin tutorial on KALP-15 in lipid bilayer, I have a
query regarding the nvt.gro that is after the NVT equillibration phase. The
mdrun was proper without any warnings or errors, but when i visuallized the
nvt.gro in VMD, i found that the peptide is intact in
2009/9/22
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Aditi Borkar wrote:
Dear Justin
Thank you. I was indeed using pressure coupling and I don't want to
simulate a protein in a droplet surrounded by vacuum
My protein is crescent shaped so if I use a regular simulation box, I
get one with a large volume. I hoped that using a shell will reduce
th
Dear Mark,
Thank you. I was indeed using pressure coupling.
My protein is crescent shaped so if I use a regular simulation box, I
get one with a large volume. I hoped that using a shell will reduce
the number of atoms in the system and will facilitate computation.
So should I just stick to the t
Stefan Hoorman wrote:
I will ty Justin's suggestion. I should have the answer by tomorrow.
As for Thomas' suggestion, well, my mdp file didn't even have the
"pull_start" flag. So I assume gromacs though I had set it to "no". But
anyway, I checked the force in each window as you mentioned and
>
> Only an idea:
> If you start your pulling simulations (to get the windows) your spring
> start at some point (0.9nm?) and then moves along the pulling direction.
> If you now take a snapshot from the trajectory the spring is at 0.9+x nm
> . When you now change *only* the 'pull_rate' two things
Aditi Borkar wrote:
Dear All,
I created a simulation box in editconf with -d 2.5. Then in genbox, I
used the -shell 1.4 option to define a 1.4 nm thick layer of solvent
around my protein. When I visualized the system in Rasmol, as
expected, there was a lot of "empty space" in the simulation box.
Aditi Borkar wrote:
Dear All,
I created a simulation box in editconf with -d 2.5. Then in genbox, I
used the -shell 1.4 option to define a 1.4 nm thick layer of solvent
around my protein. When I visualized the system in Rasmol, as
expected, there was a lot of "empty space" in the simulation bo
Dear All,
I created a simulation box in editconf with -d 2.5. Then in genbox, I
used the -shell 1.4 option to define a 1.4 nm thick layer of solvent
around my protein. When I visualized the system in Rasmol, as
expected, there was a lot of "empty space" in the simulation box.
Should this vacuum cr
Mark Abraham wrote:
Darrell Koskinen wrote:
Hi Mark,
Yes, I have had success running many GROMACS simulations with a simple
graphene sheet inside a box.
I believe I have regenerated the .tpr file from the new .mdp as the
very first command I issue is:
grompp -np $NUM_PROCS -f em.mdp -c $GRO
Vitaly V. Chaban wrote:
Hi,
Could anybody please suggest me what is the syntax of N2T files? The
only sentence I found in the manual tells that it is "atom to atomtype
translation table". What do the numbers mean?
http://www.gromacs.org/index.php?title=Documentation/Gromacs_I%2F%2FO_Files/.
> Date: Tue, 22 Sep 2009 11:19:56 +0200
> From: schl...@uni-mainz.de
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: Re: Re: Re: Re: Re: umbrella potential
>
> Only an idea:
> If you start your pulling simulations (to get the windows) your spring
> start at some point (0.9nm?) and then m
Only an idea:
If you start your pulling simulations (to get the windows) your spring
start at some point (0.9nm?) and then moves along the pulling direction.
If you now take a snapshot from the trajectory the spring is at 0.9+x nm
. When you now change *only* the 'pull_rate' two things can happen:
Darrell Koskinen wrote:
Hi Mark,
Yes, I have had success running many GROMACS simulations with a simple
graphene sheet inside a box.
I believe I have regenerated the .tpr file from the new .mdp as the very
first command I issue is:
grompp -np $NUM_PROCS -f em.mdp -c $GRO_FILE -p $TOP_FILE -o
Hi,
Could anybody please suggest me what is the syntax of N2T files? The
only sentence I found in the manual tells that it is "atom to atomtype
translation table". What do the numbers mean?
Thanks,
Vitaly
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Hi Mark,
Yes, I have had success running many GROMACS simulations with a simple graphene sheet inside a box.
I believe I have regenerated the .tpr file from the new .mdp as the very first
command I issue is:
grompp -np $NUM_PROCS -f em.mdp -c $GRO_FILE -p $TOP_FILE -o emtopol.tpr -n
index.nd
Dear David, Thanks for the reply, guess i will do some literature survey and
see if i can find some validated urea parameters.
karan
On Mon, Sep 21, 2009 at 8:51 PM, David van der Spoel
wrote:
> karan syal wrote:
>
>> Dear Justin,
>>
>> Thanks for the reply!
>>
>> I will surely try minimize the
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