I recall seeing something online about how gromacs developers have
decided to focus on increasing the overall speed and allowing
generally large timesteps (via e.g. angle constraints) vs.
implementing multiple timestepping (no mailing list ref. sorry). I
agree that this is not a logically e
- Original Message -
From: pawan raghav
Date: Wednesday, June 30, 2010 14:56
Subject: [gmx-users] REMD
To: gmx-users@gromacs.org
> Dear Justin, > > I have read manual there was an equation where T1 and T2
> are the two temperatrure will be assign but in my case I don't have different
Dear Justin,
I have read manual there was an equation where T1 and T2 are the two
temperatrure will be assign but in my case I don't have different
temperature. I have to simulate at same temperature.
Is there any other alternative to perform sampling rather than REMD. I am
working on one process
- Original Message -
From: quantrum75
Date: Wednesday, June 30, 2010 7:12
Subject: [gmx-users] mdrun_mpi issue.
To: gmx-users@gromacs.org
---
| > Hi Folks,
> I am trying to run a simulation under GMX 4.0.5. When I do a qsub of my j
Thanks Justin, this is just working amazingly
From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul
Sent: Tue 6/29/2010 6:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] automating analysis using shell scripting
Hassan Sha
Hassan Shallal wrote:
Dear Gromacs users,
This question is much more of a linux shell scripting than of Gromacs. I have several distances to measure in my produced system for which I use g_dist. I need to shell script this so I don't have to set next to the machine while measuring those dista
Dear Gromacs users,
This question is much more of a linux shell scripting than of Gromacs. I have
several distances to measure in my produced system for which I use g_dist. I
need to shell script this so I don't have to set next to the machine while
measuring those distances. The problem I fac
A couple of months ago someone mentioned a recent publication that went
through a procedure for the detection of an interface / surface between
phases for data from MD. Remember reading the publication and thinking
was pretty neat and need to come back and try it. Well, for the life of
me can't f
Hi Folks,
I am trying to run a simulation under GMX 4.0.5. When I do a qsub of my job, it
does not seem to run and gives me an error saying the library libimf.so is not
available. I tried subsequently giving/copying the library into the run path
with still the exact same error. I am attaching th
Moeed wrote:
Hello Justin,
I spent a full day to find a proper value for -d but it seems there is
no way of getting correct bond lenght and angle at the same time. With
the following commands I am getting correct bond length for the atoms
connecting two monomer units but the angle is 140.
Hello Justin,
I spent a full day to find a proper value for -d but it seems there is no
way of getting correct bond lenght and angle at the same time. With the
following commands I am getting correct bond length for the atoms connecting
two monomer units but the angle is 140. I get 110 angle only
pawan raghav wrote:
Dear Justin,
No dear I have not modelled the membrane, my protein is a simple protein
which contained a loop about 59 amino acids. So I am intrested to model
this loop through MD simulation. In this concerned I did 15 ns
simulations, but right now don't know how to perf
Dear Justin,
No dear I have not modelled the membrane, my protein is a simple protein
which contained a loop about 59 amino acids. So I am intrested to model this
loop through MD simulation. In this concerned I did 15 ns simulations, but
right now don't know how to perform sampling for my protein
tekle...@ualberta.ca wrote:
Dear Gromas users,
I want to run another set of MD simulation of my polymer in a mixed
solvent.
step 1
24 polymer molecules in a 10 * 10 * 10 nm of box.
step 2
I want to add 50% (v/v) of two solvents to this box. I have already done
an MD simulation with thei
Dear Gromas users,
I want to run another set of MD simulation of my polymer in a mixed solvent.
step 1
24 polymer molecules in a 10 * 10 * 10 nm of box.
step 2
I want to add 50% (v/v) of two solvents to this box. I have already
done an MD simulation with their individual solvents, now I wan
Hi
I need some information about how ED sampling works when
a subset of the atoms are used for covariance analysis. Basically I would like
to
move the system along the first eigenvector obtained from covariance analysis
of the
C-alpha atoms only. From the paper "Toward an Exhaustive Sampling
Hi,
The core developers have the answer for this one, but I can make an
educated guess:
Implementing it would mean a LOT of work and the rewards are small. The
latter because most particles will have rougly the same oscillation
period if one uses all-atom forcefields and turn on virtual site
Chris,
An interesting question...
BTW, is there any philosophy of gromacs developers to avoid this
algorithm in the MD engine?
Vitaly
> multiple timesteps are not possible as far as gromacs 4.0.7. NAMD can do this.
>
>
> -- original message --
>
> Is it possible to carry out multiple time st
Hi,
I don't know what you aim to study, but consider the benefits and
drawbacks of the programs and integration algorithms carefully if you
want to use the multiple timestep algorithm to perform speedy
calculations. More specifically: Is e.g NAMD with the multiple timestep
algorithm really fa
Hallo,
I would try to use the program protomol.
There are many possibilities for performing multiple timestepping.
Emanuel
>>> oguz gurbulak 29.06.10 15.41 Uhr >>>
Dear All,
Is it possible to carry out multiple time step molecular
dynamics simulations
in Gromacs
4.0. versions ? Coul
Can you please supply gen_temp and also your pressure coupling values?
Also, please supply the g_energy values that show the temperatures
changing as you suggest (with accompanying timestep info).
I'm fairly sure that what is happening is that you are simply seeing
the nose-hoover oscillati
multiple timesteps are not possible as far as gromacs 4.0.7. NAMD can do this.
-- original message --
Is it possible to carry out multiple time step molecular
dynamics simulations
in Gromacs
4.0. versions ? Could you
please give me some information about this issue ?
Thank you very much for
Hi Kun,
Can you tell more about what you are doing? What are you analyzing?
How large is the system? Which groups do you use for analysis. Etc.,
etc. Now, you might be right, but you might as well be jumping to
conclusions.
Cheers,
Tsjerk
On Tue, Jun 29, 2010 at 4:12 PM, Kun Huang wrote:
> Hi
Hi everyone:
I am using g_rdf to calculate radial distribution function. However when I
check the memory usage using top, it seems to me that the code has a huge
memory leak. My system has 4GB memory but it usually has 40MB free memory
left after the program finishes.
Does anyone have the same pr
pawan raghav wrote:
Dear Justin,
Thanks for the wonderful suggestions which is very clear and informative
but I am confused about some points below
1. Actually my protein is human mitochondrial protein so I have
used GROMOS 96 53a6 ff. is it correct? but you have mentioned about the
Th
I try to simulate a small peptide in CHCl3 there the
peptide is couplet to a heat bath at a different
temperature:
tcoupl = nose-hoover
tc-grps = Protein+PTS+AIC CHCl3
tau_t = 0.01 0.01
ref_t = 220 300
If I do so the temperature of the C
Dear All,
Is it possible to carry out multiple time step molecular
dynamics simulations
in Gromacs
4.0. versions ? Could you
please give me some information about this issue ?
Thank you very much for your attention.
Kind regards.
--
gmx-users mailing listgmx-users@grom
It is because I want to apply cmap to my own stuff. I can define my
own 2D grid potential and apply to two sequential dihedral angles by
add one line in the topol file. However, the testing result is really
unexpected.
dawei
On Tue, Jun 29, 2010 at 8:53 AM, Per Larsson wrote:
> Hi,
>
> I do not
Hi,
I do not fully understand what you are trying to do, but currently CMAP is only
available for the standard amino acid residues present in the rtp-file for the
Charmm-forcefield, and the values for the grid are specified in the
cmap.itp-file.
Do you use something else?
/Per
29 jun 2010 kl.
HI, David,
thanks for your advise. I remove the bond angle force and get same
result. It is really strange. If I set +5 on all the 24*24 grid, I
just get a inverted distribution and if I set 0 on all grid, I will
get a uniformed distribution. It is like that 27 regions are force to
have zero cmap
> Message: 5
> Date: Tue, 29 Jun 2010 11:54:12 +0330
> From: leila karami
> Subject: [gmx-users] g_msd and diffusion coefficent
> To: gmx-users@gromacs.org
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Vitaly Chaban
>
> I know using index file but gromacs say :
Hi all
pdb file for my protein was obtained by solution NMR. this file is as
follows :
ATOM 1 N GLY A 1 -25.349 -8.577 4.055 1.00 0.00
ATOM 2 CA GLY A 1 -24.037 -8.099 4.448 1.00 0.00
ATOM 3 C GLY A 1 -23.580 -6.913 3.622 1.00 0.00
ATOM
Hi,
You also need the OpenMM libraries and plugins.
For more detail see:
http://www.gromacs.org/gpu#Installing_and_running_Gromacs-GPU
--
Szilárd
On Sat, Jun 26, 2010 at 6:18 PM, Tarsis wrote:
> I'm trying to install cuda but when I export
> LD_LIBRARY_PATH=/usr/local/cuda/lib:$libcudart.so
- Original Message -
From: leila karami
Date: Tuesday, June 29, 2010 18:08
Subject: [gmx-users] g_msd and diffusion coefficent
To: gmx-users@gromacs.org
> Dear Mark Abraham> No, I want to measure something about the diffusion of my
> protein to DNA (especially to major groove of DNA)
Dear Vitaly Chaban
I know using index file but gromacs say : select only 1 group. what is this
group ? protein? or DNA?
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Hi,
Is there a standard trick in gromacs to get the atom numbers which are
located in the liquid-vapor interface?
Vitaly
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before postin
Use NDX file.
Dr. Vitaly V. Chaban
>
> in my system, there are pr, dna, water and Na and I want to obtain diffusion
> of pr in dna but when I use g_msd command, gromacs says select only 1
> group. should be this group pr or dna?
>
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.
Dear Justin,
Thanks for the wonderful suggestions which is very clear and informative but
I am confused about some points below
1. Actually my protein is human mitochondrial protein so I have used GROMOS
96 53a6 ff. is it correct? but you have mentioned about the condition
applied, so I don't und
Dear Mark Abraham
No, I want to measure something about the diffusion of my protein to
DNA (especially to major groove of DNA) in the presence of water (as
solvent).
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive a
- Original Message -
From: leila karami
Date: Tuesday, June 29, 2010 17:32
Subject: [gmx-users] g_msd and diffusion coefficent
To: gmx-users@gromacs.org
> Dear Mark Abraham > > yes. pr means protein. I want to obtain diffusion of
> protein within dna. I want to know how/how much p
Dear Mark Abraham
yes. pr means protein. I want to obtain diffusion of protein within dna. I
want to know how/how much pr diffuse to dna.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/sea
- Original Message -
From: leila karami
Date: Tuesday, June 29, 2010 16:41
Subject: [gmx-users] g_msd and diffusion coefficent
To: gmx-users@gromacs.org
> Hi gromacs users > > in my system, there are pr, dna, water and Na and I
> want to obtain diffusion of pr in dna but when I use
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