Hello,
My protein have two identical chains A and B and the backbone rmsd between
the two chains is 0.33A.
My problem is that how to select(on what basis) one chain out of the two for
md simulation, whether the selection of one of the two
chains(A or B) will make any differences to the final resul
On 8/07/2011 1:31 PM, wrote:
Hi,
I'm doing implicit solvent in gromacs 4.5.2 with amber03 force field
.I have done energy minimization .Then mdrun in NVT,but there is
always LINCS error .When I make impolicit_solvent=no,it can run
successfully. Is there a problem in the parameter settings
Dear Gromacs Developers or Users
Althoug the menu of verison 4.5.3 claims that the time-dependent of E
field (E_xt; E_yt; E_zt) has not been implemented yet, as I check the
source code of sim_util.c for the part of calc_f_el, i found the cos
of time function:
for(
Hi,
I'm doing implicit solvent in gromacs 4.5.2 with amber03 force field .I have
done energy minimization .Then mdrun in NVT,but there is always LINCS error
.When I make impolicit_solvent=no,it can run successfully. Is there a problem
in the parameter settings? How can I solve the problem?
Ste
On 8/07/2011 1:06 AM, Francesco Musiani wrote:
Dear Gromacs users,
I have the following problem: I need to calculate the potential energy
of a protein surrounded by explicit water.
In particular, I need to calculate the bond, angle, proper dihedral and
improper dihedral terms of potential energy
raghav singh wrote:
Hi Justin,
Yeah I have to remove that H from the that position to make my P open to
contact with the O atom of the next unit.
..but if you make some precise suggestion that How can I remove that
entry.. because I have tried to remove the entry from .RTP and .HDB
files an
Hi Justin,
Yeah I have to remove that H from the that position to make my P open to
contact with the O atom of the next unit.
..but if you make some precise suggestion that How can I remove that entry..
because I have tried to remove the entry from .RTP and .HDB files and in
that case it starts gi
Hi Justin,
Yeah I have to remove that H from the that position to make my P open to
contact with the O atom of the next unit.
..but if you make some precise suggestion that How can I remove that entry..
because I have tried to remove the entry from .RTP and .HDB files and in
that case it starts gi
Fabian Casteblanco wrote:
Hello Justin,
Thanks for your help.
Your response:
No, you need the [defaults] directive from the force field. If you
want to make
a completely custom entity, then build your own, although likely most of the
highest-level force field files are going to be the same.
Hello Justin,
Thanks for your help.
Your response:
No, you need the [defaults] directive from the force field. If you
want to make
a completely custom entity, then build your own, although likely most of the
highest-level force field files are going to be the same. You can always add a
new [ato
There's a quick & dirty workaround. You can write a script to "g_sas" each
frame individually, writing many output files. Then grab the results from there.
Sent from my iPhone
On Jul 7, 2011, at 9:17 PM, "Justin A. Lemkul" wrote:
>
>
> ahmet yıldırım wrote:
>> There are hydrophilic and hydr
Fabian Casteblanco wrote:
Hello Peter C. Lai,
Thanks for your help. I read your back and forth posts on the GMX
Forums with Mark Abraham. Is there any way that I can simply use it
from the topology without having to include it on the
charmm27.ff/forcefield.itp? I have to run this on a clust
errabah fatima ezzahra wrote:
Thank you so much for your help , my pdb file says that gen_seed =
473529 so i will change it to different numbers , but i saw online that
Your .mdp file, you mean?
some gen_seed = -1 and that to generate random seed is that correct ??
Yes, with -1 you will
Well, unfortunately I don't know of any step-by-step tutorial, but
from what I remember the workflow is pretty straightforward and looks
something like this:
- Download dependencies, there is precompiled OpenMM and FFTW for Windows.
- Run CMake, you'll have to set up the library dependencies manua
Hello Peter C. Lai,
Thanks for your help. I read your back and forth posts on the GMX
Forums with Mark Abraham. Is there any way that I can simply use it
from the topology without having to include it on the
charmm27.ff/forcefield.itp? I have to run this on a cluster and I
don't think I have ac
Thank you so much for your help , my pdb file says that gen_seed = 473529 so i
will change it to different numbers , but i saw online that some gen_seed = -1
and that to generate random seed is that correct ??
also please how i can control the starting initial states so that i can have
startin
just have charmm27.ff/forcefield.itp #include your new files. If you want
pdb2gmx to work, you will need to create the appropriate .rtp and/or .hdb files
too
--
Sent from my Android phone with K-9 Mail. Please excuse my brevity.
Fabian Casteblanco wrote:
Hello all,
I'm building a drug molecu
errabah fatima ezzahra wrote:
I am sorry to be asking you again but do you start with different
velocities by changing the temperature that will lead to change in
velocities, i ma new to Gromacs so i dont know where to change he
velocities, i checked the mdp file and i didn't see any veloci
I am sorry to be asking you again but do you start with different velocities
by changing the temperature that will lead to change in velocities, i ma new to
Gromacs so i dont know where to change he velocities, i checked the mdp file
and i didn't see any velocity
thank you
Fatima ezzahra
Thank you so much for your respond , i really appreciate your help
De : Justin A. Lemkul
À : Discussion list for GROMACS users
Envoyé le : Jeudi 7 Juillet 2011 14h55
Objet : Re: Re : Re : [gmx-users] Re: Hexamer problem/ The N and C termini of
peptides
erra
ahmet yıldırım wrote:
There are hydrophilic and hydrophobic SASA values versus simulation time
in the output file (area.xvg). I want to hydrophilic and hydrophobic
SASA values versus residue.
That's not implemented, but it would probably be rather easy to modify the code
to do so.
-Just
There are hydrophilic and hydrophobic SASA values versus simulation time in
the output file (area.xvg). I want to hydrophilic and hydrophobic SASA
values versus residue.
2011/7/7 Justin A. Lemkul
>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> I want to calculate hydrophilic and hyrophobic SA
ahmet yıldırım wrote:
Dear users,
I want to calculate hydrophilic and hyrophobic SASA value of each
residue in protein. I used a command as the following:
g_sas -f run.xtc -s run.tpr -or protein_protein.xvg
Select a group for calculation of surface and a group for output
select a group: 1 (
Dear users,
I want to calculate hydrophilic and hyrophobic SASA value of each residue in
protein. I used a command as the following:
g_sas -f run.xtc -s run.tpr -or protein_protein.xvg
Select a group for calculation of surface and a group for output
select a group: 1 (protein)
select a group: 2 (
errabah fatima ezzahra wrote:
*
hello
Does anybody knows why The N and C termini of peptides can be
neutralized before running simulation of peptides ?? i read this some
where in a research paper , they dont say why but they do that using
acetyl amine groops. Probably to evoid the repulsiv
hello
Does anybody knows why The N and C termini of peptides can be neutralized
before running simulation of peptides ?? i read this some where in a research
paper , they dont say why but they do that using acetyl amine groops. Probably
to evoid the repulsive interactions between the end of t
Hello all,
I'm building a drug molecule using CHARMM parameters. The thing is
that there is this new CGenFF (an extension of CHARMM, but very
similar to the old CHARMM atom types
http://mackerell.umaryland.edu/~kenno/cgenff/) that uses better
parameters for drug-like molecules. I would like to u
Hi,
Occasionally I hear that one need to use WHAM( weighed histogram analysis)
method in collaboration with Temperature-Replica exchange simulation. But, I
was not understanding why one need to use WHAM with temperature-remd
simulation.
Can someone explain me ?
Does one need to use any sor
Dear Gromacs developers or users:
I have a question about the implementation of the electrostatic field in
Gromacs (gromacs-4.5.3)
On the menu of this version, it looks that the functionality of
time-dependent has not been implemented yet.
E_x ; E_y ; E_z:
If you want to use an electric
I did not try before,
but I guess that you might need install at least the libs of mopac7,
try apt-get install libmopac7-dev
or better search your repository, there are .deb avaiable.
On Thu, Jul 7, 2011 at 11:37 AM, Yao Yao wrote:
> I am trying to compile mopac with gmx for qmmm calculation
Dear Gromacs users,
I have the following problem: I need to calculate the potential energy
of a protein surrounded by explicit water.
In particular, I need to calculate the bond, angle, proper dihedral and
improper dihedral terms of potential energy for the solute protein only.
How can I extract t
Singh wrote:
Hi Friends,
could anyone please guide me to get rid of the 5' H atom in terminal DT
nucleotide. These are my entries..
PDB : 5'DT
ATOM 1 PDT A 1 -6.726 -4.074 -28.509 1.00 0.00 P
ATOM 2 O5' DT A 1 -5.444 -3.882 -27.274 1.00 0.00
Hi Friends,
could anyone please guide me to get rid of the 5' H atom in terminal DT
nucleotide. These are my entries..
PDB : 5'DT
ATOM 1 PDT A 1 -6.726 -4.074 -28.509 1.00 0.00 P
ATOM 2 O5' DT A 1 -5.444 -3.882 -27.274 1.00 0.00 O1-
ATOM
Thank you for all your answers. It reassures me that the problem I encountered
wasn't only a secluded case.
I can also confirm that the -mol options seems to be the one making the most
consumption of the resources - without it memory usage has dropped to 20 gb.
And it could be connected to dealin
I just experienced this myself. The problem appeared to manifest
itself when I was using -mol on a molecule that straddled the box
wall. Memory usage was extremely high and the resulting MSD plot did
not show any linear behavior. Imaging the trajectory with -pbc nojump
made g_msd's memory usage
errabah fatima ezzahra wrote:
Hi everybody
i did Again run the simulation for 2000ns and the proteins were just
moving every were , they were forming the two rimers but not for along
time like in the simulation with the 200ns and 20 ns.
Justin : i did check the periodic boundary using VMD
Hi everybody
i did Againrun the simulation for 2000ns and the proteins were just moving
every were , they were forming the two rimers but not for along time like in
the simulation with the 200ns and 20 ns.
Justin : i did check the periodic boundary using VMD and it does not to seem to
be the
Dommert Florian wrote:
Hello,
I can also confirm this behaviour. Furthermore if I use an index group,
that just contains 1 molecule and compare the results from an analysis
with the flag -mol and without, then I obtain different results which
should not be the case.
It sounds like it's time
On 7/07/2011 6:25 PM, Javier Cerezo wrote:
Hi
The large peak in sodium rdf should be a consequence of the attractive
interaction between Na+ and Cl- and so it seems a reasonable plot.
Please, try to be a bit more clear and specific about your actual
problem. You can also post your command lin
Hello,
I can also confirm this behaviour. Furthermore if I use an index group,
that just contains 1 molecule and compare the results from an analysis
with the flag -mol and without, then I obtain different results which
should not be the case.
/Flo
On Thu, 2011-07-07 at 09:28 +0200, Ivan Gladic
Hi
The large peak in sodium rdf should be a consequence of the attractive
interaction between Na+ and Cl- and so it seems a reasonable plot.
Please, try to be a bit more clear and specific about your actual
problem. You can also post your command line arguments for rdf.
Also, in your mdp par
Dear All
I want to simulate a boxfilledwater that includes 10 sodium ion and 9 chloride
ion .
a chlorine fixed placein center of box simulation to see how it affects the
distribution ions .
Two graphs were obtained for the distribution of ions than to Cl fix (chlorine
fixin center of box)
Ques
Dear Justin, gmx users,
I putted a FF folder to the gromacs execution directory + changed
specbond.dat and it works (I have got isopeptide bond).
In old gromacs I needed only to made a local copy of all gromacs and made
changes in FF in its folders and not to copy FF folder to execution
directory
Dear all,
I found the same problem that Sławomir pointed out 10 days ago about
the memory usage in the computation of g_msd.
I have 100 ns simulation for 2880 water molecules. The trajectory is
savede every 1 ps: this means that I have 10 frame
I think that there is a strange memory p
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