[EMAIL PROTECTED] wrote:
> Dear friends,
> I have carried out a simulation of a protein in solution and want to
> analyse redisue wise root-mean-square-deviation (RMSD) of the protein. As
> far as I know, RMSD can be calculated by g_rms, which gives RMSD as a
> function of time, but what I expec
JMandumpal wrote:
Dear gromacs users,
I ran 100ps equilibraion, NVT, prior to running 60ps NVE to check the
energy conservation with different timesteps: 1.0fs, 1.5fs and 2.0fs,
but these NVE simulations seem not to converge even after. Following is
the command I used for running 60ps NVE :
Dear lists,
Should I use this : tpbconv -f traj.trr -s topol.tpr -e ener.edr -o tpxout.tpr
-time 100 -until 160 and then
mpirun mdrun_mpi_d -s tpxout.tpr -o pr.trr -c output_1.gro -g topol.log
If then, how do I change my paremeters, for example to remove temprature
coupling parameters in order
Dear friends,
I have carried out a simulation of a protein in solution and want to
analyse redisue wise root-mean-square-deviation (RMSD) of the protein. As
far as I know, RMSD can be calculated by g_rms, which gives RMSD as a
function of time, but what I expect is RMSD as a function of residue
Dear gromacs users,
I ran 100ps equilibraion, NVT, prior to running 60ps NVE to check the energy
conservation with different timesteps: 1.0fs, 1.5fs and 2.0fs, but these NVE
simulations seem not to converge even after. Following is the command I used
for running 60ps NVE :
---
Thanks !!
it works
Thank you very much
Best Regards
Wen-Peng Qi
Please supply us the output of trjconv.
Alternatively, use trjconv -o foo.pdb -sep.
Regards,
Yang Ye
=C6=EB=CE=C4=C5=F4 wrote:
>
> I use the trjconv -split 1.0 to split my long xtc file to seperate pdb
> files to analysis wi
Luis Javier Alvarez Noguera wrote:
Dear colleagues:
We have the cartesian coordinates of a micelle in xyz format and haven't been
able to build up the .top corresponding file with gromacs package program
x2top. There is a confusion on how to feed this program. Is there a document
or an example wh
Am Donnerstag, 27. März 2008 schrieb Priscila Capriles Goliatt:
> I would like know if the gromacs version 3.2 performs a molecular dynamic
> simulation starting with a high temperature and decreasing in each step
> until a low temperature. How I can do something like this?
Are you thinking about
Dear colleagues:
We have the cartesian coordinates of a micelle in xyz format and haven't been
able to build up the .top corresponding file with gromacs package program
x2top. There is a confusion on how to feed this program. Is there a document
or an example where we can clarify thigs such as:
1.
Yes, the LO LO in atom type should be as Justin has mentioned.
Sudheer, please note that the original post that you quote below actually
includes an example for LO LO
"LO LO 115.9994 0.000 A2.96000e-01 8.87864e-01"
Also note that similar information is available i
Berk,
> Hmm. Is this different from how other packages handle this issue? I
> have never had the recurring problems with minimization in GROMACS
> that I have in other packages. Even though, strangely enough, water is
> a common feature in most of the simulations I run.
That was backwards. I
Berk,
> I assume you are using a rigid water model, and thus constraints via SETTLE.
Yes, OK.
> Constraining is required to measure the size of the force (for convergence
> and
> step size adjustment) and to make correct steps without enormous extra
> displacements in the direction of the force
Hi everyone,
I would like know if the gromacs version 3.2 performs a molecular dynamic
simulation starting with a high temperature and decreasing in each step
until a low temperature. How I can do something like this?
Regards,
Priscila Goliatt
___
gmx-u
Hi Berk,
my volume fluctuations are relative small. For the largest and smallest
system respectively that I have been simulating the statistics are:
AverageRMSD Fluct.
207.7 nm^30.699 nm^3 0.698 nm^3
75.1 nm^30.431 nm^3 0.432 nm^3
My pressure coupling
Quoting sudheer babu <[EMAIL PROTECTED]>:
> Hi all ,
> I wanted to use OPLS-FF for POPC and Protein, I followed the procedure from
> archives and the link is
> *http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html*
> The steps I have done are
> 1. I added "atom types" from lipid.i
Hi all ,
I wanted to use OPLS-FF for POPC and Protein, I followed the procedure from
archives and the link is
*http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html*
The steps I have done are
1. I added "atom types" from lipid.itp to ffoplsaanb.itp here I got no
exponential values
Hi,
I'm a gromacs beginner and have a quick question.
My system includes a simple n-decane molecule with oplsaa force field. I'm
basically confused with
the Ryckaert-Bellemans parameters in ffoplsaabon.itp file in gromacs for
H-C-C-H alkane dihedral.
The OPLSAA parameters for H-C-C-H dihedral
Ricardo,
Please, Can you write your error messages? I think that better us understand
your situation.
Thanks,
--
Rodrigo Antonio Faccioli
Student of Post-graduation in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineer
Dear Gromacs-users,
I have been putting a protein and its hydration shell into the center of
an octahedral box and then been filling the remaining space with water
using genbox. I wanted to minimise the filled-in water, afterwards,
keeping the positions of the protein and the hydration shell fixed
Hi,
I am also starting to wonder now if you might have other problems.
Have you checked if there aren't very strong volume fluctuations?
Could you mail your mdp pressure coupling parameters?
Berk.
> Date: Thu, 27 Mar 2008 15:16:39 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> S
Please supply us the output of trjconv.
Alternatively, use trjconv -o foo.pdb -sep.
Regards,
Yang Ye
齐文鹏 wrote:
>
> I use the trjconv -split 1.0 to split my long xtc file to seperate pdb
> files to analysis with the Curves .
>
> But I cannot split files more than 1020. why? The gromacs version i
Hi everyone,
I use the trjconv -split 1.0 to split my long xtc file to seperate pdb files to
analysis with the Curves .
But I cannot split files more than 1020. why? The gromacs version is 3.3.1 and
only float precision. I have no ideas!
Pleas give me some advise!!
Thank you !!
Best Regards
Hi Berk,
I reran my simulations with the settings you suggested. Unfortunately most
of them crashed. In some of them I received the original error message:
Source code file: ns.c, line: 313
Fatal error:
Could not correct too skewed box
I did not, however, receive this message from all runs. In
> Date: Thu, 27 Mar 2008 06:41:12 -0700
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] minimization -- bugzilla or general advice?
>
> Berk,
>
> > The problem could be in the constraints.
> > Gromacs 3 constrains the forces during EM by adding c*f to the coor
Berk,
> The problem could be in the constraints.
> Gromacs 3 constrains the forces during EM by adding c*f to the coordinates,
> constraining those and then dividing the constraint displacement by c.
> This limits the accuracy.
>
> In Gromacs 4 I have implemented force constraining for LINCS and S
Hello
I'm trying to minimize a protein with the a part of it frozen.
I was wondering if it is at all possible to extract bonded energy
terms for the non-frozen region.
I can extract the coulombic and LJ energy terms but not the bond,
angle and proper dih ones...
Any suggestions?
Thanks a l
Rui Li wrote:
Dear all,
I want to know the usage of g_bond.
When I use g_bond , it prompt me to Select a group, If there are odd number of
atoms in group, it will warn.
sometimes it produces error
Fatal error:
No distribution... (i0 = 999, i1 = 1)? ? ! ! ? !
what is the meaning?
you need to defi
Dear all,
I want to know the usage of g_bond.
When I use g_bond , it prompt me to Select a group, If there are odd number of
atoms in group, it will warn.
sometimes it produces error
Fatal error:
No distribution... (i0 = 999, i1 = 1)? ? ! ! ? !
what is the meaning?
Thanks in advance!
___
> Date: Thu, 27 Mar 2008 07:54:03 +0100
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] minimization -- bugzilla or general advice?
>
> David Mobley wrote:
> > Xavier,
> >
> >> I was surprised by the value you use for emstep=1.0e-8. This is the
> >> "maximum
JMandumpal wrote:
>
>
> >Dear all,
>
> >While running a job, since there was space problem I could not write
> the xtc files. Now when I do the analysis and use the trr file it
> reports the >time values after every 5ps i.e. 2000, 2005, 2010 etc.
> However I wish to >write the xtc file using trjc
--=20
Florian Dommert
Dipl.-Phys.
Computational and Theoretical Softmatter & Biophysics group
Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University
Ruth-Moufang-Str. 1
60438 Frankfurt am Main
Phone: +49(0)69 / 798 - 47522
Fax: +49(0)69 / 798 - 47611
EMail: [EMAIL PROTECT
JMandumpal wrote:
>
>
> >Dear all,
>
> >While running a job, since there was space problem I could not write
> the xtc files. Now when I do the analysis and use the trr file it
> reports the >time values after every 5ps i.e. 2000, 2005, 2010 etc.
> However I wish to >write the xtc file using trjc
>Dear all,
>While running a job, since there was space problem I could not write the xtc
>files. Now when I do the analysis and use the trr file it reports the >time
>values after every 5ps i.e. 2000, 2005, 2010 etc. However I wish to >write the
>xtc file using trjconv such that the timestep
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