Dear Gromacs users&devs,
I just installed gromacs-4.5.7 in a Cray XE6m, the serial installation
went fine, however the mpi installation presents a problem. It
compiles fine, but the "make install" (or make install-mdrun) seems to
have problems copying the executable files to the installation
direc
ahh, i thought that the program was "skipping" as in not doing the centering
command on certain frames due to one reason or another. Ill look into your
suggestion
Thank you very much for the help.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/trjconv-center-problem-tp5007
On 4/19/13 4:37 PM, Brad Van Oosten wrote:
Ahh, yes perhaps i was unclear. The output file also has the same number of
steps.
Checking file md50_centered.xtc
Reading frame 0 time0.000
# Atoms 27392
Precision 0.001 (nm)
Last frame 5 time 10.000
Item#frames Ti
Ahh, yes perhaps i was unclear. The output file also has the same number of
steps.
Checking file md50_centered.xtc
Reading frame 0 time0.000
# Atoms 27392
Precision 0.001 (nm)
Last frame 5 time 10.000
Item#frames Timestep (ps)
Step 500012
Time
On 4/19/13 4:28 PM, Brad Van Oosten wrote:
Checking file md50.xtc
Reading frame 0 time0.000
# Atoms 27392
Precision 0.001 (nm)
Last frame 5 time 10.000
Item#frames Timestep (ps)
Step 500012
Time 500012
Lambda 0
Coords 500
Checking file md50.xtc
Reading frame 0 time0.000
# Atoms 27392
Precision 0.001 (nm)
Last frame 5 time 10.000
Item#frames Timestep (ps)
Step 500012
Time 500012
Lambda 0
Coords 500012
Velocities 0
Forces
On 4/19/13 4:19 PM, Brad Van Oosten wrote:
The trajectory file is from a consecutive run so i would hope the frames are
evenly spaced.
What does gmxcheck tell you? No reason to hope when you can prove conclusively
one way or another :)
-Justin
--
The trajectory file is from a consecutive run so i would hope the frames are
evenly spaced.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/trjconv-center-problem-tp5007473p5007475.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailin
On 4/19/13 4:14 PM, Brad Van Oosten wrote:
i find the trjconv option -center skips random frames(less then 1 % of
frames), and by random frames i mean that these frames are not equally
spaced apart in time. I have tried -center and -center -boxcenter zero
flags but both produce the same proble
i find the trjconv option -center skips random frames(less then 1 % of
frames), and by random frames i mean that these frames are not equally
spaced apart in time. I have tried -center and -center -boxcenter zero
flags but both produce the same problem.
Does anyone know a fix/workaround?
--
Vi
On 1/9/13 8:06 PM, Xu Dong Huang wrote:
Dear Justin Lemkul,
I had a correspondence with you several times in January about .gro file
formatting and I remember you suggested to me that there is a code you can use
in C to automate the spacing format in .gro file generation. I can no longer
locat
On 4/19/13 2:57 PM, Shima Arasteh wrote:
Thanks so much for your replies. I appreciate you.
Do you think that more NPT equilibration might solve the problem? or wont work?
I have no idea at what point you are in your procedure that is crashing. I'm
not going to make some blind assessment
Thanks so much for your replies. I appreciate you.
Do you think that more NPT equilibration might solve the problem? or wont work?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, April 19, 2013 11:23 PM
Subject: Re:
On 4/19/13 2:25 PM, Nuria Cirauqui Diaz wrote:
Hi all,
I am trying to run a simulation of a protein in a water-vacuum-water box,
which simulates quite well the membrane environment. I did it some years
ago in amber, but know I am trying in grommacs and got the following answer
when I try to ru
On 4/19/13 2:49 PM, Shima Arasteh wrote:
The energy minimization has been done and the result is as follow:
Steepest Descents converged to Fmax < 100 in 8971 steps
Potential Energy = -1.5253394e+06
Maximum force = 9.2729095e+01 on atom 4719
Norm of force = 3.5977371e+00
But by runn
The energy minimization has been done and the result is as follow:
Steepest Descents converged to Fmax < 100 in 8971 steps
Potential Energy = -1.5253394e+06
Maximum force = 9.2729095e+01 on atom 4719
Norm of force = 3.5977371e+00
But by running mdrun, I get this fatal error:
1 particle
Hi all,
I am trying to run a simulation of a protein in a water-vacuum-water box,
which simulates quite well the membrane environment. I did it some years
ago in amber, but know I am trying in grommacs and got the following answer
when I try to run the fist "mdp" file:
ERROR: The cut-off length i
Dear Mark,
Thanks for the pages.
Now it is clear to me that because the shared libraries maybe are not
identical during compilation, I am getting different value for energies.
However, I have to perform single point energy calculation for a lot of
structure and the only thing that I care about is
On 4/19/13 1:18 PM, Shima Arasteh wrote:
Lets check the minim.mdp settings:
( ff applied is charmm36)
define = -DPOSRES
integrator= steep
emtol= 100.0
emstep= 0.01
nsteps= 5
nstlist= 1
ns_type= grid
rlist= 1.2
rlistlong
Dear All users
I want to use amber ff and there are some particles in my system that
non bonded interaction between them is buckingham,
Can I simulate this system in gromacs with different cut-off?
--
Sincerely
Ali Alizadeh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.groma
Lets check the minim.mdp settings:
( ff applied is charmm36)
define = -DPOSRES
integrator = steep
emtol = 100.0
emstep = 0.01
nsteps = 5
nstlist = 1
ns_type = grid
rlist = 1.2
rlistlong = 1.4
Thanks,
I've posted a summary of my build process (OpenMPI and Gromacs 4.6.1 using
Intel compilers) in case it's helpful to anyone else:
http://flakrat.blogspot.com/2013/04/how-to-compile-gromacs-461-with-openmpi.html
Mike
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:g
:-)
OK, thanks.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, April 19, 2013 8:42 PM
Subject: Re: [gmx-users] unstable system
On 4/19/13 11:55 AM, Shima Arasteh wrote:
> All right.
> And if minimization doesnt f
On 4/19/13 11:55 AM, Shima Arasteh wrote:
All right.
And if minimization doesnt fix such a problem, what would be the solution?
However I have not tried it on my own system yet.
It's a waste of time to delve into hypotheticals. Please try the advice you've
been given and report back if ne
All right.
And if minimization doesnt fix such a problem, what would be the solution?
However I have not tried it on my own system yet.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Friday, April 19, 2013
On 4/19/13 11:43 AM, Shima Arasteh wrote:
Thanks for your reply.
I' d like to know if I need to remove all position restraints before
MDRUN?means that the last step of npt should be done without position
restraints?
Whatever makes sense for your system. There is no universal answer to ho
if you only want the pdb file at a specific moment you can use -dump
trjconv -f traj.xtc -s file.tpr -o pdb_at_time.pdb -dump 10
the "pdb_at_time.pdb" file will be the structure at 10 ps.
You can then write a script to go through all your simulation.
cheers
Fra
On Fri, 19 Apr 2013, at 12:16 PM
Thanks for your reply.
I' d like to know if I need to remove all position restraints before
MDRUN?means that the last step of npt should be done without position
restraints?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent:
On 4/19/13 11:26 AM, Shima Arasteh wrote:
Hi,
I tried to equilibrate my system by setting timestep=1 fts and decreasing the
position restraints step by step.
But when I go to MDRUN step, it doesnt work and some pdb files are printed.
what is printed in my log file is as follow:
Hi,
I tried to equilibrate my system by setting timestep=1 fts and decreasing the
position restraints step by step.
But when I go to MDRUN step, it doesnt work and some pdb files are printed.
what is printed in my log file is as follow:
Step Time Lambda
On 4/19/13 10:45 AM, 라지브간디 wrote:
Hello gromacs.
I wanna simulate the heme contain proteins which has bond FE-NE2 from HIS as it
already found in specbond section.
When i use pdb2gmx, I could see the links of these but in topology file but not
parameter information which detects from ffbo
Hello gromacs.
I wanna simulate the heme contain proteins which has bond FE-NE2 from HIS as it
already found in specbond section.
When i use pdb2gmx, I could see the links of these but in topology file but not
parameter information which detects from ffbonded.itp.
I also checked the ffbon
Hi,
unfortunately state_prev.cpt are different too (checked with gmxcheck). So, the only way to restart
is the old fashion?
thanks
and
On 04/19/2013 04:13 PM, Mark Abraham wrote:
This is part of what state_prev.cpt is for - if only some of the new .cpt
files have made it to disk, you still
This is part of what state_prev.cpt is for - if only some of the new .cpt
files have made it to disk, you still have a full set of matching .cpt
files, but not with consistent names. Use gmxcheck to see the times.
Mark
On Fri, Apr 19, 2013 at 3:24 PM, andrea spitaleri
wrote:
> Hi there,
>
> I a
Hi there,
I am performing a remd (8 replica) using gromacs-4.5.3
Unfortunately, the job crashed for a problem with our cluster. We attempted to restart the
simulation using the checkpoint files, but two on the eight have different time frame.
To restart the simulation, I used the old feature of
On Apr 19, 2013 2:50 PM, "Fahimeh Baftizadeh" <
fahimeh.baftiza...@googlemail.com> wrote:
>
> Hi thanks for your reply, and sorry to be late since I am living 9 hours
> behind you :)
>
> I tried but still I get different energies. I check tpr files, according
to
> gmxcheck they are identical ...
>
Hi thanks for your reply, and sorry to be late since I am living 9 hours
behind you :)
I tried but still I get different energies. I check tpr files, according to
gmxcheck they are identical ...
But they give me different energies in different computers...
here is what I do:
$Mygrompp -f nvt.mdp
Dear,
I have made a 10ns prodution MD, The set dt=0.002，nstxtcout = 500 in
mdp file. I have made 10ns prodution MD, I want to extract frames from the
molecular dynamics simulations at regular intervals of 10ps and keep the file
as individual pdb file i want to use the follow command
On 4/19/13 8:03 AM, aixintiankong wrote:
At 2013-04-14 11:07:39,aixintiankong wrote:
Dear,
I have made a 10ns prodution MD, I want to extract frames from the
molecular dynamics simulations at regular intervals of 10ps and keep the file
as individual pdb file. The dt=0.002，n
At 2013-04-14 11:07:39,aixintiankong wrote:
Dear,
I have made a 10ns prodution MD, I want to extract frames from the
molecular dynamics simulations at regular intervals of 10ps and keep the file
as individual pdb file. The dt=0.002，nstxtcout = 500，i want to use the
follow comm
On 4/19/13 7:37 AM, Giuseppe wrote:
Dear Justin,
thank you very much for replying. When I run the editconf tool I set for
sure the right box vectors (6.23910 6.17970 6.91950) so that in the
system.gro file (according to the nomenclature of your tutorial) the box
vectors from the protein st
Dear Justin,
thank you very much for replying. When I run the editconf tool I set for
sure the right box vectors (6.23910 6.17970 6.91950) so that in the
system.gro file (according to the nomenclature of your tutorial) the box
vectors from the protein structure and from the membrane are the s
Have you tried the -reprod option?
Andrish
Fahimeh Baftizadeh wrote
> Hello,
>
> I have a 2 tpr files which are identical. Then I am doing a single step MD
> (I put n_step=0) simulation just to compute the total energy of a certain
> configuration.
>
> These tpr files give me different energy
Hi GROMACS users,
GROMACS 4.5.7 is officially released. It contains some bug fixes,
particularly for the md-vv integrator.
You can find the code, release notes, and installation instructions at the
links below.
ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.7.tar.gz
http://www.gromacs.org/About_G
On 4/19/13 2:46 AM, 라지브간디 wrote:
Dear Justin,
I understand all the visualization programs guess the chemical bonds..etc. When
i use ngmx i can able to see the bonds which i mentioned in topology but none
of the other program such as vmd, pymol, chimera fails to shows them. Is there
anyway
On Fri, Apr 19, 2013 at 3:30 AM, Fahimeh Baftizadeh <
fahimeh.baftiza...@googlemail.com> wrote:
> Hello,
>
> I have a 2 tpr files which are identical.
This is true only if gmxcheck agrees with you :-)
> Then I am doing a single step MD
> (I put n_step=0) simulation just to compute the total en
Dear gmx,
I am facing a problem during energy minimization. I got to know from the gmx
search that these error aries when the parameters are not assigned well.
My problem is when i run without using virtual site, its runs without any
problem but if use virtual site for the ligand it gives th
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