On Monday 01,October,2012 01:44 PM, 仝督读 wrote:
Hi everyone,
I am doing a DNA simulation in a long simulation box (the lengthen of z is
much larger than x and y). So I want to constrain the DNA molecule lying
along the z axis. But I don't know how to realize this in GROMACS.
Actually I
On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote:
Dear all,
I am attempting to calculate the viscosity of a liquid binary system of
500 molecules (3050 atoms), via g_tcaf command.
The system is equilibrated. The list of command I use is:
/g_covar -f traj.trr -s topol.tpr -n
what's going on.
Ο χρήστης lina lina.lastn...@gmail.com έγραψε:
On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote:
Dear all,
I am attempting to calculate the viscosity of a liquid binary system of
500 molecules (3050 atoms), via g_tcaf command.
The system is equilibrated
precision means double precision? I see you use single
precision.
I have never tried this one, perhaps someone else may give you some
suggestions.
Best regards,
Ο χρήστης lina lina.lastn...@gmail.com έγραψε:
On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote:
The -dt flag
On Mon, Apr 16, 2012 at 11:01 PM, sai nitin sainit...@gmail.com wrote:
Hi all,
I have done complex (protein + ligand) complex from autodock software using
this complex im trying to follow
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html
tutorial
Hi,
A quick question, how can I change the .xtc file which beginning at 0,
end at 1 ns to beginning at 5ns and end at 6ns.
Thanks for any suggestions,
Best regards,
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+0800, lina wrote:
Hi,
A quick question, how can I change the .xtc file which beginning at 0,
end at 1 ns to beginning at 5ns and end at 6ns.
Thanks for any suggestions,
Best regards,
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On Thu, Apr 5, 2012 at 11:50 AM, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
In the on-line tutorial on lysozyme
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html),
there is a command
trjconv -s md_0_1.tpr -f md_0_1.xtc -o
Hi,
suppose I lost original .tpr file,
can I get tpr file from the .xtc file ? I mean from the .xtc or trr
file, not by re-run grompp to generate tpr file.
Thanks ahead,
Best regards,
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Please
On Thu, Apr 5, 2012 at 6:07 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 05/04/12, lina lina.lastn...@gmail.com wrote:
On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai p...@uab.edu wrote:
trjcat -settime or trjconv -t0
Thank you, a further question, a trjcat-ed xtc file, which timestamp
On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett acootbr...@yahoo.com wrote:
Dear All,
For the different protonation state of HIS, what are there 3-letter code for
GROMACS? And how about -SH and -S-S- codon? Or do you have a web link for me
to read? Do we still have any other confusing amino
On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila oina...@gmail.com wrote:
We are trying to do simulation of lysozyme in water.
step with problem : energy minimization.
command given: [root@localhost gromacs-4.0.5]# grompp -f minim.mdp -c
1AKI_solv_ions.gro -p topol.top -o em.tpr
On Wed, Mar 21, 2012 at 11:36 PM, Kukol, Andreas a.ku...@herts.ac.uk wrote:
Hello,
Upon continuing a replica exchange MD simulation using the command
mdrun -cpi state.cpt -append -s tpr_remd20ns_.tpr -multi 48 -replex 1
-cpt 60 -x xtcRemd_20ns.xtc -c afterRemd_20ns.gro -g
On Thu, Mar 22, 2012 at 11:54 AM, Spring buds winterho...@gmail.com wrote:
Hi
A protein sits on the top of another protein (not docking). I then used
pdb2gmx command to generate the topology. Surprisingly, i got five files,
as given below: I think the two proteins are not connected each
On Sat, Mar 10, 2012 at 7:14 PM, Atila Petrosian
atila.petros...@gmail.com wrote:
Dear all
When I use g_dist -f *.trr -s *.tpr -n *.ndx -o dist.xvg -dist 0.5,
program was done without error, but it don't create output file
(dist.xvg) in the directory in which g_dist tool was run.
What is
On Sat, Mar 10, 2012 at 9:17 PM, Atila Petrosian
atila.petros...@gmail.com wrote:
Dear Lina
Thanks for your reply.
Without the -dist 0.5, I get the -o dist.xvg output, but I need list
of the all atoms in group 2 closer than dist to the center of mass of
group 1.
It print on the terminal
On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
atila.petros...@gmail.com wrote:
Dear Lina
There is not any things related to list of atoms on the terminal.
t: 100 83 ILE 845 CG1 1.60274 (nm)
t: 100 83 ILE 846 CG2 1.63838 (nm)
t: 100 83 ILE 847 CD 1.59769 (nm)
t: 100 83 ILE 848 C
On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
atila.petros...@gmail.com wrote:
Dear Lina
There is not any things related to list of atoms on the terminal.
Might your distance -dist so large.
try a smaller one and see.
Best regards
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On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 2/03/2012 6:52 PM, lina wrote:
Hi,
is the old dssp not compatible with the gromacs 4.5.5 ?
I am confused,
Thanks,
Best regards,
The new DSSP is not compatible with any GROMACS
Ha ... the dssp complain
Hi,
is the old dssp not compatible with the gromacs 4.5.5 ?
I am confused,
Thanks,
Best regards,
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On 1 Mar, 2012, at 1:01, Steven Neumann s.neuman...@gmail.com wrote:
Dear Gmx Users,
I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. The
problem I face is PBC which I cannot get rid of. I used:
1. First make your molecules whole if you want them whole
On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann s.neuman...@gmail.com wrote:
Thank you Vedat!
Why do you use -DFLEXIBLE in md and in em?
Why dont you use constraint algorithm (LINCS) in your simulation?
Otherwise, the system is easily explode with lots of LINCS warning.
Also thanks Vedat
Hi,
I don't know how to extract the position like the x y z with t or r with t.
Thanks for any suggestions,
Best regards,
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On Thu, Feb 9, 2012 at 8:44 PM, rar...@ens-cachan.fr wrote:
Dear Gromacs users,
I have been trying to simulate a Protein-DNA complex using gromacs, but each
time I have been facing problems. I would like to point out that both the
Protein and DNA have been modeled and after that docked in
On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim ilmare...@gmail.com wrote:
Hi,
I have a simulation result from 0 to 50ns after equilibration run.
I want to divide this data set equally into 10blocks (10ns each) and get
block averaged MSD curve (average of 10 blocks).
I would try some external
On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar aiswarya.pa...@gmail.com wrote:
Dear Gromacs users,
I have a MD simulated protein and i take frame from this and remove water
and add water implicit in the interface and want to do energy minimization
but while doing the minimization i get
On Friday 03,February,2012 09:56 PM, francesca vitalini wrote:
Yes but those tips are not for bash scripts... :(
You'd better post what you have done so far about this script,
probably someone can help you improve or refine it.
2012/2/3 Mark Abraham mark.abra...@anu.edu.au
-f ../xtc/300-${i}.xtc -s ../../dynamin_dimer_phfitted.pdb -o
../cg_gro/300-${i}.gro -pbc index.txt
done
very stupidly I just need to type 0 all the time in the interactive
window that trjconv opens.
Any help?
Thanks
2012/2/3 lina lina.lastn...@gmail.com mailto:lina.lastn...@gmail.com
On Fri, Feb 3, 2012 at 12:54 PM, Vishwambhar Bhandare
vishway...@gmail.com wrote:
Hello,
I am getting error given below,
wht we can do for this?
Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2gmx.c, line:
655
Fatal error:
Atom 'H5T in residue
On Thu, Feb 2, 2012 at 12:36 PM, Alex Seling selin...@msu.edu wrote:
Hello,
I've recently been having trouble with my simulations blowing up.
Specifically,
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase
On Mon, Jan 30, 2012 at 5:43 PM, Steven Neumann s.neuman...@gmail.com wrote:
Dear Gmx Users,
I run the simulation of protein with 10 ligands (200 ns). In total I should
have total of 4000 frames as I set up:
nsteps = 1
dt = 0.002
nstxout = 25000
I used trjconv -f md.trr -o
did you write this script yourself?
On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik mehmet63...@hotmail.com wrote:
hi! lina my script this please tell me where is wrong...thanks
#!/bin/bash
# Set some environment variables
FREE_ENERGY=/home/mkiytak/Free_Energy1
echo Free energy
On Mon, Jan 30, 2012 at 9:22 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
did you write this script yourself?
This script appears to be based on one that I provided in the free energy
tutorial, but there are some differences (including one of the mistakes you
Your tutorials
On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik mehmet63...@hotmail.com wrote:
hi again capacity of my harddisk 600 GB ı try again ..the program
gave me below message...
Reading file md0.tpr, VERSION 4.5.4 (single precision)
Starting 8 threads
NOTE: The load imbalance in PME FFT and
On Sat, Jan 28, 2012 at 9:17 PM, parto haghighi
parto.haghi...@gmail.com wrote:
Dear gmx-users
I am working on lipid membrane+drug system.I should do umbrella
sampling in this procedure:
1.cat drug and lipid
2.energy minimization
3.run npt
4.run md_pull
I want to pull drug into the
Hi,
are there some tips of quick adding missing atoms ( namely hydrogens,
non-titrable ones, or some ligands ones) ?
Thanks,
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Hi,
which gromacs force field shares the high quasi-compatibility with
the amber force field.
I checked the heme only exists in gromos and the charmn
while gbsa only shows in amber and oplsaa,
truth is that I don't know how to get the gbsa parameter for heme,
Thanks for any suggestions,
Best
On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
gianl...@u.washington.edu wrote:
Dear gromacs users list,
I noticed that gromacs can perform simulations with an implicit solvent
model using a GBSA method. Is it compatible with the CHARMM22 force field?
look for gbsa.itp showed
On Mon, Jan 23, 2012 at 9:56 PM, Víctor victor.gil.sepulv...@gmail.com wrote:
Dear all,
I've been trying to do a rmsd matrix of two different trajectories by using
g_rms (with -f traj1 and -f2 traj2). I'm wondering if the algorithm g_rms
uses does something like this:
for each frame f1 in
On Tue, Jan 24, 2012 at 12:08 AM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
gianl...@u.washington.edu wrote:
Dear gromacs users list,
I noticed that gromacs can perform simulations with an implicit solvent
model using
On 24 Jan, 2012, at 1:53, Spring buds winterho...@gmail.com wrote:
Dear Gromacs users,
Greetings!!!
I am very new users and I am trying to install grmacs 4.5.5 or 3.3.3 for past
four days. But still I am not able to. So I would like to ask some questions
which are below.
1.My
On Tue, Jan 24, 2012 at 11:42 AM, Spring buds winterho...@gmail.com wrote:
Hi lina,
Thanks for reply. could you tell me how to remove completly the gromacs
installation?
Which commands have you issued?
try make uninstall in the directory where you used make install
before. like Path_to
Hi,
Failed to lock: md.log. No locks available.
still the same problem I met before,
once I terminated, resume not work, there is a md.log file.
$ mount
/dev/sda1 on / type ext3 (rw)
none on /proc type proc (rw)
none on /sys type sysfs (rw)
none on /dev/pts type devpts (rw,gid=5,mode=620)
On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 13/01/2012 7:08 PM, lina wrote:
Hi,
Failed to lock: md.log. No locks available.
mdrun locks various files at various points. If it can't then GROMACS won't
continue, but the problem lies with the file system
On Fri, Jan 13, 2012 at 7:04 PM, Jianguo Li ljg...@yahoo.com.sg wrote:
There is a solution in this mailing list sometime before:
mv md.log to some other folder and copy it back.
Jianguo
I tried, not work.
Thanks,
From: lina lina.lastn...@gmail.com
On Thursday 12,January,2012 09:36 AM, yp sun wrote:
Dear Sir,
I want to unscribe there emails, thank.
http://lists.gromacs.org/mailman/listinfo/gmx-users
at the bottom, fill in your email address and click Unsubscribe.
Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology Immunology
On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:
Hi,
I am trying to run a REMD of a peptide. But while executing the
following command after nvt and npt equilibration , I am getting the
following error:-
mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
mdrun_mpi: error while
Hi,
I met a very untamed simulation system.
when I tried to run a short MD, it's collapsed with LINCS Warnings, It's
under 317K
so I used energy minimizations after NVT, and run another NVT_2 again.
(In vacuum, no NPT being applied here).
after that NVT_2, mainly increased the steps, run
] /lib64/libpthread.so.0 [0x399440e7c0]
[hostname-c06:07555] [ 1]
/home/lina/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x1cc1)
[0x2b7249a92d61]
[hostname-c06:07555] [ 2]
/home/lina/lib/libgmx_mpi.so.6(do_nonbonded+0xe8) [0x2b72499d99d8]
[hostname-c06:07555] [ 3]
/home/lina/lib/libmd_mpi.so
On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
gianluca.sant...@ibs.fr wrote:
Hi gmx_users,
is there any tutorial for implicit solvent simulation available?
Hi,
I tried it few days ago.
1] pdb2gmx the water model choose none.
2] after editconf, go to energy minimization directly
* It's
On Thu, Dec 8, 2011 at 11:26 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
gianluca.sant...@ibs.fr wrote:
Hi gmx_users,
is there any tutorial for implicit solvent simulation available?
Hi,
I tried it few days ago.
1
On Sun, Dec 4, 2011 at 3:04 PM, Alex Jemulin alexbioi...@yahoo.com wrote:
Dear all,
I'd like to convert an xpm file to delimited CSV , because I need to import
values in excel.
Any suggestion?
Try to write some scripts to do this.
Thanks
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The Y-size of the box (1.999239) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (2) times the
smallest allowed cell size (1.00)
I don't understand the fatal error message it has been given during a
simple run,
I tested with large box already, during
https://docs.google.com/open?id=0B93SVRfpVVg3NTVjMmY0NzEtM2UzOC00MDEwLWI2OWMtZjEyZDQ5NzM1YWVh
I uploaded the files here.
is it the box still small?
Thanks,
On Thu, Dec 1, 2011 at 12:25 AM, lina lina.lastn...@gmail.com wrote:
The Y-size of the box (1.999239) times the triclinic skew factor
On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 1/12/2011 3:25 AM, lina wrote:
The Y-size of the box (1.999239) times the triclinic skew factor
(1.00) is smaller than the number of DD cells (2) times the
smallest allowed cell size (1.00)
I don't
/git-build/gromacs/src/gromacs/mdlib/ns.c, line: 2544
Fatal error:
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the
cut-off.
On Thu, Dec 1, 2011 at 11:38 AM, lina lina.lastn...@gmail.com wrote:
On Thu, Dec 1, 2011
On Sat, Nov 26, 2011 at 11:17 PM, chris.ne...@utoronto.ca wrote:
When people do this for lipid bilayers, they compute depth-dependent
diffusion profiles (often diffusion is computed separately for lateral
diffusion and diffusion along the bilayer normal). Sounds like you might do
something
On Thu, Nov 24, 2011 at 5:16 PM, cuong nguyen nvcuon...@gmail.com wrote:
Dear,
I create a box of water with 10 MIBC molecules on two opposite surfaces.
then I used the command grompp -f input_min.mdp -o min.tpr -c box1.g96 to
creat .tpr file before using the command genion -s min.tpr -o
need more information, please feel free to let me know.
Best regards,
As you workaround you should be able to run with mdrun -noappend.
Roland
On Sun, Nov 13, 2011 at 10:43 AM, lina lina.lastn...@gmail.com wrote:
Hi,
This is the first time I met:
Fatal error:
Failed to lock: md.log
On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG yujan2...@gmail.com wrote:
Hi there
I am trying to build up a topology file for a tetra nitrogen molecule using
Gromos UA and OPLS UA force field. Following are the molecules.
1. for C
|
Hi,
This is the first time I met:
Fatal error:
Failed to lock: md.log. No locks available
the disk is not saturated,
md.log is normal,
The job was stopped months ago, and now I planned to resume it with
all the necessary files kept intact.
Thanks for pointing out which parts I should
are you
using?
As you workaround you should be able to run with mdrun -noappend.
Thanks,
There is no problem running a mdrun without appending.
Best regards,
Roland
On Sun, Nov 13, 2011 at 10:43 AM, lina lina.lastn...@gmail.com wrote:
Hi,
This is the first time I met:
Fatal error:
Failed
On Tue, Nov 1, 2011 at 3:33 PM, Efrat Exlrod efrat.exl...@biu.ac.il wrote:
Hi There!
Is it possible to run mdrun from a shared directory and set the working
directory to a local directory on the computer on which it runs, in order to
decrease NFS load?
Yes. I attached a generic script, you
On Sat, Oct 29, 2011 at 12:51 AM, Victor nicegrom...@live.cl wrote:
Hello gmx-users
I have compiled gromacs on Debian/Linux wiht the option --with-x but the
ngmx binary has not been generated. I don´t have gnome or kde installed, but
I have installed xserver-xorg and I can export VMD with
On Mon, Oct 31, 2011 at 9:28 AM, Sanku M msank...@yahoo.com wrote:
Hi,
I just compiled gromacs 4.5.4 in a cluster. But, I find that if I try to
make use of threading introduced in gromacs 4.5.x series, it does not work.
After issuing command like mdrun -v -s , I expected that for my 8-core
On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Lina,
Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump
Hope it helps,
Hi,
Thanks.
I tried trjconv_g -fit translation -pbc nojump, ideally it should work.
but still not,
after I
On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Lina,
My previous reply was from before I looked at the graph. Have you
considered that the molecule might be taking a stroll and turn back,
Ha ... stroll?!
or goes to another side of the protein? Have you looked
Hi,
I have a problem using
trjconv_g -pbc nojump
or
trjconv_g -pbc nojump -center
I even tried the -pbc whole.
The system is protein with a small molecular, for the first time
period, when I checked on pymol.
they are together, but later they apart, after show cell, protein
inside the cell,
On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
j.marzine...@imperial.ac.uk wrote:
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of lina [lina.lastn...@gmail.com]
Sent: Thursday, October 27, 2011 10:47 AM
To: Discussion
On Fri, Oct 28, 2011 at 11:47 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 28/10/2011 2:39 PM, lina wrote:
On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
j.marzine...@imperial.ac.uk wrote:
From: gmx-users-boun...@gromacs.org [gmx-users-boun
On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Lina,
Make sure to use a reference in which the molecules are together (clustered)
the way you want them.
I used the initial mdrun .tpr. After checking the generated pdb (total
51 frames), the first 28/29 frames
On Sat, Oct 15, 2011 at 2:11 PM, Xiaoxiao He xxia...@ust.hk wrote:
Dear all,
I'm doing an slow-growth alchemical free energy perturbation calculation
of the formation of a disulfide bridge between two Cysteines with Gromacs.
I've had tried different ways to combine the topology of both state A
On Sat, Oct 15, 2011 at 2:58 AM, James Starlight jmsstarli...@gmail.com wrote:
Dear Gromacs users!
I have couple of questions about some Gromacs features.
1- I'm looking for tutorial where I could find clear example of force fied
based Normal Mode Analysis via Gromacs
E.g on first step I
On Thu, Oct 13, 2011 at 5:16 PM, Ahmad Randy run_...@yahoo.com wrote:
Hi All,
I understand that there were already some discussions about new DSSP exec
with do_dssp in gromacs-4.5.4. I just want to make clear, is it true that
this two DSSP and do_dssp do not compatible each other?
I was
On Wed, Oct 12, 2011 at 1:20 AM, Poojari, Chetan c.pooj...@fz-juelich.dewrote:
Hi,
I have protein completely inserted into lipid membrane and would like to
study order parameter around the protein as well as away from the protein.
For this I would like to slice my membrane into parts.
I
On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote:
Hello,
I have a system with 128 emi (cations) and 128 Cl (anions). I run the
simulation for 20 ns.
I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.
trjconv use -dt 5000
I don't want to save snap shot for
Hi,
How do I use the history input in the make_ndx prompt,
such as before I input
name 32 A2
name 33 A3
up arrow showed me: ^[[A
Alt+up arrow showed me: ^[[1;3A
Just curious,
Thanks,
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On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA ithayar...@gmail.com wrote:
only 59 particle variation found out of 230 ligand coordinates.
On 8 October 2011 12:22, ITHAYARAJA ithayar...@gmail.com wrote:
Dear Sir,
I am actually simulating my protein with its ligand so I incorporated all
On Sep 25, 2011, at 0:33, raj vvindv.vvi...@gmail.com wrote:
Hello,
I would like to calculate the concentration distribution of atoms along the x
and y axis from the trajectory. Can anybody suggest me a tool to calculate
this?
g_rdf ?!
regards,
Raj
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Best Regards,
lina
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works well.
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lina
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to each nodes, all is fully running.
The storage is NFS, I/O flow can't be choked for hours.
Really headache, sometimes it works.
I have had no clue about it.
Thanks for any suggestions,
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lina
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be some reason there which I don't know.
Thanks,
On Sun, Sep 18, 2011 at 4:35 PM, lina lina.lastn...@gmail.com wrote:
Hi,
Very sporadically and also with high frequent,
The job I submitted only running without writing (this job is not
un-started one, mainly one I stopped and rerun).
Before
just try to figure out slowly.
Thanks for your answering,
Jianguo
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*From:* lina lina.lastn...@gmail.com
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Sunday, 18 September 2011 5:13 PM
*Subject:* [gmx-users] Re: about non-writing issue
, just running.
Thanks for providing any clue for me to examine.
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lina
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Please
On Mon, Sep 12, 2011 at 8:33 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
Hi,
I am confused, why the job is running,
but they did not write the .edr, .log .xtc ... files.
Everything showed so normal, just not writing,
when I used thread, all is fine, the writing is normal
On Mon, Sep 12, 2011 at 8:35 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 12/09/2011 10:23 PM, lina wrote:
Hi,
I am confused, why the job is running,
but they did not write the .edr, .log .xtc ... files.
Everything showed so normal, just not writing,
when I used thread, all
Temperature [lina@hostname
You may notice that the [lina@hostname] did not start in a new line.
there is md_step31441735.cpt
and md_prev.cpt
what is the final step stored in the md_prev.cpt? How do I check ?
are there some chance to resume?
Thanks ahead,
Best regards,
lina
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On Sat, Sep 10, 2011 at 5:05 PM, lina lina.lastn...@gmail.com wrote:
Hi,
My job terminated due to the storage out of the quote given by
administrator,
here the md.log is unusual, so when I resume the job, the results won't
append on it. but still running...
Here is the tail of md.log
On Sat, Sep 10, 2011 at 10:00 PM, Moeed lecie...@googlemail.com wrote:
Thank you for your input. I am going to run for another 15 ns to see if the
little jumps vanish.
Best,
g_rdf -bin
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On Sat, Sep 10, 2011 at 8:45 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
Hi,
My job terminated due to the storage out of the quote given by
administrator,
here the md.log is unusual, so when I resume the job, the results won't
append on it. but still running...
Here
Hi,
are there someone love to share one md.mdp file for GPU version?
Thanks ahead,
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lina
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On Fri, Sep 9, 2011 at 8:48 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
Hi,
are there someone love to share one md.mdp file for GPU version?
All the details are here:
http://www.gromacs.org/**Downloads/Installation_**
Instructions/GPUs?highlight=**gpuhttp
? Read http://www.gromacs.org/Support/Mailing_Lists
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lina
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lina
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lina
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the manual, ...the specified concentration as computed from
the volume of the cell...
the cell? Has anyone tried to calculate the concentration back?
( I guess might the way I calculate was wrong? the Avogadro's Constant
= 6.0221415 × 10^23 mol-1)
Thanks with best regards,
lina
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