Have you installed the
CUDA Toolkit 4.0 ?
I have never tried, just guessed.
lina
On Mon, Apr 25, 2011 at 9:17 AM, Claus Valka wrote:
> Hello,
>
> I'm interested in knowing the level of development about gromacs supporting
> the opencl framework language.
>
> I hav
In latest version of gromacs (4.5.4 or earlier)
The amber force fields were provided.
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s/lib:${LD_LIBRARY_PATH}
# export LD_LIBRARY_PATH=/usr/local/lapack/lib:${LD_LIBRARY_PATH}
# export LD_LIBRARY_PATH=/usr/local/salapack/lib:${LD_LIBRARY_PATH}
You are welcome,
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Hi,
For group A, b, C.
It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
But I don't know how to get the number of residues of b forming both
with A and B at the same time. namely b-A&C, not with AC group.
Thanks,
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lina
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On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul wrote:
>
>
> lina wrote:
>>
>> Hi,
>>
>> For group A, b, C.
>>
>> It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
>>
>> But I don't know how to get the nu
",
b-C : "51 95 2 1",
84, 95?
Thanks,
On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul wrote:
>
>
> lina wrote:
>>
>> Hi,
>>
>> For group A, b, C.
>>
>> It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
>&
I got it. I should have outputted the -hbn file.
Thanks,
On Thu, May 12, 2011 at 1:09 PM, lina wrote:
> /* y-label: "Hydrogen Bond Index" */
>
> is it relevant to the total number of hydrogen bonds?
>
> such as
> /* XPM */
> /* x-label: "Time (ps)&qu
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2011/5/12 Justin A. Lemkul :
>
>
> lina wrote:
>>
>> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx
>>
>> LiGA & LİGB:
>
> This is not correct. You need to use | rather than &. Using logical and
> (&) means the index group will contain a
On May 29, 2011, at 20:45, rashi.pari...@gmail.com wrote:
> Hi all..
> I want to ask if it is possible to restart the md run if due to power problem
> final md run not completed means initiating md from where is stop due to any
> reason?
Suppose your .tpr is topol.tpr
mdrun -cpi state.cpt
Or
ing!
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>
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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
I
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 loadi
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)
usbfs
On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham 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, b
On Fri, Jan 13, 2012 at 7:04 PM, Jianguo Li 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
> To: Discussion list
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,
Bes
On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
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
amber03.ff/forcefield.itp
ambe
On Mon, Jan 23, 2012 at 9:56 PM, Víctor 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 traj1:
> for each fram
On Tue, Jan 24, 2012 at 12:08 AM, Justin A. Lemkul wrote:
>
>
> lina wrote:
>>
>> On Mon, Jan 23, 2012 at 10:01 AM, Gianluca Interlandi
>> wrote:
>>>
>>> Dear gromacs users list,
>>>
>>> I noticed that gromacs can perform simulation
On 24 Jan, 2012, at 1:53, Spring buds 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 laptop is a dual
On Tue, Jan 24, 2012 at 11:42 AM, Spring buds 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//groma
Hi,
are there some tips of quick adding missing atoms ( namely hydrogens,
non-titrable ones, or some ligands ones) ?
Thanks,
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On Sat, Jan 28, 2012 at 9:17 PM, parto haghighi
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 membrane but gromacs pus
On Mon, Jan 30, 2012 at 1:18 AM, murat özçelik 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 solve is 1211%.
>
On Mon, Jan 30, 2012 at 5:43 PM, Steven Neumann 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 mdnojump.xtc -
did you write this script yourself?
On Mon, Jan 30, 2012 at 6:56 PM, murat özçelik 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
>
On Mon, Jan 30, 2012 at 9:22 PM, Justin A. Lemkul 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 t
On Thu, Feb 2, 2012 at 12:36 PM, Alex Seling 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 the tab
On Fri, Feb 3, 2012 at 12:54 PM, Vishwambhar Bhandare
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 A 1 was n
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 mailto:mark.abra...@anu.edu.au>>
onv -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 mailto:lina.lastn...@gmail.com>>
On Thu, Feb 9, 2012 at 8:44 PM, 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 order to obtain a
On Thu, Feb 9, 2012 at 7:25 PM, Kiwoong Kim 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 software. excel.
On Thu, Feb 9, 2012 at 6:17 PM, aiswarya pawar 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 errors. The steps follow
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,
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On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann 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 for sharing,
Best r
On 1 Mar, 2012, at 1:01, Steven Neumann 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 (system).
> trjconv -
Hi,
is the old dssp not compatible with the gromacs 4.5.5 ?
I am confused,
Thanks,
Best regards,
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On Fri, Mar 2, 2012 at 3:55 PM, Mark Abraham 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,
>
>
> T
On Sat, Mar 10, 2012 at 7:14 PM, Atila Petrosian
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 reason of this case?
On Sat, Mar 10, 2012 at 9:17 PM, Atila Petrosian
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 termin
On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
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 1.8202 (nm)
t
On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
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
> --
> gmx-users mailing list gmx-
On Thu, Mar 22, 2012 at 11:54 AM, Spring buds 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 other. is it
> possib
On Wed, Mar 21, 2012 at 11:36 PM, Kukol, Andreas 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 logRemd_20ns.log -v -e
> ed
On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila 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
>
>
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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4PM +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,
>> --
>> gmx-users mailing list
On Thu, Apr 5, 2012 at 11:50 AM, Acoot Brett 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 md_0_1_noPBC.xtc -pbc mol -u
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 wrote:
>
>
> On 05/04/12, lina wrote:
>
> On Thu, Apr 5, 2012 at 4:42 PM, Peter C. Lai wrote:
>> trjcat -settime or trjconv -t0
>
> Thank you, a further question, a trjcat-ed xtc file, which timestamp like
>
>
On Thu, Apr 5, 2012 at 7:14 PM, Acoot Brett 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 acids?
In pdb2gmx -h
On Mon, Apr 16, 2012 at 11:01 PM, sai nitin 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
>
> But when
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.t
short time period. namely -e 200 to
see what's going on.
> Ο χρήστης lina 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 (3
the full 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 έγραψε:
>
> On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote:
>> Th
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
man/listinfo/gmx-users
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>
> Mark
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rce = 2.89751132744731e+04 on atom 8524
Norm of force = 2.18622026854678e+02
Thanks for any advice,
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On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul wrote:
>
>
> lina wrote:
>>
>> Hi,
>>
>> Form the begining to 5 steps, during EM, all exit in atom 8524,
>> how do I check it further? I mean, from which parts to examine?
>> I also switched to d
On Wed, Jul 27, 2011 at 9:06 PM, Justin A. Lemkul wrote:
>
>
> lina wrote:
>>
>> On Wed, Jul 27, 2011 at 7:29 PM, Justin A. Lemkul wrote:
>>>
>>> lina wrote:
>>>>
>>>> Hi,
>>>>
>>>> Form the begining to 5000
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I read 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 re
; shared object file: No such file or directory
>
>
>
> How to solve this problem?
>
>
>
> Best wishes,
>
> Afsaneh
>
>
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the ar
On Thu, Aug 11, 2011 at 10:41 PM, Mark Abraham wrote:
> On 12/08/2011 12:37 AM, lina wrote:
>>
>> Hi,
>>
>> after using genion -conc 0.1
>>
>> certain number of Na and Cl were added in solvent.
>>
>> but when I tried to calculate back, namely,
hing.
> There is just one problem that stays nonetheless; in how far does the
> bulk concentration you use as target correspond to the local
> concentration you might need to use? Solutes, membranes and voids may
> alter the local concentration significantly.
>
> By the way, Lina, i
-23=121/6.022/9.369=0.214 mol/L?
But before when I used -conc, the number I chose maybe 0.1 or 0.15
mol/L, but not 0.2mol/L.
Here if consider the water, certainly the water volumn will be greatly
smaller than the box volumn, so the concentration will reach very
high?
I might be wrong in som
On Fri, Aug 12, 2011 at 8:08 AM, Mark Abraham wrote:
> On 12/08/2011 2:22 AM, lina wrote:
>>
>> On Thu, Aug 11, 2011 at 11:35 PM, Tsjerk Wassenaar
>> wrote:
>>>
>>> Hi,
>>>
>>>>> I'd be amazed if the error was in the code an
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Best Regards,
lina
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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 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
se the
> www interface or send it to gmx-users-requ...@gromacs.org.
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lina
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Please search the arc
n. Total EnergyTemperature [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,
l
On Sat, Sep 10, 2011 at 5:05 PM, 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 is the
On Sat, Sep 10, 2011 at 10:00 PM, Moeed 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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Please search the ar
On Sat, Sep 10, 2011 at 8:45 PM, Justin A. Lemkul 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
, just running.
Thanks for providing any clue for me to examine.
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lina
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On Mon, Sep 12, 2011 at 8:33 PM, Justin A. Lemkul 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,
On Mon, Sep 12, 2011 at 8:35 PM, Mark Abraham wrote:
> 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 no
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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some reason there which I don't know.
Thanks,
On Sun, Sep 18, 2011 at 4:35 PM, lina 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).
>
l root
again.
So just try to figure out slowly.
Thanks for your answering,
>
> Jianguo
>
>
> --
> *From:* lina
> *To:* Discussion list for GROMACS users
> *Sent:* Sunday, 18 September 2011 5:13 PM
> *Subject:* [gmx-users] Re: about non-writ
B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB
mdrun_g -v -deffnm em
works well.
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lina
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st. Use the
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ailman/listinfo/gmx-users
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On Sep 25, 2011, at 0:33, raj 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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> gmx-users mailing listgmx-users@gromac
Could you write me which are the commands to execute up to MD run?
>
The links Justin provided are very useful. It's not a bad idea to do some
tutor to be familiar with those procedures.
>
> Bests
>
> 2011/9/22 lina
>
>> On Thu, Sep 22, 2011 at 11:34 AM, elisa carl
On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal wrote:
> 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 128 ion-pairs. H
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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