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
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
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
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
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 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 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
>
>
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 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
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
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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Please search the archive a
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
>
>
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 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 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 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 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 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 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
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 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 -
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
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 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
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 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
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 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>>
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 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 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
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 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 -
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 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
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 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
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 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 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 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
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 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
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
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 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
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
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 11:26 PM, Justin A. Lemkul wrote:
>
>
> lina wrote:
>>
>> On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
>> wrote:
>>>
>>> Hi gmx_users,
>>> is there any tutorial for implicit solvent simulation available?
>>
&
On Thu, Dec 8, 2011 at 9:50 PM, Gianluca Santoni
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 important to relax the sy
On Sun, Dec 4, 2011 at 3:04 PM, Alex Jemulin 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
>
> --
> gmx-users mailing list gmx-users@gromacs.org
> http:
/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 wrote:
> On Thu, Dec 1, 2011 at 7:45 AM, Mark Abra
On Thu, Dec 1, 2011 at 7:45 AM, Mark Abraham 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)
&
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 wrote:
> The Y-size of the box (1.999239) times the triclinic skew factor
> (1.00) is s
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 editconf
On Sat, Nov 26, 2011 at 11:17 PM, 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 similar. I doubt that
On Thu, Nov 24, 2011 at 5:16 PM, cuong nguyen 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 add.gro
> -nname Cl
f you 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 wrote:
>>
>> Hi,
>>
>> This is the first time I met:
>
MACS 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 wrote:
>>
>> Hi,
>>
>> This
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 examine,
On Sun, Nov 13, 2011 at 10:26 AM, XUEMING TANG 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
> |
> A. C-C-C
On Tue, Nov 1, 2011 at 3:33 PM, Efrat Exlrod 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 can modify from
On Mon, Oct 31, 2011 at 9:28 AM, Sanku M 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
> processor whic
On Sat, Oct 29, 2011 at 12:51 AM, Victor 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 ssh.
> Do I need
On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar 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 yo
On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar 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,
af
On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar 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 fra
On Fri, Oct 28, 2011 at 11:47 AM, Mark Abraham wrote:
> On 28/10/2011 2:39 PM, lina wrote:
>>
>> On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
>> wrote:
>>>
>>>
>>> From: gmx-users-boun...@gromacs.org
On Thu, Oct 27, 2011 at 6:11 PM, Marzinek, Jan
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: Discussio
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, wh
On Sat, Oct 15, 2011 at 2:11 PM, Xiaoxiao He 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 and
> st
On Sat, Oct 15, 2011 at 2:58 AM, James Starlight 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 would like to
On Thu, Oct 13, 2011 at 5:16 PM, Ahmad Randy 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 running in Ub
On Wed, Oct 12, 2011 at 1:20 AM, Poojari, Chetan wrote:
> 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 tried the followi
On Sat, Oct 8, 2011 at 3:10 PM, ITHAYARAJA wrote:
> only 59 particle variation found out of 230 ligand coordinates.
>
> On 8 October 2011 12:22, ITHAYARAJA wrote:
>
>> Dear Sir,
>>
>>
>> I am actually simulating my protein with its ligand so I incorporated all
>> ligand (3) coordinates to my pro
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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Pl
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
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 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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lina
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B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB
mdrun_g -v -deffnm em
works well.
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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
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).
>
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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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
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,
, just running.
Thanks for providing any clue for me to examine.
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Please
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
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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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
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
se the
> www interface or send it to gmx-users-requ...@gromacs.org.
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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
Hi,
are there someone love to share one md.mdp file for GPU version?
Thanks ahead,
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gromacs.org/mailman/listinfo/gmx-users
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