Hi all,
I need to do simulation which same as protein-ligand tutorial by Justin.
The different is i'm using my protein and the ligand was zinc.
I already follow everything in that tutorial and suddenly when i want
to heat my protein by using the nvt.mdp there was an error state like
below :
Fatal
Hi Justin,
Thank you so much. We were trying to use version 4.5.5 with OpenMM because
I was silly. I mistakenly thought 4.6.x was in beta, but apparently I did
not read the release page: 4.6.1 has been out for some time now.
Version 4.6.1 has made our GPU lives a lot easier. Thank you so, so
Dear Jianguo, XAvier, and Dallas:
Thank you for your great suggestions. I am making progress, but still have not
found an efficient way
to do this. I don;t have any particular questions in this post, but wanted to
provide an update and
also to see if anybody has any additional ideas based on wha
On 5/8/13 7:18 PM, zugunder wrote:
May I ask you to share the content of your m2p?
The size of the matrix elements is subjective; it depends on what dimensions of
the matrix you want. My usual settings are xbox = 0.05, ybox = 2.0, but that's
for my systems, which are relatively small alon
May I ask you to share the content of your m2p?
The problem here is that using defaults (no -di) I at least can see some eps
image via evince for example, but when I use m2p consisting of these 2
lines:
xbox = 0.2 ; x-size of a matrix element
ybox
It is a really bad idea to use standard tip3p with charmm36 lipids (see the
Piggot paper that you referenced and also Sapay, N. et al. 2010 J. Comp. Chem.
32, 1400-1410 + probably others).
dt 0.001 with nstlist 5 seems like overkill on the nstlist update frequency
(not a problem though).
Here'
On 5/8/13 6:59 PM, zugunder wrote:
But don't you know where I could find the default settings used in xpm to eps
conversion (without di flag)?
The default values simply indicate that each element occupies 1 pixel, such that
you have some matrix that is N residues by some tens of thousands (m
But don't you know where I could find the default settings used in xpm to eps
conversion (without di flag)?
I used the m2p from the example and tried to change some parameters to take
a look what happens, but I can't see any image at all now :-(
Thank you.
--
View this message in context:
http
On 5/8/13 6:24 PM, zugunder wrote:
OK, thank you, now it is clear.
So, that's what I've done so far:
1. Got a dsspold binary for Linux (unfortunately, 32bit only).
2. Renamed it into dssp, moved to /usr/local/bin and made it executable with
chmod a+x
3. Because of dsspold being 32bit (giving
OK, thank you, now it is clear.
So, that's what I've done so far:
1. Got a dsspold binary for Linux (unfortunately, 32bit only).
2. Renamed it into dssp, moved to /usr/local/bin and made it executable with
chmod a+x
3. Because of dsspold being 32bit (giving an error on a wrong ELF
descriptor) I i
On 5/8/13 5:33 PM, zugunder wrote:
Thank you Justin, but I am afraid I do not understand what you mean.
I am using gromacs 4.5.7 and there are no traces of -var option in its
manual (actually, for 4.5.6); moreover, if I try to specify -ver in the
command I get an error on an invalid command li
Thank you Justin, but I am afraid I do not understand what you mean.
I am using gromacs 4.5.7 and there are no traces of -var option in its
manual (actually, for 4.5.6); moreover, if I try to specify -ver in the
command I get an error on an invalid command line argument. So I suppose,
4.5 can't do
On 5/8/13 4:20 PM, zugunder wrote:
And it seems to me more strange as there is no option "-na" - neither in
dssp, nor in do_dssp.
Or do I missing something? Just in case, here is my command:
$ g_do_dssp -s md_input_extended_to50ns.tpr -f md_product.xtc
where:
.tpr - after I extended the pro
And it seems to me more strange as there is no option "-na" - neither in
dssp, nor in do_dssp.
Or do I missing something? Just in case, here is my command:
$ g_do_dssp -s md_input_extended_to50ns.tpr -f md_product.xtc
where:
.tpr - after I extended the product tun a couple of times
.xtc - uncha
Le 08/05/13 19:33, Christoph Junghans a écrit :
Date: Wed, 08 May 2013 16:34:46 +0200
From: Julian Garrec
Subject: Re: [gmx-users] Langevin thermostat implementation in GROMACS
vs AMBER
To: Discussion list for GROMACS users
Message-ID: <518a6286.8020...@epfl.ch>
Content-Type: text/plai
No, it is there:
$ cd /usr/local/bin
[user@localhost bin]$ ls
dssp vmd
And I had made it executable with chmod a+x
Thank you.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/A-problem-with-do-dssp-command-tp5008049p5008055.html
Sent from the GROMACS Users Forum mailing li
On 5/8/13 3:25 PM, zugunder wrote:
OK, thanks a lot, got it.
But suddenly I got an unexpected error executing do_dssp:
Program g_do_dssp, VERSION 4.5.7
Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/tools/do_dssp.c,
line: 572
Fatal error:
Failed to execute command: /usr/local/bin/
OK, thanks a lot, got it.
But suddenly I got an unexpected error executing do_dssp:
Program g_do_dssp, VERSION 4.5.7
Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/tools/do_dssp.c,
line: 572
Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddKypQH4 ddgk6w8G >
/dev/null
On 5/8/13 3:03 PM, zugunder wrote:
Sorry guys, just figured it out:
correct syntax is g_do_dssp :-)
Maybe, it would worth correcting the online manual for GROMACS (which is for
4.6.1 version now)? do_dssp and editconf are mentioned there without "g_"
prefix, unlike many other commands...
Pr
Sorry guys, just figured it out:
correct syntax is g_do_dssp :-)
Maybe, it would worth correcting the online manual for GROMACS (which is for
4.6.1 version now)? do_dssp and editconf are mentioned there without "g_"
prefix, unlike many other commands...
Thank you.
--
View this message in conte
On 5/8/13 2:55 PM, zugunder wrote:
Hi,
Hi, I have a rather odd problem running do_dssp:
$ do_dssp -h
bash: do_dssp: command not found
I am running GROMACS 4.5.7 under SL 6.3 and everything else seems to work
fine.
DSSP is also installed and should be OK:
$ dssp -h
DSSP 2.0.4 options:
-h
Hi,
Hi, I have a rather odd problem running do_dssp:
$ do_dssp -h
bash: do_dssp: command not found
I am running GROMACS 4.5.7 under SL 6.3 and everything else seems to work
fine.
DSSP is also installed and should be OK:
$ dssp -h
DSSP 2.0.4 options:
-h [ --help ] Display help message
> Date: Wed, 08 May 2013 16:34:46 +0200
> From: Julian Garrec
> Subject: Re: [gmx-users] Langevin thermostat implementation in GROMACS
> vs AMBER
> To: Discussion list for GROMACS users
> Message-ID: <518a6286.8020...@epfl.ch>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/8/13 12:44 PM, Gmx QA wrote:
Thanks Justin, those are good points.
A quick follow up, would you (or someone else) consider the APL-values I
have for my mixed bilayer system to be good, just ok-ish or plain wrong?
I have no basis for making such an assessment, but I know there is litera
Thanks Justin, those are good points.
A quick follow up, would you (or someone else) consider the APL-values I
have for my mixed bilayer system to be good, just ok-ish or plain wrong?
THANKS
2013/5/8 Justin Lemkul
>
>
> On 5/8/13 11:09 AM, Gmx QA wrote:
>
>> Hi gmx-users,
>>
>> I've been exp
On 5/8/13 11:09 AM, Gmx QA wrote:
Hi gmx-users,
I've been experimenting with simulations of mixed bilayers (512 lipids in
total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and
have a couple of questions. I know this has been discussed before, but I'd
appreciate some input
Hi,
I "fixed" an issue with the 1/visc output in 4.5.4, but incorretly.
I filed a bug report and a fix, you can easily correct your numbers:
http://redmine.gromacs.org/issues/1244
https://gerrit.gromacs.org/#/c/2370/
Thanks for reporting this.
Cheers,
Berk
> Date: Thu, 11 Apr 2013 16:55:37
Hi,
On Wed, May 8, 2013 at 4:44 PM, Albert wrote:
> I am trying to run g_select with command:
>
> g_select -f md.xtc -s md.pdb -os water.xvg -sf selection.dat
>
> in the selection.dat I defined the following:
>
> watero= name 0 and resname T3P;
> close = water0 and within 0.6 of resid 50;
> clos
Yes, all steps were completed successfully.
About your tips, OK sir.
I' m going to go through the minimization and NVT and NPT again. Lets get my
result, then will post the exact commands.
Thanks for your suggestions.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: S
Hi gmx-users,
I've been experimenting with simulations of mixed bilayers (512 lipids in
total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and
have a couple of questions. I know this has been discussed before, but I'd
appreciate some input nonetheless :-)
The relevant section
Hi everyone,
I want to calculate the LJ potential with different Cut-off for simulation
in a reduced unit (LJ unit).
For example, the cut-off for LJ potential of A-A, A-B, and B-B is 1.12246
(repulsive), 1.12246, and 2.5 （attractive, respectively;
However, it seems that the Cut-off only can
No suggestion ?? :)
In my post I forgot to say that my system contains explicit water.
I'm still very curious about the difference in implementation in AMBER
and GROMACS. And I still don't really understand the meanning of tau-t
in LD and how it is related to other (well defined) quantities s
Dear:
I am trying to run g_select with command:
g_select -f md.xtc -s md.pdb -os water.xvg -sf selection.dat
in the selection.dat I defined the following:
watero= name 0 and resname T3P;
close = water0 and within 0.6 of resid 50;
close;
my residue 50 is in the deep pocket of protein and the
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On 5/8/13 9:19 AM, Sainitin Donakonda wrote:
Hello,
I am trying to secondary structure analysis using DSSP in gromacs so i
followed this procedure
First I downloaded dssp
wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O
~/dssp
this gave dssp executable file in my home
/home/dssp seems like a strange path. Are you sure you set DSSP correctly?
Erik
On 8 May 2013, at 15:19, Sainitin Donakonda wrote:
> Hello,
>
> I am trying to secondary structure analysis using DSSP in gromacs so i
> followed this procedure
>
> First I downloaded dssp
>
> wget ftp://ftp.cmb
Hello,
I am trying to secondary structure analysis using DSSP in gromacs so i
followed this procedure
First I downloaded dssp
wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O
~/dssp
this gave dssp executable file in my home directory
I checked ./dssp ...it works
Then i s
On 5/8/13 2:35 AM, Shima Arasteh wrote:
OK.
1. Exact commands given in the preparation protocol (EM and equilibration)
EM:
# grompp -f minim.mdp -c input.gro -p topol.top -o minim.tpr
#mdrun -deffnm minim
NVT:
#grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
#mdrun -deffnm n
On 5/8/13 3:07 AM, Subramaniam Boopathi wrote:
Dear Sir,
I am succesfully run molecules upto energy minimization, in case of
position restrain md step , i have following, could you help to overcome
the A charge group moved too far between two domain decomposition steps.
Step 1, time 0
On 5/8/13 8:16 AM, Arunima Shilpi wrote:
Hello Sir
While running command for perl distances.pl.. system gets hanged...while
processing particular group file...
I will be thankful to you if you can guide me in debugging the error
If you created groups.txt in accordance with what the tutori
Hello Sir
While running command for perl distances.pl.. system gets hanged...while
processing particular group file...
I will be thankful to you if you can guide me in debugging the error
--
Thanking You with Regards.
Arunima Shilpi
Ph. D Research Scholar(Cancer & Epigenetics)
Department of
Sir
Yes, trjconv works without tpr. Thanks for that.
I want to see the distribution of anion around cation. Is it not possible
to see an averaged spatial distribution of all anions around all cations?
Do I need to make a selection of a single cation molecule?
I did the selection of a single cati
Message: 5
Date: Wed, 8 May 2013 08:25:33 +0200
From: Tsjerk Wassenaar
Subject: Re: [gmx-users] PCA_RMS fluctuation per residue?
To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain; charset=UTF-8
Thank you for the reply Tsjerk.
Could you tell me how i can visu
Dear Sir,
I am succesfully run molecules upto energy minimization, in case of
position restrain md step , i have following, could you help to overcome
the A charge group moved too far between two domain decomposition steps.
Step 1, time 0.002 (ps) LINCS WARNING
relative constraint deviati
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