Dear GMX users,
I ran across a nice web page, I believe from a brazilian group, for generating membranes of any compnents (pdb). This was months ago, and after a few days of trying, I cannot find the page again. It was capable of makeing bilayers, as well as other shapes, including small
Thank you Justin.
With regards,
Indu
On Tue, Aug 12, 2014 at 5:08 PM, Justin Lemkul jalem...@vt.edu wrote:
On 8/12/14, 4:58 AM, Indu Kumari wrote:
Grompp terminated and shows following warning and notes:
NOTE 1 [file topol.top, line 57]:
System has non-zero total charge: -0.675997
Hello:
I am trying to run gromacs in a script with following command line:
make_ndx -f input.gro EOF
1|13
q
EOF
I am just wondering how can we record the log file for such kind of command?
thank you very much.
Albert
--
Gromacs Users mailing list
* Please search the archive at
text/html; charset=UTF-8: Unrecognized
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
Hi Kester:
thx a lot
It works fine ;-)
best
ALbert
On 08/13/2014 09:18 AM, Kester Wong wrote:
Hi Albert,
Maybe you can use the command as follows:
make_ndx -f input.gro output.log
It might work
--
Gromacs Users mailing list
* Please search the archive at
Hi everyone,
I would like to monitor water dynamics in the protein's hydration layer eg.
calculation of mean square displacement, order parameter etc. In this
regard I have couple of questions:
I was going through the user list regarding calculation of mean square
displacement. I believe while
On Wed, Aug 13, 2014 at 1:55 PM, Pappu Kumar papu...@yahoo.com wrote:
Thanks for your info. I am planning to buy one upcoming Haswell E-5820K to
use with 2x GTX 780Ti if feasible. So there will be six threads/GPU. I am
wondering if it will be good enough or I should go for 2x GTX 780.
Did you
Dear Gromacs users,
I am analyzing the RMSD evolution of a trajectory with g_rms and
clustering it with g_cluster (GROMOS, cutoff 0.1). I am noticing
something quite odd in the RMSD distribution. I link here the RMSD
evolution over time , the cluster ID over time, and the RMSD
distribution
Hi Massimo,
You have two clusters, both with low within-cluster RMSD. This shows up as
the first peak in the RMSD distribution. The second peak is the
between-clusters RMSD.
Cheers,
Tsjerk
On Wed, Aug 13, 2014 at 3:14 PM, ms deviceran...@gmail.com wrote:
Dear Gromacs users,
I am
Hi Tsjerk,
On 8/13/14 3:19 PM, Tsjerk Wassenaar wrote:
You have two clusters, both with low within-cluster RMSD. This shows up as
the first peak in the RMSD distribution. The second peak is the
between-clusters RMSD.
I am sorry, but I don't understand anything here - what does
within-cluster
H Massimo,
The RMSD over time is the RMSD against a single reference structure. For
clustering you use the RMSD matrix, which has all pairwise RMSDs. The
distribution you show is the distribution of RMSD values in that matrix.
Cheers,
Tsjerk
On Wed, Aug 13, 2014 at 3:44 PM, ms
On 8/13/14 4:01 PM, Tsjerk Wassenaar wrote:
H Massimo,
The RMSD over time is the RMSD against a single reference structure. For
clustering you use the RMSD matrix, which has all pairwise RMSDs. The
distribution you show is the distribution of RMSD values in that matrix.
Aha! This makes much
On 8/13/14, 10:11 AM, ms wrote:
On 8/13/14 4:01 PM, Tsjerk Wassenaar wrote:
H Massimo,
The RMSD over time is the RMSD against a single reference structure. For
clustering you use the RMSD matrix, which has all pairwise RMSDs. The
distribution you show is the distribution of RMSD values in
On 8/13/14, 9:05 AM, Batdorj Batsaikhan wrote:
Dear gmx users,
I want to calculate free energy calculations for protein and water system.
There are many free energy calculation tutorials for small molecule and water
system. I want to make free energy calculations for a protein and water
On 8/13/14, 5:40 AM, neha bharti wrote:
Hello Justin
Thank you very much for your help.
You have asked me that Are the coordinates of lig.pdb identical to those
of lig_princ_rotate.pdb?
The coordinates are not exactly the same. There is some variations. I have
also check by some
On 8/12/14, 10:45 PM, Alex s wrote:
http://www.mediafire.com/view/63k3pi3k3hahnu3/snapshots(2).docxhttp://www.mediafire.com/view/02dk2kwj6tec939/mdp.txt
hope this helps
Note the massive change in your box along z. Something has gone terribly wrong
in the simulation. Is your unit cell
On 8/13/14 4:17 PM, Justin Lemkul wrote:
Aha! This makes much more sense then, thanks!
Is there a Gromacs command to get the histogram of RMSD against a single
reference structure, then?
You can construct histograms of any time series with g_analyze -dist.
OK, I forgot that. Thanks a lot,
I should've mentioned that the those snapshots are of different system set ups.
The first snapshot is for a system I set up by doubling the size of lipid box
and placing the polymer just above the membrane. The second snaphshot is for a
another system where I left the lipid box size as it was
On 8/13/14, 10:45 AM, Alex s wrote:
I should've mentioned that the those snapshots are of different system set
ups. The first snapshot is for a system I set up by doubling the size of
lipid box and placing the polymer just above the membrane. The second
A little context next time, please.
On 8/13/14, 11:19 AM, Swapnil Kate wrote:
hello,
I am trying to generate free energy of solvation using g_bar gromacs tool,
i have carried out all steps given in manual for solvation energy, but when i
am trying to use g_bar command it shows 'nothing to calculate'.
what can be the possible
I obtained all of my forcefield, coordinate and topology files from the MARTINI
website.
Date: Wed, 13 Aug 2014 11:29:52 -0400
From: jalem...@vt.edu
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Polymer not diffusing into membrane
On 8/13/14, 10:45 AM, Alex s wrote:
I should've
On 8/13/14, 12:22 PM, Wainwright, Josh wrote:
The lipid I'd like to use is called DPhPG, or officially
2,3-di-O-phytanyl-sn-glycero-1-phosphoryl-3'-sn-glycerol.
A similar lipid, PhPC, is already present in CHARMM36, so generating parameters
for your lipid should be fairly straightforward.
I'm currently looking in the merged.rpt file but cannot find the lipid (PhPC)
you recommended. Am I looking in the right place? Is there somewhere online I
could find the lipid?
Thanks,
?
Josh
--
Gromacs Users mailing list
* Please search the archive at
Hi again.
Some of my friends said that gromacs had lower numerical stability than
amber, and occasionally has mysterious error in energy.
Is that still true? Does the implementation of Integrator cause more
resonance effect?
I am trying to run NVE simulation with the single precision version,
On 8/13/14, 2:19 PM, Johnny Lu wrote:
Hi again.
Some of my friends said that gromacs had lower numerical stability than
amber, and occasionally has mysterious error in energy.
I have never seen convincing evidence to support such a claim. Some people have
stated that they have found
Hello Stephan,
Do you mean PACKMOL?
http://www.ime.unicamp.br/~martinez/packmol/
VIctor
2014-08-13 0:58 GMT-05:00 lloyd riggs lloyd.ri...@gmx.ch:
Dear GMX users,
I ran across a nice web page, I believe from a brazilian group, for
generating membranes of any compnents (pdb). This was
Thank you very much. Yes I did.
Stephan
Gesendet:Mittwoch, 13. August 2014 um 23:09 Uhr
Von:Victor Rosas Garcia rosas.vic...@gmail.com
An:gmx-us...@gromacs.org
Betreff:Re: [gmx-users] Membrane simulations
Hello Stephan,
Do you mean PACKMOL?
http://www.ime.unicamp.br/~martinez/packmol/
27 matches
Mail list logo
