Dear all,
I ran MD simulations of a small molecule and clustered structurally
similar frames together. I wanted to find the radius of gyration of all
the members of each cluster.
To do the same, I used the command:
$ g_gyrate -f cluster.xtc -s full.tpr -o cluster_rg.xvg
Here, the file "cluster.
Hello,
I recently changed the number of cpus I was pairing with each gpu and I
noticed a significant slowdown, more than I would have expected simply due
to a reduction in the number of cpus.
>From the log file it appears that the GPU is resting for a large amount of
time. Is there something I ca
Dear users,
I am planing to simulate how small organic molecules (i.e. pyrene and
phenanthrene) bind to bile salts in the gut using GROMACS. However, there are
diverse groups of bile salts in the intestinal systems. Could someone give me
some suggestion on choosing one typical type of bile sal
Hi Justin,
Thanks for your advice. Since we are using a forcefield which could only
incorporate with gromacs 3.3.1, we have no choice but to prepare the system
in the old version, then run it with the latest version of gromacs.
Yes, indeed the option should be with -DPOSRES instead. And the topol
Dear users,
I ran the Perl script for Umbrella Sampling Tutorial 3, and it generated an
incomplete summary_distances.dat :
summary_distances.dat :
00.505
10.507
20.504
30.510
40.505
50.500
60.499
70.509
80.505
90.504
100.510
110.505
120.509
13
Hello Users,
I am planning to do a bilayer simulation with asymmetric ion concentrations
using slab boundaries. I am trying to modify the concentration of each
ionic species on each side of the bilayer, however, I am struggling to find
a technique that will allow me to effectively manipulate the c
Dear Gromacs users,
I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow
me to create a new *.gro file containing the protein and the N closest
water molecules to the protein
, starting from a system of a solvated protein
?
Best,
Jose Borreguero
--
Gromacs Users mailing li
> 在 2017年6月7日,16:26,gromacs.org_gmx-users-requ...@maillist.sys.kth.se 写道:
>
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Finally I managed to find the exact syntax for the rdf calculation by
adding " -ref 'com of group g1' " at the end of the command-line:
gmx rdf -f cgs.gro -s cgs.tpr -o rdf.xvg -xy -ref 'com of group g1'
On Thu, Jun 8, 2017 at 12:56 AM, Sajjad Kavyani
wrote:
> Dear experts,
> Recently I a
Dear experts,
Recently I ask a question entitled "RDF of a group around CNT axis" in the
mailing list in order to find proper command-line for it it turns out that
the "-xy" option can help
But I encounter an unusual problem therefore I decided to ask another
question
It turns out that the gmx rdf
On 6/7/17 4:18 PM, Alex wrote:
Hi all,
I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane
with a narrow pore and an ion. The configurations correspond to various
heights "above" the membrane (0 to 1.5 nm).
In one case, the ion is K+, in another Na+. In both cases the re
Hi all,
I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane
with a narrow pore and an ion. The configurations correspond to various
heights "above" the membrane (0 to 1.5 nm).
In one case, the ion is K+, in another Na+. In both cases the results are
fairly reasonable, but th
Please do not reply to the whole digest.
On 6/7/17 2:46 PM, Shi Li wrote:
On 6/7/17 1:20 PM, Li, Shi wrote:
Dear GMX users,
I have a pure solvent system A with 100 molecules. Then I randomly removed
10 molecules out of the box, but keep the box size. Now I want to do a gmx
insert-molecule to
Dear list
I am attempting to pull a small molecule though a bilayer using the pull
geometry cylinder with gromacs v 2016.
This is the relevant portion of my mdp-file:
pull = yes
pull-ngroups = 2
pull-ncoords = 1
pull-coord1-groups = 1 2
pull-gro
> 在 2017年6月7日,13:31,gromacs.org_gmx-users-requ...@maillist.sys.kth.se 写道:
>
> Send gromacs.org_gmx-users mailing list submissions to
> gromacs.org_gmx-users@maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://maillist.sys.kth.se/mailman/listinf
I noticed that the gmx rdf some how cannot find the center of mass (COM)
for the CNT because after that I manually put a single particle in the COM
of the CNT and calculated the rdf around it (with -xy option), the gmx rdf
resulted the expected value which is a sharp peak at the radius of the cnt.
Dear Joao,
Thank you very much for your support. I am following Justin's tutorial but
simulating a fragment of antibody (Fab).
I will try the different water models.
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Thu, Ju
Just one more thing. If you're following Justin's tutorial, I guess you're
using lysozyme. This protein will not deviate very much from it's crystal
structure at 27ºC, let alone at -40ºC (*in the context of a molecular
dynamics simulation**). I understand that it may be possible to
experimentally u
On 6/7/17 1:20 PM, Li, Shi wrote:
Dear GMX users,
I have a pure solvent system A with 100 molecules. Then I randomly removed
10 molecules out of the box, but keep the box size. Now I want to do a gmx
insert-molecule to insert 10 molecule B into the system box. The problem is
molecule B is slig
Dear GMX users,
I have a pure solvent system A with 100 molecules. Then I randomly removed
10 molecules out of the box, but keep the box size. Now I want to do a gmx
insert-molecule to insert 10 molecule B into the system box. The problem is
molecule B is slightly larger than molecule A. So in som
Higher complexity water models such as TIP5P and so on are able to better
reproduce bulk water properties (please check the paper I linked in my
earlier email). However, these models require more computational effort
(due to the increased number of interactions) and may not work well in
conjunctio
Dear Justin,
Thank you very much. I will try the possible water models.
Do you know if there are water models to resemble frozen state?
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng";<272699...@qq.com>;
Date: Thu, Jun 8, 2017 00:50 AM
To: "ZHANG
On 6/7/17 12:50 PM, ZHANG Cheng wrote:
Dear Joao,
Thank you for your help and the paper link.
I was following Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
On that page, it says "spc216.gro as the solvent configuration for SP
Dear Joao,
Thank you for your help and the paper link.
I was following Justin's tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E,
or TIP3P water", and it outputs
Dear Srinivas,
That's absolutely right, I want to calculate the RDF of a certain
group around the central axis of a nanotube.
And as I know that the RDF of the CNT around its axis is just a sharp peak
at the radius, I just tested the command-line parameters for this case, to
specify that which comm
On 6/7/17 10:05 AM, Mohammad Roostaie wrote:
Dear Mark,
I was using version 5.1.4, but I got this error when using "gmx mdrun":
tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted
I tried version 5.0.4, too, and I got the same error. Hence, I decided to use
the 4.5.5
Hello,
"spc216.gro" is not a water model, it's just a pre-equilibrated simulation
box (300 K and 1 bar) with the coordinates of 216 3-site water molecules.
SPC and TIP3P are two examples of 3-site water models. Water model
properties are well studied and tabled (e.g.
http://aip.scitation.org/doi/1
If I understand you correctly: you want to calculate the RDF of a certain
group (NOT part of the nanotube) around the central axis of a nanotube?
The way I do these calculations is to use the gmx trjconv tool to isolate a
trajectory file of ONLY the gropus I am interested in and run my
calculation
Dear Mark,
I was using version 5.1.4, but I got this error when using "gmx mdrun":
tMPI error: malloc failure in tMPI (out of memory) (in valid comm)Aborted
I tried version 5.0.4, too, and I got the same error. Hence, I decided to use
the 4.5.5 version which does not give me that error.
Mohammad
Dear Gromacs,
I would like to simulate the protein at subzero condition in aqueous buffer, to
see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I
ask what is the valid temperature range for water "spc216.gro" ? If I run the
simulation at -40 C, does it still assume the
Dear all,
Is there any way of scaling the Coulombic and/or van der Waals interactions
between a protein-ligand system and simultaneously doing Normal Mode analysis
on the perturbed system while scaling, perhaps using free-energy code in
Gromacs?
Thanking in anticipation,
Best Regards,
Bhagye
Dear experts,
I want to calculate rdf of a certain group around the axis of a cnt, but I
do not know what are the proper parameters to choose in the command-line.
To test the parameters, I calculated the rdf of cnt itself around its axis
which must be a sharp peak at the cnt radius.
I tested the fo
On 6/7/17 8:36 AM, saranya wrote:
I have already done simulation for protein and drug interacted protein
complexes for 100ns. I just checked out the pressure of my system by using
gmx energy command, but the calculated pressure is quite altered (20,000
pressure bar).
Moreover, when I calculated
Thank you Mark.
Let me explain my scenario here - Umbrella sampling simulations with 15
windows are run using -multi option to obtain PMFs. I have not noticed
any issues with the output files (trr, pullf etc.) yet. I have carried
out WHAM analysis using gmx wham option and obtained smooth PMFs
I have already done simulation for protein and drug interacted protein
complexes for 100ns. I just checked out the pressure of my system by using
gmx energy command, but the calculated pressure is quite altered (20,000
pressure bar).
Moreover, when I calculated the temperature of my system, the res
Hi Group
I have been trying to run a simulation that contains both 3-10 and alpha
helical peptides.
I am using "AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et
al., Proteins 78, 1950-58, 2010)" forcefield.
Over the course of simulation, the 3-10 helix is changing to alpha as
sugg
Hi Mark,
I think I solved the problem. It should be DPOSRES instead of POSRES. The
define command should be implemented as "define = -DPOSRES". Finally, the
chainX_porse.itp should be included in the master topology file, not
chainX-pace.top.
Thanks again by the way.
Simon
2017-06-07 19:18 GMT+
On 6/6/17 4:01 PM, RAHUL SURESH wrote:
Dear Justin
I think I have confused so much.
Let me try to put it in simple way.
1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of
monomer(just protein) to explain stability?
RMSD may be an indicator of something going on but by
On 6/7/17 7:18 AM, Simon Kit Sang Chu wrote:
Hi Mark,
Thanks for your prompt reply. What surprises me is that a change of "define
= POSRES" could cause a problem. The full output from grompp is -
checking input for internal consistency...
calling cpp...
cpp: error: POSRES: No such file or dir
Hi Mark,
Thanks for your prompt reply. What surprises me is that a change of "define
= POSRES" could cause a problem. The full output from grompp is -
checking input for internal consistency...
calling cpp...
cpp: error: POSRES: No such file or directory
cpp: warning: ‘-x c’ after last input file
Hi,
gmx mdrun -multidir is a good way to run a group of similar but otherwise
uncoupled simulations - they remain uncoupled unless you choose something
that couples them, such as replica exchange. gmx mdrun -multi is a bit less
reliable with output files.
Mark
On Wed, Jun 7, 2017 at 12:34 PM Deb
Dear Users,
I have doubts regarding simulating multiple systems using mdrun '-multi'
option.
I have seen that people have used this option for replica exchange (with
'-replex' option, of course) where information are exchanged between the
systems. In case of different systems (such as differ
Hi all!
For those of you who are interested in molecular visualization and
modeling with Blender and MembraneEditor, we conduct a Hands-on workshop
at the Integrative Bioinformatics conference in Odense/University of
Southern Denmark! The conference will be 22.-23.6., the workshop at
Saturday, 24.
Thank you Dear Mark.
Its my pleasure taking your time. ;-)
On Wed, Jun 7, 2017 at 2:25 PM, Mark Abraham
wrote:
> Hi,
>
> This is why you should actually copy and paste your command lines so you
> don't waste your time ;-) And mine.
>
> Unless you wrote your entire system to your xtc file, your
Hi,
This is why you should actually copy and paste your command lines so you
don't waste your time ;-) And mine.
Unless you wrote your entire system to your xtc file, your tpr has more
atoms than your xtc, and thus probably some more dihedrals. Make a matching
subset of your tpr using gmx convert
Dear Mark
Thank you
gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg
This was my command..
I didn't choose any dihedral particularly
On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham
wrote:
> Hi,
>
> Sounds like your choice of dihedrals doesn't match your system. How did you
> select them?
>
Hi,
On Wed, 7 Jun 2017 06:37 G R wrote:
> Dear all,
>
> I want to calculate the relaxation of pure water cell at room temperature
> and at freezing point, monitoring its equilibration in volume and in
> potential energy. I have 3 question: 1) Can I use packmol for my initial
> configuration?
M
Hi,
You might want to measure the autocorrelation time of RMSD from your
reference structure. Then you'll have an idea how long you have to wait to
make a statistically independent observation.
Mark
On Tue, 6 Jun 2017 08:25 Apramita Chand wrote:
> Dear Mark,
> Thanks for your reply. I think yo
Hi,
You almost certainly don't want to use version 4.5.5. It's many years old,
slow and contains many bugs that have been fixed. Get a new version
installed ;-)
Mark
On Tue, 6 Jun 2017 17:49 João Henriques
wrote:
> Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I
> mean
Hi,
Please read the advice on system preparation on the GROMACS webpage. You
probably have clashing atoms or missing atoms (check all the warnings!)
Mark
On Tue, 6 Jun 2017 20:19 Pandya, Akash wrote:
> Hi all,
>
> I have used the steepest descent method to minimise my system. It kept
> saying
Hi,
Sounds like your choice of dihedrals doesn't match your system. How did you
select them?
Mark
On Wed, 7 Jun 2017 08:41 RAHUL SURESH wrote:
> Dear Users
>
> When I try to execute ramachandran plot analysis, I get the following note
> like "Dihedral around 5809,5816 not found in topology. Us
Hi,
We can't tell, because position restraints are an attribute of
moleculetypes and those are hidden in your itp files and you didn't share
which moleculetype grompp reported was the problem. Please copy and paste
terminal output to make a useful description.
You'll need to include the position
Dear all,
I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I use
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