Hi Nahren,
You can try the .g96 format for this, which has high precision. To
understand the format, convert something to .g96 and replace the
coordinates with the eigenvectors.
Hope it helps,
Tsjerk
On Fri, Nov 1, 2013 at 4:10 AM, nahren manuel wrote:
> Dear GMX Users,
>
> I performed an AN
i am a newbie to gromacs, trying to generate a new rtp entry for my
residue.
Bonds, dihedrals of .rtp file has gb_XX
what is gb_XX numbers? how can get informations about that?
How to define those velues for my residues?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.
Dear GMX Users,
I performed an ANM calculation at
http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi
It returned me eigenvectors in the following format (where the second and
third column represent first and second eigenvector)
1 0.010551 -0.048553
1 -0.022038 -0.042918
1 0.107906 0.045
Dear all,
I would like to assess the probability distribution of particle bond
distance/length over the entire run, specifically I want to collect possibly a
histogram representation or even a regular plot. Would using g_bond be the
correct way to obtain the probability distribution? Or is ther
Hi All,
I am considering setting up a small cluster to run Gromacs jobs. The aim
would be to maximise ns/day/$ for smallish systems of 15-30,000 atoms. Can
anybody provide advice/benchmarks/anecdotes about what type of current hardware
provides the best performance/price? Would it be somet
On 10/31/13 7:03 PM, Ehsan Sadeghi wrote:
Thanks Justin,
Here is the steps that I followed:
pdb2gmx -f eth.pdb -o eth.gro -p eth.top
pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top
editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5
genbox -cp box.gro -cs spc216.gro -c
Thanks Justin,
Here is the steps that I followed:
pdb2gmx -f eth.pdb -o eth.gro -p eth.top
pdb2gmx -f ionomer-4.pdb -o ionomer4.gro -p ionomer4.top
editconf -f ionomer4.gro -o box.gro -bt dodecahedron -d 0.5
genbox -cp box.gro -cs spc216.gro -ci eth.gro -nmol 1000 -o solvated.gro
I got th
On 10/31/13 5:03 PM, Xu Dong Huang wrote:
@ Justin,
Excellent advice. Thank you! And for the equilibrium angle, what is the
approximate range I can define it to be? Say target is 90 degrees, should I
define maybe 130 and let it oscillate? I guess question is how far is too far
off?
This is
@ Justin,
Excellent advice. Thank you!
And for the equilibrium angle, what is the approximate range I can define it to
be? Say target is 90 degrees, should I define maybe 130 and let it oscillate? I
guess question is how far is too far off?
Thanks,
On Oct 31, 2013, at 4:48 PM, Justin Lemkul w
On 10/31/13 4:44 PM, Xu Dong Huang wrote:
@ Justin,
I did not define [angles] in the topology but I do have the angles result
from All-atom run using OPLS forcefield. The reason for me not to include it
in MARTINI forcefield topology is because I wanted to see if it will produce
similar angle
@ Justin,
I did not define [angles] in the topology but I do have the angles result from
All-atom run using OPLS forcefield. The reason for me not to include it in
MARTINI forcefield topology is because I wanted to see if it will produce
similar angle result of atom 1&2, 1&3 and 2&3 in martini
Thank you, Justin!
I did intend to use h-bonds for the CHARMM36 simulations and all-bonds
elsewhere (depending on the FF). I just wanted some clarity before I
proceeded.
On Fri, Nov 1, 2013 at 1:49 AM, Justin Lemkul wrote:
>
>
> On 10/31/13 2:21 PM, rajat desikan wrote:
>
>> Hi,
>> In the CHARM
On 10/31/13 4:22 PM, Xu Dong Huang wrote:
@ Justin,
That doesn’t sound very good. I tried it as he suggested using make_ndx, it
seems to work, but it’s not reporting the result I want. When I use g_angle
using the index i created, I chose the group I want to assess (My compound is
very simple
@ Justin,
That doesn’t sound very good. I tried it as he suggested using make_ndx, it
seems to work, but it’s not reporting the result I want. When I use g_angle
using the index i created, I chose the group I want to assess (My compound is
very simple in Martini, it’s only represented by 3 atom
On 10/31/13 2:21 PM, rajat desikan wrote:
Hi,
In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds
are constrained for the lipid simulations using SHAKE (excerpt from the
paper below)
"Consistent for all of these simulations was the use of a 1 fs time step
and constraining
On 10/31/13 2:25 PM, Ehsan Sadeghi wrote:
Hi gmx users,
I want to solvate nafion molecules in a 3:1 ethanol water solution. I used
genbox with -ci option to add ethanol to water when generating the box, but
it did not work. Then, first I solvated the ethanol in water, and then added
What "di
On 10/31/13 3:59 PM, Riccardo Concu wrote:
Dear Xu,
you have to use the make_ndx option if I'm not wrong.
The syntax should be make_ndx -f xxx.gro -o index.ndx
make_ndx is not particularly useful for angles. To get it to recapitulate the
function of mk_angndx, it's as much work as writing t
On 10/31/13 3:52 PM, Xu Dong Huang wrote:
Dear all,
so after I opened angle.ndx file in a text editor, the file appears to be
blank. How can I properly make a index file since the command I issued seems to
produce a blank index file? Is there something wrong with my input regarding
npt.tpr?
Dear Xu,
you have to use the make_ndx option if I'm not wrong.
The syntax should be make_ndx -f xxx.gro -o index.ndx
Cheers,
-Original Message-
From: Xu Dong Huang
Sent: Thursday, October 31, 2013 8:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] No group in index f
Dear all,
so after I opened angle.ndx file in a text editor, the file appears to be
blank. How can I properly make a index file since the command I issued seems to
produce a blank index file? Is there something wrong with my input regarding
npt.tpr?
Thanks for your input,
Xu Huang
On Oct 31
Dear Ehsan,
Did you try to pack your box with packmol? I have a similar system and
packmol pack my system quite well and in a random way.
Regards,
Riccardo
-Original Message-
From: Ehsan Sadeghi
Sent: Thursday, October 31, 2013 7:25 PM
To: Discussion list for GROMACS users
Subject: [g
Hi gmx users,
I want to solvate nafion molecules in a 3:1 ethanol water solution. I used
genbox with -ci option to add ethanol to water when generating the box, but it
did not work. Then, first I solvated the ethanol in water, and then added the
nafion to the system, but these 3 molecules each
Hi,
In the CHARMM36 paper (Klauda et al., JPCB 2010), only the hydrogen bonds
are constrained for the lipid simulations using SHAKE (excerpt from the
paper below)
"Consistent for all of these simulations was the use of a 1 fs time step
and constraining of the hydrogen atoms using the SHAKE algorit
On 10/31/13 1:36 PM, Xu Dong Huang wrote:
Dear all.
Since I am interested in finding the average angle, dihedrals in my system, I
attempted to use g_angle, but then I realized I need to make index file using
mk_angndx,
I issued the following:
mk_angndx -s npt.tpr -n angle.ndx
and then i us
Dear all.
Since I am interested in finding the average angle, dihedrals in my system, I
attempted to use g_angle, but then I realized I need to make index file using
mk_angndx,
I issued the following:
mk_angndx -s npt.tpr -n angle.ndx
and then i used g_angle -f not.xtc -n angle.ndx -ov angle.x
On 10/31/13 11:40 AM, Nilesh Dhumal wrote:
Could you tell how can I get rid of following warning?
WARNING 1 [file test.top, line 263]:
The bond in molecule-type BMI between atoms 10 C10 and 23 H23 has an
estimated oscillational period of 1.2e-03 ps, which is less than 5 times
the tim
Could you tell how can I get rid of following warning?
WARNING 1 [file test.top, line 263]:
The bond in molecule-type BMI between atoms 10 C10 and 23 H23 has an
estimated oscillational period of 1.2e-03 ps, which is less than 5 times
the time step of 1.0e-03 ps.
Maybe you forgot to change
Dear Justin,
I ran a short simulation (200ps) with the cool down under NVT and now it
seems the system is working. In addition, I removed from the NVT options
the tc for all the groups.
Thank you,
Riccardo
El jue, 31-10-2013 a las 08:31 -0400, Justin Lemkul escribió:
>
> On 10/31/13 8:25 AM, Ricca
On 10/31/13 10:30 AM, Nilesh Dhumal wrote:
Hello,
I am running a equilibration simulation for ionic liquids at 400 K.
I am getting following note.
The sum of the two largest charge group radii (0.213127) is larger than
rlist (1.00) - rvdw (0.90)
Could you tell what is the prob
Hello,
I am running a equilibration simulation for ionic liquids at 400 K.
I am getting following note.
The sum of the two largest charge group radii (0.213127) is larger than
rlist (1.00) - rvdw (0.90)
Could you tell what is the problem? I am using Gromacs VERSION 4.5.5 .
I used
I think ProDy can do this. It is a python module for analysis of
structures that can be downloaded from http://www.csb.pitt.edu/ProDy/
I'm not sure it can read xtc but you can probably use it after converting
trajectories to pdb.
>> On 10/30/13 11:26 AM, Knapp Bernhard wrote:
>>> Hi users,
>>>
>>>
On 10/31/13 8:25 AM, Riccardo Concu wrote:
Dear all, I'm having some problems during the cool-down process after
the NVT.
I'm running the NVT process at a T of 500K for 3ns and everything is
going well but when I cool down the system blows up. I am running the
cool down for 100ps, I tried to ru
Dear all, I'm having some problems during the cool-down process after
the NVT.
I'm running the NVT process at a T of 500K for 3ns and everything is
going well but when I cool down the system blows up. I am running the
cool down for 100ps, I tried to run the process for longer time (500 ps)
and dec
On 10/31/13 4:57 AM, fantasticqhl wrote:
Dear Justin,
*Thanks very much for your reply! Here is my minim.mdp I used:*
/; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (ste
On 10/31/13 6:26 AM, Hossein Lanjanian wrote:
Hi
I'm going to study the molecular dynamics of an RNA(which has stem-loop
structure) by comparison the native RNA structure and it's mutant to find
the conformation changes of 3D structure. This RNA comprises 70
nucleotides. Do you think that it w
Hi
I'm going to study the molecular dynamics of an RNA(which has stem-loop
structure) by comparison the native RNA structure and it's mutant to find
the conformation changes of 3D structure. This RNA comprises 70
nucleotides. Do you think that it would be possible in Gromacs.
--
gmx-users mailing
On 10/30/13 11:26 AM, Knapp Bernhard wrote:
Hi users,
I was wondering if there is an easy and quick way to get a frame-wise
binding
energy between 2 groups of chains (chain ABC vs DE) in an existing
trajectory.
This is not indented to be an actual binding free energy approach but
rather a
rou
Dear Justin,
*Thanks very much for your reply! Here is my minim.mdp I used:*
/; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol
Dear Justin,
*Thanks very much for your reply! Here is my minim.mdp I used:*
/; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol
39 matches
Mail list logo
