I reckon ngmx is installed by default if you install GROMACS properly. Read the
GROMACS manual Appendix D, page 215.
And if you really need a better visualisation software you better install some
other visualization software like VMD or PyMol.
-Original Message-
From:
hi
I'm simulating gold nanoparticle interaction with amino acids.
I would like first equilibrate the nanoparticle and freeze it. Then I
equilibrate protein .Meaning that I want equilibrate them separatelywhile both
of them are in one box full of water. And after equilibrium phase I start
Bogdan,
thank you for so detailed explanation. Now it's only intresting to me
if it possible to change vdw radius (assuming it as the distance from
center of atom to it outer electronic shell)? E.g I want to change
such value for each node in my lattice model (e.g for CH2 united atom
that value
On 1/17/13 1:19 AM, sarah k wrote:
Dear all,
1- I’m trying to simulate a DNA-ligand complex. I have to use AMBER force
field for the DNA structure. I have used PRODRG to get the required files
and parameters of my ligand. PRODRG generates GROMOS based files.
Consequently, when I add the
On 1/17/13 1:25 AM, Devika N T wrote:
Thank you Emanuel
I have followed the path only usr/share/gromacs/top -- but was missing
Then I followed /usr/local/gromacs/share/gromacs/top - I could find
residuetype.dat
Previously I was having gromacs version 4.0.7, now I have installed 4.5.5.
So I
On 1/17/13 4:41 AM, fatemeh ramezani wrote:
hi
I'm simulating gold nanoparticle interaction with amino acids.
I would like first equilibrate the nanoparticle and freeze it. Then I
equilibrate protein .Meaning that I want equilibrate them separatelywhile both
of them are in one box full of
Thank you Justin, but there is still something I do not understand. Could you
please help me with it?
I believe that with the line
-CB CA1 +CB +CA1 gd_34
in aminoacids.rtp I am defining the torsion the program is complaining
about. I also tried with a line
-CH3 CH1 +CH2 +CH1 gd_34
On 1/17/13 5:40 AM, escajarro wrote:
Thank you Justin, but there is still something I do not understand. Could you
please help me with it?
I believe that with the line
-CB CA1 +CB +CA1 gd_34
in aminoacids.rtp I am defining the torsion the program is complaining
about. I also tried
Thank you!
That clarifies it, I will redefine the residues. This definition was good
enough for an all-atom force field, but it seems that not for this.
--
View this message in context:
http://gromacs.5086.n6.nabble.com/No-default-Proper-Dih-types-tp4442749p5004659.html
Sent from the GROMACS
On Thu, Jan 17, 2013 at 10:59 AM, James Starlight
jmsstarli...@gmail.com wrote:
thank you for so detailed explanation.
You're welcome. Now it's up to you to use it :)
Now it's only intresting to me
if it possible to change vdw radius (assuming it as the distance from
center of atom to it
Dear all,
we'd need to convert a trajectory in .xtc format (and the related
topology file) to a format that could be read by Amber program (I'd need
to perform MM-PBSA calculations).
We tried to do it using VMD, but failed to produce a correct trajectory
to be read by MMPBSA.py tool. It
On 1/17/13 6:22 AM, Anna Marabotti wrote:
Dear all,
we'd need to convert a trajectory in .xtc format (and the related topology file)
to a format that could be read by Amber program (I'd need to perform MM-PBSA
calculations).
We tried to do it using VMD, but failed to produce a correct
On Jan 17, 2013, at 12:27 , Justin Lemkul wrote:
On 1/17/13 6:22 AM, Anna Marabotti wrote:
Dear all,
we'd need to convert a trajectory in .xtc format (and the related topology
file)
to a format that could be read by Amber program (I'd need to perform MM-PBSA
calculations).
We tried
Dear all,
I have been trying to calculate and plot the secondary structure of helix
movements during the simulation on time through g_helix, g_helix orient,
g_principle and g_mindist but none of them shown the helix movements.
Is there any other tool can elaborate the helix movements ? Plz
Bogdan,
thanks againfor explanation.
So if I have force field with the C6/C12 terms (instead of
sigma\epsilon) I need to express sigma (which correspond to the Rmin
in LJ equation) as the (C12/C6)^0.5. Than if I want to increase sigma
( and consequently to increase vdw radius of my atom) I
On 1/17/13 7:37 AM, 라지브간디 wrote:
Dear all,
I have been trying to calculate and plot the secondary structure of helix
movements during the simulation on time through g_helix, g_helix orient,
g_principle and g_mindist but none of them shown the helix movements.
Is there any other tool can
On Thu, Jan 17, 2013 at 1:51 PM, James Starlight jmsstarli...@gmail.com wrote:
So if I have force field with the C6/C12 terms (instead of
sigma\epsilon) I need to express sigma (which correspond to the Rmin
in LJ equation) as the (C12/C6)^0.5. Than if I want to increase sigma
( and
Dear Gromacs Developers!
Using sd1 integrator I've obtain good performance with the core-5 +
GTX 670 ( 13ns\per day) for the system of 60k atoms. That results on
30% better than with the sd integrator.
Buit on my another work-station which differs only by slower GPU ( GT
640). I've obtained
Bogdan,
It's not clear for me how I could change sigma with fixed epsilon in
case of using (A/R)^12-(A/R)^6 form of LJ. In that case sigma and
epsion depends both on A and B so changing A or B we will influence
both sigma and epsilon.
James
2013/1/17 Bogdan Costescu bcoste...@gmail.com:
On
On 1/17/13 9:51 AM, James Starlight wrote:
Bogdan,
It's not clear for me how I could change sigma with fixed epsilon in
case of using (A/R)^12-(A/R)^6 form of LJ. In that case sigma and
epsion depends both on A and B so changing A or B we will influence
both sigma and epsilon.
From manual
Hi,
Please use the fix I put on the redmine issue, as that's even faster and you
can use sd again.
We should probably rephrase the note a bit in case the GPU has more work to do
than the CPU.
In your case there is simple no work to do for the CPU.
Ideally we would let the CPU handle some
On 1/17/13 9:54 AM, Marcelo Depolo wrote:
Well, Justin,
I tried to generate the .tpr using single precision and I got the same
warning. I also tried to use gmxcheck using the command line below:
*$ gmxcheck -e prt_cg.edr -m cg.tex*
Unfortunately, I got the same warning and no log file.
Dear Justin Thank you for your Previous Reply Mail
I am using GridMAt MD Script When I run the APL Headgroup
Calculation It runs well But I Have got Output With the Following Comment in
My Command Prompt
looking for offending protein atoms...
There
On 1/17/13 10:56 AM, vidhya sankar wrote:
Dear Justin Thank you for your Previous Reply Mail
I am using GridMAt MD Script When I run the APL
Headgroup Calculation It runs well But I Have got Output With the Following
Comment in My Command Prompt
looking for
1. For separate equilibration of AU and Protein, I'm using this em.mdp file for
equilibration in step 1, that Protein and SOL are frozen:
title = n.pdb
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
dt
In addition to LINCS warning during last simulation I obtained the
next warning from mdrun (again that was when calmodulin reached close
compact conformation)
WARNING: Listed nonbonded interaction between particles 1230 and 1249
at distance 3f which is larger than the table limit 3f nm.
This is
On 1/17/13 1:24 PM, James Starlight wrote:
In addition to LINCS warning during last simulation I obtained the
next warning from mdrun (again that was when calmodulin reached close
compact conformation)
WARNING: Listed nonbonded interaction between particles 1230 and 1249
at distance 3f which
Justin,
so following to that equation the alteration of sigma will affect on
both C6 and C12 ( attractive and repuslive terms). I dont quite
understand how such modifications of the c6 and c12 params will change
vdw radius of atom. I need some example to understand it :(
James
2013/1/17 Justin
On 1/17/13 12:15 PM, fatemeh ramezani wrote:
1. For separate equilibration of AU and Protein, I'm using this em.mdp file for
equilibration in step 1, that Protein and SOL are frozen:
This is not an equilibration, this is an energy minimization, which will likely
not accomplish much with so
On 1/17/13 1:31 PM, James Starlight wrote:
Justin,
so following to that equation the alteration of sigma will affect on
both C6 and C12 ( attractive and repuslive terms). I dont quite
understand how such modifications of the c6 and c12 params will change
vdw radius of atom. I need some
Justin,
so its exacly what I mean! I dont find any relationship between LJ
equation in any form and vdw radius of atom. But is it possible to
modify vdw radius exactly ? E.g I have united atom as a node which
vdw must be 1.5 A. I want to decrease it to 1 A. What should I do
for it ?
James
On 1/17/13 2:05 PM, James Starlight wrote:
Justin,
so its exacly what I mean! I dont find any relationship between LJ
equation in any form and vdw radius of atom. But is it possible to
modify vdw radius exactly ? E.g I have united atom as a node which
vdw must be 1.5 A. I want to decrease
Dear Justin thanks for your reply and,
Please help me to correct the settings of .mdp files step by step .
By these em.mdp files if I freeze only protein for the first time and after
minimization I use the result .pdb file for second step of minimization that
I freeze AU atoms in it,
On 1/17/13 2:48 PM, fatemeh ramezani wrote:
Dear Justin thanks for your reply and,
Please help me to correct the settings of .mdp files step by step .
I did that in my previous reply.
By these em.mdp files if I freeze only protein for the first time and after
minimization I use the result
Dear Justin,
For example, In hemoglobin (A-H helix), the particular E and F helix gets
moved during the MD simulation, I would like to calculate this helix
movements/rotation angle? Thanks.
You'll have to define what you mean by helix movements. Everything moves in a
simulation, but what is
Please use an appropriate subject line and delete irrelevant parts of the
digest.
On 1/17/13 8:42 PM, 라지브간디 wrote:
Dear Justin,
For example, In hemoglobin (A-H helix), the particular E and F helix gets
moved during the MD simulation, I would like to calculate this helix
p{margin:0;padding:0;}
Dear Justin,
For example, In hemoglobin (A-H helix), the particular E and F helix gets moved
during the MD simulation, I would like to calculate this helix
movements/rotation angle? Thanks.
Dear all,
I have been trying to calculate and plot the secondary
37 matches
Mail list logo
