Hi,
Define an itp file which has the non-bonded info. Then define a mdp (md
parameter file) and also make a structure file (gro). Also you need a
topology file (top) which corresponds to the structure file.
You will have to do some background work. Manual should be your friend.
amit
On Sat,
hi
do I need any .pdb file for making .gro and .top file?
I make .pdb file with hyperchem software and then I used pdb2gmx command in
order to make .gro and .top files. but I think my way is wrong. is it true?
is there anybody that done this simulation?
leila
On Sun, Nov 21, 2010 at 11:24
- Original Message -
From: leila separdar separdar.le...@gmail.com
Date: Sunday, November 21, 2010 19:15
Subject: Re: [gmx-users] request
To: Discussion list for GROMACS users gmx-users@gromacs.org
hi
do I need any .pdb file for making .gro and .top file?
I make .pdb file
Hi all,
I was going through the very nicely presented tutorial by Justin (on KALP-15
in DPPC). I have one question regarding the non-bonded cut-offs. It seems
that people use many different values of non-bonded cut-off (varying from
0.9 nm to 1.2 nm or probably more). How should i choose the
Thank mark for comments, but I have check the structure after energy
minimization through ramachandran plot and found 82% residues were lies in
core region. After performed position restrained dynamics it reduced to 52%
in core region also 1 bad contact was found. I have taken SPC water model
then
Hi,
Today I use serach and find this topic.
I got confused.
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
According the page of extending simulation, in GROMACS ver.4, the commend is:
tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -s next.tpr -cpi
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello,
I haven't read the mails before, but as long as you are not in
equilibrium I do not think that PR coupling is the best way to go.
Furthermore PR is very sensitive to constraints and the time step, so
perhaps 2fs is too large. Try to perform a
Hi,
I had done 10ns simulation,
by dssp, can see the beta-sheet appeared very apparently, before it's
alpha-helix.
there were 5000 frames, I based on the time of the picture got from dssp, I can
guess around which frames is supposed to have those beta sheets.
After I took few frames which I
Zhe, here's what comes to my mind. It certainly requires a whole bunch
of testing, but if you really must calculate this then you could give
it a try.
In order to keep 2 plates planar, it seems to me that the distance
between the planes must be controlled at 3 or more points (3 points
On 21/11/2010 11:43 PM, #ZHAO LINA# wrote:
Hi,
I had done 10ns simulation,
by dssp, can see the beta-sheet appeared very apparently, before it's
alpha-helix.
there were 5000 frames, I based on the time of the picture got from
dssp, I can guess around which frames is supposed to have those
On 21/11/2010 9:09 PM, pawan raghav wrote:
Thank mark for comments, but I have check the structure after energy
minimization through ramachandran plot and found 82% residues were
lies in core region. After performed position restrained dynamics it
reduced to 52% in core region also 1 bad
On 21/11/2010 10:58 PM, Hsin-Lin Chiang wrote:
Hi,
Today I use serach and find this topic.
I got confused.
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
According the page of extending simulation, in GROMACS ver.4, the commend
is:
tpbconv -s previous.tpr
On 21/11/2010 2:34 AM, Spitaleri Andrea wrote:
Hi there,
I am encountering a weird problem with a REMD simulation using 4.5.3. The total
simulation is 50ns with 5 replica, and I do in two runs: 25ns and then
continuing to 50ns (walltime queue). The first run is okay, the continue run
(the
On 21/11/2010 8:45 PM, Amit Choubey wrote:
Hi all,
I was going through the very nicely presented tutorial by Justin (on
KALP-15 in DPPC). I have one question regarding the non-bonded
cut-offs. It seems that people use many different values of non-bonded
cut-off (varying from 0.9 nm to 1.2 nm
Quoting Mark Abraham mark.abra...@anu.edu.au:
On 21/11/2010 8:45 PM, Amit Choubey wrote:
Hi all,
I was going through the very nicely presented tutorial by Justin (on
KALP-15 in DPPC). I have one question regarding the non-bonded
cut-offs. It seems that people use many different values
Hi,
yes sure. Basically I do:
1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 - i get the first 5x25ns
of remd simulation (five xtc every 5ps and five trr every 20ps, for each
replica). I check those files by gmxcheck and they are fine. no errors.
2. for i in 'seq 1 5'; tpbconv -s
Thank you Mark and Justin. Yes i did check the reference of your tutorial,
but its just that there are so many groups using same FF but different
cut-off lengths.
amit
On Sun, Nov 21, 2010 at 10:22 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Quoting Mark Abraham mark.abra...@anu.edu.au:
On
do_dssp -f traj.xtc -s topol.tpr -o ss.xpm
trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump
Took several frames, here, such as model 1000, model 3000 and model 5000, and
named as 1000.pbd, 3000.pdb and 5000.pdb
pymol 3000.pdb
intra_fit protein and (name c,n,ca)
show cartoon
all
Hi, Mark
So, You mean I can get correct extending simulation without using -e ede
and -t trr in GROMACS ver.4.
Then I can set my mind at rest.
Thank you for your reply.
Hsin-Lin
Hi,
Today I use serach and find this topic.
I got confused.
Hi Chris,
Thank you so much for the idea! It is a good idea of using umbrella
sampling technique. But I am not sure whether it is just a matter of
averaging 3 PMFs as the final result.
To be physical, we need the 2 plates to be parallel to each other at
any time, right? With 3 pull groups (or
- Original Message -
From: Hsin-Lin Chiang jian...@phys.sinica.edu.tw
Date: Monday, November 22, 2010 14:51
Subject: Re: [gmx-users] extending simulation without cpt file
To: gmx-users@gromacs.org
Hi, Mark
So, You mean I can get correct extending simulation without
using -e ede
Thank you for the discussion. I am basically having a similar problem:
position restraining (PR) 2 plates in NPT and the system blow up
(posted here:
http://lists.gromacs.org/pipermail/gmx-users/2010-November/055975.html).
I will try to use smaller time step to see whether the situation
becomes
On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea
spitaleri.and...@hsr.itwrote:
Hi,
yes sure. Basically I do:
1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 - i get the first
5x25ns of remd simulation (five xtc every 5ps and five trr every 20ps, for
each replica). I check those files
Thanks a lot for the replies.
What we would like to have are the pairwise forces. I, however, was not
sure if gromacs saves the pairwise forces to the trajectory file or not
(I now figured out with gmxdump that atomic forces are saved).
I also came across the mdrun -rerun option, but I was not
Dear all,
Can anybody tell me how to incorporate potassium ion parameters in GROMACS
for GROMOS53a6 forcefield.
Thanking you in anticipation.
With regards,
Jignesh
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive
25 matches
Mail list logo
