Hi Justin,
I had used only Gromos 43 a1 from initially for proteins, but i saw the
-ff gmx in the Drug enzyme tutorial, so i tried using this optiion for
protein ligand comp[ex simultaitons, also the simulation was able to be
performed with -ff gmx for some ligands without the atom type not
I have got the formyl parameters through swissparam site (http://swissparam.ch/
) . Then I seperate the formyl from other residues. After it , I got the
topology for this and then I included the .itp file in it . Now I' d like to
know how can I become sure that the formyl group is applied in
Oh my god! :-)
The situation seems going complicated! :-(
Let me explain what I'm gonna do in detail:
I have formyl residue as the N-terminus in my protein (.pdb file) ! As you
know, the topology database in CHARMM27 doesn't have formyl. So I got its
parameter as an .itp file through
Dear colleagues,
Has anyone run simulation with heme moiety in GROMACS with AMBER FF before?
I have a problem running it. I need the topology parameters for the heme.
Thanks
Peterson
--
View this message in context:
In general, NVE is tricky business, since small integration errors build up and
cause energy drift in the long run. Do you see energy drift too? In my
experience one needs double precision and a shorter timestep than what you
employ. But that is of course system dependent.
Erik
9 maj 2012
I think you should still have COM removal. This compensates for numerical
errors coming from the integrator. If you remove the COM of your system the COM
of the solute is still allowed to move, it's just that there is not net
movement of the entire system.
Erik
9 maj 2012 kl. 06.58 skrev
Dear Gmx Users,
I am running TPI of the water in the system containing free amino acids.
Steps:
1. I run the NPT simulation of 100 ns to equilibrate the system.
2. I added 1 extra water molecule to the final pdb file (converted from
gro) and to topology
3. I creaded tpi.tpr using grompp using
On 5/9/12 4:48 AM, Shima Arasteh wrote:
Oh my god! :-)
The situation seems going complicated! :-(
Let me explain what I'm gonna do in detail:
I have formyl residue as the N-terminus in my protein (.pdb file) ! As you know,
the topology database in CHARMM27 doesn't have formyl. So I got its
On 5/9/12 3:13 AM, Sarath Kumar Baskaran wrote:
Hi Justin,
I had used only Gromos 43 a1 from initially for proteins, but i saw the -ff gmx
in the Drug enzyme tutorial, so i tried using this optiion for protein ligand
comp[ex simultaitons, also the simulation was able to be performed with -ff
Hi all,
I try to build go model(which uses only c-alpha atoms), my pdb
contains only c-alpha atoms extracted from the original pdb file ,when i
use pdb2gmx command on c-alpha containing pdb file it gives the following
error.
Atom N is used in an interaction of type atom in
On 5/9/12 8:37 AM, mohan maruthi sena wrote:
Hi all,
I try to build go model(which uses only c-alpha atoms), my pdb
contains only c-alpha atoms extracted from the original pdb file ,when i use
pdb2gmx command on c-alpha containing pdb file it gives the following error.
Hi Steven
As I remember, TPI is based on the calculation of the potential at every
conformation from the already computed simulation (inserting the
particle in every snapshot), so velocities are not used.
Anyway, use both and see if there are any differences.
Javier
El 09/05/12 11:27,
thank you Javier, I will try both in this case.
On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo j...@um.es wrote:
Hi Steven
As I remember, TPI is based on the calculation of the potential at every
conformation from the already computed simulation (inserting the particle
in every snapshot),
Dear Gmx Users,
My surface is made of different atoms (Fe, Na, H). I would like to create
bonds between them so the surface will be stable. Is there a command in
gromacs to create [ bonds ] and to add to your topology?
I tried to use specbond.dat but none bonds were created. It could be
manually
On Tue, May 8, 2012 at 2:04 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
Yeah, that .rtp comment looks totally wrong. After looking at the code I
think:
* Column 5: 1 means keep all generated dihedrals,
* 0 means permit generated dihedrals to have their parameters
*
hello gmx users,
I am sorry for bothering you but I was searching mailing list and no
results. I have a problem with my test particle insertion as I run the
workflow I described previously with my mdp:
title = Test Particle Insertion
; Run parameters
integrator = tpi
nsteps =
What's your command line?
El 09/05/12 15:49, Steven Neumann escribió:
title = Test Particle Insertion
; Run parameters
integrator = tpi
nsteps = 5000; 100 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress .trr output ; output coordinates
grompp -f tpi.mdp -c tpi.pdb -p topol.top -o tpi.tpr
where tpi.pdb is a file with extra water molecule as well as topol.top.
Then:
mdrun –s tpi.tpr -rerun md.trr -deffnm tpi -tpi tpi.xvg -tpid tpid.xvg
On Wed, May 9, 2012 at 2:56 PM, Javier Cerezo j...@um.es wrote:
What's your command line?
Sorry, I saw now the command line you've posted. Did you check your trr
with gmxcheck?
El 09/05/12 15:49, Steven Neumann escribió:
hello gmx users,
I am sorry for bothering you but I was searching mailing list and no
results. I have a problem with my test particle insertion as I run the
OK, I have to build a .rtp file. But I'd like to know if I should make it
corresponding to relation between.itp and .rtp files format?
Cheers,
Shima
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent:
Checking file md.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time0.000
# Atoms 2569
Last frame 2000 time 10.000
Item#frames Timestep (ps)
Step 200150
Time 200150
Lambda200150
Coords 0
Velocities
On 5/9/12 10:02 AM, Shima Arasteh wrote:
OK, I have to build a .rtp file. But I'd like to know if I should make it
corresponding to relation between.itp and .rtp files format?
Start by reading the manual and looking at existing examples. The formats are
largely unrelated, but the content
I added one water molecule in my topology to all water molecules:
[ molecules ]
; Compound#mols
Alanine40
SOL 724
Maybe I should add aditional line like:
[ molecules ]
; Compound#mols
Alanine40
SOL 723
SOL 1
The trr file has something wrong. Look at Coords, it has 0 frames
You may have forgotten to set nstxout to a non-zero value?
Javier
El 09/05/12 16:10, Steven Neumann escribió:
I added one water molecule in my topology to all water molecules:
[ molecules ]
; Compound#mols
Alanine
Thank you! I have missed it somehow. I can still use my xtc trajectory.
Steven
On Wed, May 9, 2012 at 3:16 PM, Javier Cerezo j...@um.es wrote:
The trr file has something wrong. Look at Coords, it has 0 frames
You may have forgotten to set nstxout to a non-zero value?
Javier
El 09/05/12
On Tue, 2012-05-08 at 11:38 -0700, Milinda Samaraweera wrote:
Hi Guys
I was using the program http://q4md-forcefieldtools.org/RED/ to
derrive ESP based charges for some molecules that I study. Is this a
correct method to do so if not please let me know what are the other
methods that are
Dear Gmx Users,
My plane surface is made of atoms. I would like to restrain positions
between them so they will move all togehter or create bonds between them.
Would you advise how to do this in the easiest way?
Steven
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gmx-users mailing listgmx-users@gromacs.org
On 5/9/12 11:34 AM, Steven Neumann wrote:
Dear Gmx Users,
My plane surface is made of atoms. I would like to restrain positions between
them so they will move all togehter or create bonds between them. Would you
advise how to do this in the easiest way?
If you need to restrain positions
Dear all,
my coarse grained simulations contain a cubic box
with 16 peptides. After 85ns peptides aggregate but because of PBC I
have problem in analyzing some data like radius of gyration and
clustering. I searched mailing list to solve this problem by trjconv. I
examined its different
On 5/9/12 11:59 AM, Faezeh Kargar wrote:
Dear all,
my coarse grained simulations contain a cubic box with 16 peptides. After 85ns
peptides aggregate but because of PBC I have problem in analyzing some data like
radius of gyration and clustering. I searched mailing list to solve this problem
Dear all,
I want to calculate the ion solvation free energy (e.g. an ion
Na+ solvated in a water box) using Bennett Acceptance Ratio (BAR)
method, following the tutorial by Justin A. Lemkul. However, if I turn
off the Coulombic interaction, the total charge of my system would not
neutral at
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