Hi Thanasis, Chris,
I read the first while there was only one :p I agree that most people
(including me) will not readily go through eight lengthy posts as an
introduction to an issue. But the issue raised does seem in need of
attention. Not mine though :p
Also, the stream-of-consciousness approac
remember to change the
pbc = xyz from pbc = no.
lina
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Tsjerk Wassenaar [tsje...@gmail.com]
Sent: Tuesday, June 22, 2010 12:04 PM
To: Discussion list for GROMACS
Hi Nayef,
Can you
- copy-paste the sequence of commands as you have typed them in (not
as you think you typed them in or as they're given in the tutorial)
- provide the output of 'tail 1qlz-water.gro'
Cheers,
Tsjerk
On Mon, Jun 21, 2010 at 9:49 PM, Nayef Daher wrote:
> Hi,
>
> I have the same
Take that replica on the left that shows a bimodal histogram. Now plot
a time series of the displacement: x-axis = time and y-axis =
displacement along reaction coord. Is it jumping back and forth
between two regions of sampling? Probably not... more likely it starts
near one maximum and tr
I am doing US . Yes, histograms of population densities along the reaction
coordinate. Please find the pull settings. Sampled for 800ps.(nsteps =
40). Pull_init will vary for each frame, depends on the window spacing.
pull = umbrella
pull_geometry= position
pull
Hi,
I am reconstructing atomic details from coarse-grained MD structure using
gromacs-reverse.
I am following reverse transform tutorial at MARTINI Website and also this paper
http://www3.interscience.wiley.com/cgi-bin/fulltext/123244279/HTMLSTART
I am unable to find g_dihfix program to restra
Moeed wrote:
Hello Justin,
As you pointed out at the end of former message my real problem is
generation of a properly formatted structure file for PE. Within last
few weeks I tried to obtain the structure file using that known link...
but that was not helpful to me since those residues ne
Hello Justin,
As you pointed out at the end of former message my real problem is
generation of a properly formatted structure file for PE. Within last few
weeks I tried to obtain the structure file using that known link... but that
was not helpful to me since those residues need atom numbering..Hd
Hi,
I have the same problem as listed below back in February. I am using
the latest gromacs version (4.0.7) and tried the solution below by
entering
genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro
instead of making the output as pdb file. Yet the same result occurs
w
munu...@yahoo.com wrote:
Hi
I want to add acetyl group at the N and C terminal of my protein.
i.e. CH3-C=O NH QQQ NH CH3 by removing the NH3+ and COO- at the N and C
terminal.
Please suggest what steps I have to follow.
There are no programs in Gromacs that will do that. You may find s
Hi
I want to add acetyl group at the N and C terminal of my protein.
i.e. CH3-C=O NH QQQ NH CH3 by removing the NH3+ and COO- at the N and C
terminal.
Please suggest what steps I have to follow.
regards
M. Baskar
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.
You're right, although I did not realize this at first. I got confused
(again) by the global numbering. Regarding the off-by-one numbering, I
can figure out what is meant there and that was not really my question.
Thanks Berk, and sorry for the confusion.
Chris.
I coded this and I looked a
Hi,
I coded this and I looked at the code again.
pbcatom is always the global, system wide atom number.
But it seems that mdrun forgets to add one to the atom number
or maybe this is part of the mdrun output scheme of starting numbering at 0.
We would have to check this.
As far as I can see that
Dear Gromacs user,
Still another problem...
How can I manage the mutation upon a Trp?
The mutation ALA-GLY does not cause any problem but the trasformation
TRP-ALA seems uneasy.
The Segmentation Fault error occurs suddenly I try to run the mdrun
with lambda=1, with lambda=0.99 it take 6 step bef
Please clarify:
Are doing SMD or are you doing US? If you're doing SMD then you should
not be using WHAM and you should not really be able to generate any
sampling histograms.
Are the histograms that you are referring to population densities of
the sampling along your reaction coordinate?
Dear Thanasis:
8 posts on the same topic? I didn't even read them. If you want some
help, I'd suggest that you start with a new subject line and post a
single email containing all relevant information.
You can see how it looks at the bottom of this list:
http://lists.gromacs.org/pipermail
Thanks, Justin. I appreciate this. I will go with the first option of creating
a *.rtp file and manually change the subsequent *.top file to put in the morse
potential.
Thanks again.
o.
--- On Mon, 6/21/10, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] Help with de
Omololu Akin-Ojo wrote:
Hi,
I obtained parameters for a Morse potential between Oxygen molecule and
Iron in heme (from ab initio calculations). How can I use this
potential with the GROMOS96 parameters?
I thought of a couple of options:
1) Define a new residue -- OXYHEM using the same pa
Hi,
I obtained parameters for a Morse potential between Oxygen molecule and Iron in
heme (from ab initio calculations). How can I use this potential with the
GROMOS96 parameters?
I thought of a couple of options:
1) Define a new residue -- OXYHEM using the same parameters for HEME as in
ffG4
Amin,
the -np flag is not necessary any more for grompp in Gromacs 4.0.
For mdrun, just use something like
mpirun -np 4 mdrun -s topol.tpr
Carsten
On Jun 21, 2010, at 2:00 PM, Amin Arabbagheri wrote:
> Hi all,
>
> I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package
>
Use grompp normally, without the -np flag. Then run mdrun_mpi with your
normal parameters as mpirun -np x mdrun_mpi -deffnm xx
On Mon, Jun 21, 2010 at 2:00 PM, Amin Arabbagheri wrote:
> Hi all,
>
> I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic
> package manager.
> I want to
Amin Arabbagheri wrote:
Hi all,
I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic
package manager.
I want to run a simulation in parallel on a multi processor, single PC,
but to compile via grompp, it doesn't accept -np flag, and also , using
-np in mdrun, it still runs a
Hi all,
I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package
manager.
I want to run a simulation in parallel on a multi processor, single PC, but to
compile via grompp, it doesn't accept -np flag, and also , using -np in mdrun,
it still runs as a single job.
Thanks a lot
hi gmx-users
sorry for this pack of emails. the page has not a good format. you can find my
text included to this email.
thanks
hi gmx-users
In order to discover the miscalculation that gromacs computes in a system of
450 molecules in vacuum and after a gmx-user guidance i ran a simulation of o
2) deleting the [pairs] and all the lines below
I)from md.log
Step Time Lambda 0 0.0 0.0
Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.:
Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol)
3) deleting only the last line of the [pairs]
I)from md.log
Step Time Lambda 0 0.0 0.0
Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.:
Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol)
A
1)leaving the top file as it is above
I)from md.log
Step Time Lambda 0 0.0 0.0
Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.:
Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol)
Angle Ryc
hi gmx-users
In order to discover the miscalculation that gromacs computes in a system of
450 molecules in vacuum and after a gmx-user guidance i ran a simulation of one
molecule in vacuum just to calculate by hand all the energies. the mdp file
that i use is
; VARIOUS PREPROCESSING OPTIONStitl
3) deleting only the last line of the [pairs]
I)from md.log
Step Time Lambda 0 0.0 0.0
Grid: 3 x 3 x 3 cellsLong Range LJ corr.: 3.8522e-03Long Range LJ corr.:
Epot -0.00732091, Pres: -0.00379895, Vir: 0.00732091 Energies (kJ/mol)
i did three simulations
1) leaving the top file as it is above2) deleting the [pairs] and all the
lines below3) deleting only the last line of the [pairs]
the results with usage of the command gmxdump -s topol.tpr | lessfor step 0 are
below
1)leaving the top file as it is above
I)from md.log
Ste
hi gmx-users
In order to discover the miscalculation that gromacs computes in a system of
450 molecules in vacuum and after a gmx-user guidance i ran a simulation of one
molecule in vacuum just to calculate by hand all the energies. the mdp file
that i use is
; VARIOUS PREPROCESSING OPTIONStitl
Hi Friends,
When i did the Umbrella sampling of frames from an SMD (of ligand
transport), I am getting bimodal histograms in some cases.
Do you think this is because , the force constant that i used is very low (i
used pull_k1=1000).? Are these bimodal peaks may cause any deviation in my
PMF resu
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