As far as I know it should not be included. Make a tpr file new .top and
input file and run the mdrun with -rerun option as described here.
http://manual.gromacs.org/online/mdp_opt.html#run;
Cheers,
Rajesh
On Thu, Jun 20, 2013 at 3:08 PM, Phan, Anh T. anhp...@ou.edu wrote:
Dear GMX Users,
Dear Anh,
You need to construct a .tpr file for the mdrun -rerun with:
- a .gro file with the ligand to be inserted at the end, which _must_ be
geometrically centered at 0,0,0 ;
- a matching .top file (which means with the ligand topology
appropriately inserted) ;
- a .mdp file
Thank you very much! I just saw your response.
As I run it in NPT ensemble the plot with volume is important for me.
Please, See the plot:
http://speedy.sh/CJn5b/tpiN.jpg
So does the fluctuating red curve make any sesnse then if it does not
consider volume?
Another thing: this is chemical
About the red curve, I guess fluctuations might be directly related to
volume fluctuations, you can extract the volume over time from g_energy
(boxXX*boxYY**boxZZ) and compare. (just another comment, now I am not
very sure about the f. that precedes the red line legend..)
About the
On Wed, May 16, 2012 at 10:28 AM, Javier Cerezo j...@um.es wrote:
About the red curve, I guess fluctuations might be directly related to
volume fluctuations, you can extract the volume over time from g_energy
(boxXX*boxYY**boxZZ) and compare. (just another comment, now I am not very
sure
Hi
Well, according to the link you pointed out, the Widom technique gives
you the excess chemical potential, as we discussed. mu and mu_ideal (in
your link) are not calculated, those are just the reference states
between which the Widom technique calculates the excess chem pot.
As I said, I
Hi Steven.
1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?
It is not not divided by nm3. The legend for y axis is not appropriate
for your plot. Keep in mind that the same graph is used to represent
lots of quantities (you can plot all of them with xmgrace -nxy
On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/14/12 11:53 AM, Steven Neumann wrote:
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical potential? The
tpi.xvg
files consists of:
@ s0 legend -kT log(Ve\S-\xb\f{}U\N/V)
@ s1 legend f.
On 5/14/12 11:53 AM, Steven Neumann wrote:
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical potential? The tpi.xvg
files consists of:
@ s0 legend -kT log(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4
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),
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
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
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
Hi,
Yes, I implemented it in git master.
Berk
From: schn...@uni-heidelberg.de
Date: Mon, 15 Mar 2010 14:52:38 +0100
To: gmx-users@gromacs.org
Subject: [gmx-users] test particle insertion with PME
Hi all,
has the combination of tpi (test particle insertion) and PME (particle
mesh
YH wrote:
Dear Dr. Saavedra,
I would like to ask your help for my use of Gromacs.
Now I run the Gromacs 4.05 on 16 node computer, but always meet the problems
like the following.
Would you please tell me how to sovle it.
Thank you very much in advanc,
James, Wang(Dr.)
Dalian
groups). This is the
reason why I wanted to use two energy groups in the test particle.
For curiosity, does Gromacs use the Cavity Insertion Widom method?
Thanks for the advice !
Harry G.
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Test Particle Insertion Problem
occurring cavities.
Berk
Date: Fri, 15 May 2009 07:50:52 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
Harry Saavedra wrote:
Dear All,
I run a test molecule insertion simulation using Gromacs 4.0.3
Harry Saavedra wrote:
Dear All,
I run a test molecule insertion simulation using Gromacs 4.0.3. All the
molecules of the system work with two energy groups (two tabulated
potentials), and every atom belongs to a different charge group; but
Gromacs shows an error message:
grompp...
Andrei Neamtu wrote:
Hello,
Where can be found more information on test particle insertion method
as implemented in gromacs? It is possible to use molecules as test
particles?
Have you search the manual? It answers your second question.
Mark
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