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 wit
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. wrote:
> Dear GMX Users,
> My name is
Dear GMX Users,
My name is Anh Phan, a PhD student at University of Oklahoma.
I would like to calculate excess chemical potential of one gas molecule in
water solvent using Widom test particle insertion with Gromacs.
In this method, I will insert this gas molecule at a random position in each
con
test
*test*
/test/
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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
On Wed, May 16, 2012 at 10:28 AM, Javier Cerezo 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 about the
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 interpret
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 poten
On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul 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(/)"
>> @ s1 legend "f. -kT log"
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 -nx
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(/)"
@ s1 legend "f. -kT log"
@ s2 legend "f. "
@ s3 legend "f. V"
@ s4 legend "f. "
@ s5 legend "f. "
@ s6 legend
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical potential? The
tpi.xvg files consists of:
@ s0 legend "-kT log(/)"
@ s1 legend "f. -kT log"
@ s2 legend "f. "
@ s3 legend "f. V"
@ s4 legend "f. "
@ s5 legend "f. "
@ s6 legend "f. "
@ s7 legend "f. "
@ s8 legend "f. "
@
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 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 16
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
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
Wh
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
Velocities2
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
work
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 wrote:
> What's your command line?
>
> El 09
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
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 = 5000
thank you Javier, I will try both in this case.
On Wed, May 9, 2012 at 1:45 PM, Javier Cerezo 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), so velo
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, Steve
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 new
Hi everyone. I am trying to do test particle insertion in a cavity with the
tpic option. The manual says that the trajectory file should have one extra
coordinate for the cavity location. I have a trajectory from an md run that
I would like to use. How do I get the extra coordinate in there, and wh
ok
Date: Sat, 17 Dec 2011 16:33:25 +0530
From: priya.thiyagaraja...@gmail.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Test mail
Greetings, THis is a mail to test my gromacs mailing list connection
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gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman
Greetings, THis is a mail to test my gromacs mailing list connection
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscr
Could it be this:
http://www.mail-archive.com/gmx-users@gromacs.org/msg35107.html
I've posted a few times on the fact that this tool is broken for
constant pressure simulations.
I'm not sure why both even and odd would be under the overall average,
but it seems possible.
Chris.
-- origi
Hi all.
I've noticed an unexpected behaviour using g_density. I have a
trajectory (with time step 2) and it is split into two subsets (using
trjconv) with, lets say, even and odd steps respectively. According
the the algorithm I expected that the density obtained with the
original traject
My messages haven't been going through since yesterday, testing to see if this
one makes it.
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (54
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Hi,
this is a test to see whether the mailing list works.
Cheers,
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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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 inse
Hi all,
has the combination of tpi (test particle insertion) and PME (particle
mesh Ewald) already been implemented into any GROMACS version?
Eamnuel
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Please search the archive at http://www.
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.)
> Da
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 university of Technology,
Bert wrote:
Dear gmx-users,
I have done a test using test suit 4.0.4, and I got some failures as follows.
All 16 simple tests PASSED
FAILED. Check files in aminoacids
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water
Those fail frequently on normal install
Bert wrote:
Dear gmx-users,
I have done a test using test suit 4.0.4, and I got some failures as follows.
All 16 simple tests PASSED
FAILED. Check files in aminoacids
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water
4 out of 14 complex tests FAILED
Chec
Dear gmx-users,
I have done a test using test suit 4.0.4, and I got some failures as follows.
All 16 simple tests PASSED
FAILED. Check files in aminoacids
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water
4 out of 14 complex tests FAILED
FAILED. Check files in
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
ously
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
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...
> mdr
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...
> mdrun ...
Program mdrun, VE
Thanks, Justin. Then does it mean I cannot use the program to do simulation
at this point? any suggestion on it?
Johnny
Date: Fri, 08 May 2009 12:31:31 -0400
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users
Message-ID: <4a045e63.1
s can comment at this point as to the reason
for the missing energy term.
-Justin
Thanks
Johnny
Message: 1
Date: Thu, 07 May 2009 21:50:45 -0400
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users
Message-ID: <4a038ff5.3030...@vt
Vir-ZY step 50: -2207.77, step 50: -2608.41
Vir-ZZ step 50: -1482.41, step 50: -680.999
Thanks
Johnny
Message: 1
Date: Thu, 07 May 2009 21:50:45 -0400
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Test-set
To: Discussion list for GRO
Sorry, but I only performed a couple of runs using the test-set, so
don't have a lot of experience, but when I did and got some fails all
the information was there to help point out what the issue was.
Doesn't the files in the subdirectories for each of the tests provide
details of why that partic
), hardware, and
anything else necessary to diagnose the problem.
-Justin
-Johnny
Message: 1
Date: Thu, 07 May 2009 12:44:23 -0400
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users
Message-ID: <4a030fe7.2030...@vt.edu>
Content-
Vir-ZZ step 50: -1482.41, step 50: -680.999
Files read succesfully
-Johnny
Message: 1
Date: Thu, 07 May 2009 12:44:23 -0400
From: "Justin A. Lemkul"
Subject: Re: [gmx-users] Test-set
To: Discussion list for GROMACS users
Message-ID: <4a030fe7.2030...@vt
Any clues from any of the other *.out files?
-Justin
Zhanglin Ni wrote:
Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in t
Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in the energy files
Files read succesfully
"
what the problem could be. Thanks.
TECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] test molecule insertion
>
> Hi
> I have trouble inserting molecules for test particle insertion (with
> atoms there is no problem at all).
> I have defined my conf.gro, topology and index files, but it keeps
> say
Hi
I have trouble inserting molecules for test particle insertion (with
atoms there is no problem at all).
I have defined my conf.gro, topology and index files, but it keeps
saying that
"Number of atoms in trajectory (7000) is not equal the number in the run
input file (7005) minus the number o
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
___
gmx
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?
Thank you a lot,
Andrei
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Is there a test set available for Gromacs 4?
I looked here and found 3.3.2 and 3.3.3:
ftp://ftp.gromacs.org/pub/tests/
Thanks, Mike
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[EMAIL PROTECTED] wrote:
Dear gmx-users,
I just updated my operating system to Centos 5.1 and Gromacs to version
3.3.3 and faced some problems with test-set (gmxtest-3.3.2.tgz). I can
pass all the double precision tests (./gmxtest.pl -double all), but
number of single precision tests are fail
Dear gmx-users,
I just updated my operating system to Centos 5.1 and Gromacs to
version 3.3.3 and faced some problems with test-set
(gmxtest-3.3.2.tgz). I can pass all the double precision tests
(./gmxtest.pl -double all), but number of single precision tests are
failed (./gmxtest.pl all)
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