The other issue... I am using tables as an input in my protein coarse
grained model based on atomistic simulations. I used Boltzmann inversion
and fitted the curve into the 6th order polynomial then in angle_a*.xvg I
used -f ' (x) so the derivative of my polynomial.
My question: Do I need to use
Hi Ankita,
No, the file contains the 3Nx3N covariance matrix, row by row, split over
triplets, mass weighted if you did the analysis mass-weighted. But for
C-alpha only there is no difference between mass-weighted and
non-mass-weighted, except for global scaling.
Cheers,
Tsjerk
On Mon, Jul
Hi Tsjerk,
Thank you very much. It was extremely helpful.
Kind regards
Ankita
On Monday, July 1, 2013, Tsjerk Wassenaar wrote:
Hi Ankita,
No, the file contains the 3Nx3N covariance matrix, row by row, split over
triplets, mass weighted if you did the analysis mass-weighted. But for
If you use periodic boundary conditions, there is no need that the
protein stays at one side of the box.
For the pulling simulation: Read the chapters 6.4 (explains the
pull-code) and 7.3.21 (explains the mdp-paramters).
Additional information you an also get from Justin Tutorial for Umbrella
Thank you!
It's work. But another problem has appeared.
Apparently this is some error associated with ORCA connecting:
Back Off! I just backed up md.log to ./#md.log.5#
Reading file topol.tpr, VERSION 4.6 (single precision)
Using 1 MPI thread
QM/MM calculation requested.
Layer 0
nr of QM atoms
On 6/26/13 7:02 AM, DavidPO wrote:
Thank you!
It's work. But another problem has appeared.
Apparently this is some error associated with ORCA connecting:
Back Off! I just backed up md.log to ./#md.log.5#
Reading file topol.tpr, VERSION 4.6 (single precision)
Using 1 MPI thread
QM/MM
O'Neill, David wrote
Hello Users,
Recently I have been trying to implement the use of tabulated potentials
in GROMACS to an system of argon atoms.
I run a NVE simulation of 1000 argon atoms and then plot the potential
energy from the output.
ar.itp :
[ defaults ]
; nbfunc
Thank you both, Michael and Justin,
I have found more documentation and examples about expanded ensemble, so I
think I want to be more documented before try it. Also, I will also follow
Justin’s advice about checking the problem with my charge groups and dd
before I continue with the
Hi everybody,
My runs keep crashing despite energy minimisation and fiddling around with
nstlist values. I have been looking in the Gromacs manual particularly the
interaction ranges in the domain decomposition section, which mentions that
simulations can stop with error messages about missing
On 6/26/13 8:39 PM, Neha wrote:
Hi everybody,
My runs keep crashing despite energy minimisation and fiddling around with
nstlist values. I have been looking in the Gromacs manual particularly the
interaction ranges in the domain decomposition section, which mentions that
simulations can stop
Hi Justin,
Thank you for your answer. I’m performing several tests to see what is the
best for my system. The reason I decided not to couple the intramolecular
interactions is because I think that the annihilation of the molecule will
lead to very extreme configurations and that will affect my
Hi, Sonia-
Gromacs 4.6.2 (some bug fixes vs 4.6.1) with the example files you
point out from Alchemistry.org should work well for expanded ensemble.
David Mobley and I have been validating expanded ensemble and replica
exchange, and the files posted there now are stable for all sizes of
systems,
On 6/25/13 4:36 PM, Sonia Aguilera wrote:
Hi Justin,
Thank you for your answer. I’m performing several tests to see what is the
best for my system. The reason I decided not to couple the intramolecular
interactions is because I think that the annihilation of the molecule will
lead to very
Please keep all Gromacs-related questions on the gmx-users mailing list. I am
not a private help service.
On 6/26/13 12:05 AM, Dwey wrote:
HI Justin,
Thanks for your suggestions about GPU/CPU load imbalance.
I actually dug into Archive. It concludes that a single and faster GPU is better
I am using Red Hat Enterprise Linux 5.5
Raji
On 6/20/13 5:16 PM, gmx-users-requ...@gromacs.org
gmx-users-requ...@gromacs.org wrote:
Send gmx-users mailing list submissions to
gmx-users@gromacs.org
To subscribe or unsubscribe via the World Wide Web, visit
Yes, that command works and the entry 13 is recognized as 'SOL'
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Re-gmx-users-Digest-Vol-110-Issue-114-tp5009358p5009361.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing list
On 6/24/13 11:36 AM, raji_yu wrote:
Yes, that command works and the entry 13 is recognized as 'SOL'
OK, then you need to figure out why your shell doesn't understand the difference
between an input stream and a command, otherwise you have to do all your
selections via echo, which can be
On 6/23/13 1:13 AM, Dwey wrote:
Hi Justin,
Thank you for sharing your experience with me.
As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box
and I am able to reproduce a similar result ( DG= -9.30 kJmol-1).
Gromacs ver 4.5.5 and 4.6.2 both are compiled from source
Hi Justin,
Thank you for sharing your experience with me.
As suggested, Gromacs ver 4.5.5 is compiled within the same Linux box
and I am able to reproduce a similar result ( DG= -9.30 kJmol-1).
Gromacs ver 4.5.5 and 4.6.2 both are compiled from source codes, while
Gromacs ver 4.5.7 as
Dear Rajesh and Damas,
Thank you for your help.
I will try now.
Thanks again.
Sincerely,
Anh
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of gmx-users-requ...@gromacs.org
Sent: Thursday, June 20, 2013 10:19 PM
To:
Justin Lemkul wrote
What was the outcome of EM before this? What if you try NVT before NPT?
Have
you tried reducing the timestep or the value of nstlist?
I would try everything with ref_p = 1.0 instead of zero to make sure you
can get
a normal setup to work.
-Justin
The membrane
Hello.
I followed your advice and tried different versions of GROMACS (4.5.6,
4.6.2). All of them give one and the same error:
Program mdrun, VERSION 4.5.6 (or 4.6.2)
Source code file: /home/timofeev/GROMACS/gromacs-4.5.6/src/mdlib/qmmm.c,
line: 710
Fatal error:
Ab-initio calculation only
On 6/18/13 10:12 PM, Neha wrote:
Hi,
Well, I tried running a simulation at ref_p to 1.0 and got the same error as
earlier, so it doesn't seem to be that. That was the only thing I changed in
the mdp file, so I am still not sure as to where the problem is.
Please post a full .mdp file;
On 6/19/13 6:11 AM, DavidPO wrote:
Hello.
I followed your advice and tried different versions of GROMACS (4.5.6,
4.6.2). All of them give one and the same error:
OK, good to know.
Program mdrun, VERSION 4.5.6 (or 4.6.2)
Source code file:
On 6/19/13 6:11 AM, DavidPO wrote:
Hello.
I followed your advice and tried different versions of GROMACS (4.5.6,
4.6.2). All of them give one and the same error:
Program mdrun, VERSION 4.5.6 (or 4.6.2)
Source code file: /home/timofeev/GROMACS/gromacs-4.5.6/src/mdlib/qmmm.c,
line: 710
Fatal
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit= 0.0
dt = 0.02
nsteps =
On 6/19/13 9:25 AM, Neha wrote:
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit= 0.0
dt =
Please keep the discussion on the gmx-users mailing list.
On 6/19/13 12:14 PM, Raji Viswanathan wrote:
Dear Justin,
Thanks for your response regarding running demo with gromacs. Do I need to have
ngmx installed or can I use most functionalities of gromacs without installing
gromacs?
I
On 19.06.2013 15:25, Neha wrote:
Here's the full mdp file. Please let me know if you need anymore information
and thank you so much for helping!
dt = 0.02
Should be 0.03 according to S. Marrinks own remarks
(but wouldn't change your experience)
nstcomm
Addendum:
On 19.06.2013 23:16, Mirco Wahab wrote:
...
MARTINI W is a strongly associating fluid and will freeze
trough your box in no time even when setting negative pressure
below 300K. In newer Gromacs versions (from 4.6) there seems
to be additional shift (?) in the potential, so the water
Dear Szilard,
Thanks for your message. Your help is priceless and helps advance science more
than many publications. I extend that to many experts who kindly and promptly
answer questions in the mailing list. I wish that could be valued when
evaluating a CV. Sorry for the digression...
The
it sends back a fatal error if you don't put in a tp file.
I'm more than happy to send in a tpr file, I just need to figure out how to
generate it.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/g-sas-on-pdb-files-tp5009248p5009250.html
Sent from the GROMACS Users Forum
On 6/18/13 8:22 AM, erin.cutts wrote:
it sends back a fatal error if you don't put in a tp file.
I'm more than happy to send in a tpr file, I just need to figure out how to
generate it.
Refer to any tutorial. A .tpr file is a run input file that Gromacs uses for a
simulation.
-Justin
Hi everybody,
It seems that my runs still are crashing. I even decided not to switch over
to Parinello-Rahman and continue doing the simulation with a Berendsen
barostat and it shuts off after a period of time. I am extremely puzzled as
to why this is happening especially since Berendsen is
Hi,
Well, I tried running a simulation at ref_p to 1.0 and got the same error as
earlier, so it doesn't seem to be that. That was the only thing I changed in
the mdp file, so I am still not sure as to where the problem is.
Justin Lemkul wrote
On 6/18/13 3:13 PM, Neha wrote:
Hi everybody!
I
Hi, Tsjerk
You asked me a good question.
Ya, sometime it accords my imagination to tell if it right or not. That's
not the correct way.
Maybe it near boundary, like at the boundary of dangerous. So let me have
such question.
maggin
--
View this message in context:
Hi,Tsjerk,
Oh, that's it !
Thank you very much for your kind help!
maggin
--
View this message in context:
http://gromacs.5086.x6.nabble.com/a-snapshot-of-NVT-tp5009206p5009211.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing list
On Jun 17, 2013 5:50 AM, maggin maggin.c...@gmail.com wrote:
Hi, Alaina
Before you install GMX4.5.5, did you install cmake-2.8.8 and fftw-3.3.2 ?
Installing cmake for an autotools build isn't going to help ;-)
Mark
maggin
--
View this message in context:
On Mon, Jun 17, 2013 at 8:12 AM, maggin maggin.c...@gmail.com wrote:
Hi, Tsjerk
You asked me a good question.
Ya, sometime it accords my imagination to tell if it right or not. That's
not the correct way.
Maybe it near boundary, like at the boundary of dangerous. So let me have
such
...@gmail.com
Date: 17/06/2013 04:50 (GMT+00:00)
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: Gromacs 4.5.5
Hi, Alaina
Before you install GMX4.5.5, did you install cmake-2.8.8 and fftw-3.3.2 ?
maggin
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Gromacs-4-5-5
for GROMACS users gmx-users@gromacs.org
Subject: Re: [gmx-users] Re: Gromacs 4.5.5
Hello Maggin,
I re-installed both cmake and fftw. Now I no longer have an output from grep
-i error make. log. However I still can't get past the same stage in Making
all in man 7.
Sent from my Ultrafast
Hello, Justin.
I try to find information about it, but all examples is old and there is
nothing about it in new manuals.
I will be very grateful if you describe me a procedure of connecting orca
library to mdrun.
David
--
View this message in context:
On 6/17/13 7:16 AM, DavidPO wrote:
Hello, Justin.
I try to find information about it, but all examples is old and there is
nothing about it in new manuals.
I will be very grateful if you describe me a procedure of connecting orca
library to mdrun.
At this point, you don't need a tutorial
+0200
From: Mark Abraham mark.j.abra...@gmail.com
Subject: Re: [gmx-users] RE: Re: RE: About the binary identical
results by restarting from the checkpoint file
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
camnumaqbjd5lvcroybd4-qf04p4dn+wdpabnbdv4ge
On 6/17/13 4:13 PM, Dariush Mohammadyani wrote:
Dear Justin,
I have sent a post on GROMACS-user and did not get any answer.
Could you please help me out to find the answer?
I did not see the original post, but that doesn't really matter. Please keep
all Gromacs-related questions on the
Hi, Justin
the structure of 19532ps shows as
http://gromacs.5086.x6.nabble.com/file/n5009235/aa2.png
the structure of md_0_1 shows as
http://gromacs.5086.x6.nabble.com/file/n5009235/cc.png
So, how can I fix the structure of 19532ps like md_0_1 ?
Thank you very much!
maggin
--
View
On 6/17/13 9:59 PM, maggin wrote:
Hi, Justin
the structure of 19532ps shows as
http://gromacs.5086.x6.nabble.com/file/n5009235/aa2.png
the structure of md_0_1 shows as
http://gromacs.5086.x6.nabble.com/file/n5009235/cc.png
So, how can I fix the structure of 19532ps like md_0_1 ?
As I
Hi, Justin,
use:
trjconv -dump 19532 -pbc nojump -s md_0_1.tpr -f md_0_1.xtc
get:
http://gromacs.5086.x6.nabble.com/file/n5009238/dd.png
Thank you veru much!
maggin
--
View this message in context:
Hi, Alaina
Before you install GMX4.5.5, did you install cmake-2.8.8 and fftw-3.3.2 ?
maggin
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Gromacs-4-5-5-tp5009198p5009203.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing
Subject: Re: [gmx-users] RE: About the binary identical results by
restarting from the checkpoint file
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
CAMNuMARBEZ=m=Y_M1=c5pzncgwv438mveydosf56r6ytc68...@mail.gmail.com
Content-Type: text/plain; charset=ISO
-users] RE: About the binary identical results by
restarting from the checkpoint file
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
CAMNuMARBEZ=m=Y_M1=
c5pzncgwv438mveydosf56r6ytc68...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Hi, Tsjerk,
I have one question that in what situation people do constraint ?
Thank you very much!
maggin
--
View this message in context:
http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009144.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
Hi Maggin,
The constraints are typically used during MD simulation to allow larger
time steps.
Cheers,
Tsjerk
On Fri, Jun 14, 2013 at 9:39 AM, maggin maggin.c...@gmail.com wrote:
Hi, Tsjerk,
I have one question that in what situation people do constraint ?
Thank you very much!
maggin
On Fri, Jun 14, 2013 at 12:52 AM, Cuiying Jian cuiying_j...@hotmail.comwrote:
Hi GROMACS Users,
I am sorry if you are bothered by my second post about this topic. But the
fact is that I tested restarting simulations with .cpt files by GROMACS
4.6.1. and I still cannot get binary identical
Hi, Tsjerk,
Oh, so that's it . Thank you very much!
maggin
--
View this message in context:
http://gromacs.5086.x6.nabble.com/distance-restraints-tp5008938p5009146.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
Hi, Justin,
At md step, protein run out of box, if it will better that set position
constraint, let protein at center of box?
Thank you very much!
maggin
--
View this message in context:
http://gromacs.5086.x6.nabble.com/refcoord-scaling-com-tp5009141p5009150.html
Sent from the GROMACS
Hi, Justin,
Thank you very much for your help!
Another question is when we do steep minimization, if it will be better
first do steep with constraint, then do steep without constraint?
Thank you very much!
maggin
--
View this message in context:
Constraints make the job of the minimizer more difficult. If the starting
configuration is bad enough that the EM step might be really useful, give
the potential energy surface a free run without constraints. And then in
such cases do a preliminary NVT with dt=0.0005 and no constraints to get
Hi, Justin,
If I use Pymol to set up a mutation of 1dx0.pdb, If it best do Steepest
Descents in vacuo first ?
Thank you very much!
maggin
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Steepest-Descents-in-vacuo-tp5009143p5009153.html
Sent from the GROMACS Users Forum
HI Maggin,
The Pressure came from NPT simulation, I apologize for the lack of
annotation. Here are some of the outputs of your suggested checks of
equilibrium
https://docs.google.com/spreadsheet/ccc?key=0Ao2bINpUakZ-dHpiZG9SOXhkX0JGNXlqTHBfQ1kwbncusp=sharing
I'm currently looking into the rvdw
On 6/14/13 6:33 AM, maggin wrote:
Hi, Justin,
At md step, protein run out of box, if it will better that set position
constraint, let protein at center of box?
There is no such thing as outside of an infinite system using periodic
boundary conditions.
On 6/14/13 7:22 AM, maggin wrote:
Hi, Justin,
If I use Pymol to set up a mutation of 1dx0.pdb, If it best do Steepest
Descents in vacuo first ?
I have no idea. There are many ways you can probably dream up to proceed with
any system. For normal proteins in water, I never waste time with
On 6/14/13 10:45 AM, Parker de Waal wrote:
HI Maggin,
The Pressure came from NPT simulation, I apologize for the lack of
annotation. Here are some of the outputs of your suggested checks of
equilibrium
Hi Mark,
Sorry for my carelessness. I check my email again and see your reply. I get
your point that my problem may be (at least part of) caused by RNG of the
thermostat.
Thanks again and sorry for my careless bothering.
Cheers,
Cuiying
On Fri, Jun 14, 2013 at 12:52 AM, Cuiying
or should i be doing U+V*ref_p = H?
More specifically, U + V*ref_p = H
H isn't really meaningful thing. I mean, you can define something
such that H* = H, but that's not really thermodynamics.
sorry I always have issues deciding how to talk about this stuff, so
thanks
for
On 2013-06-14 19:28, Jeffery Perkins wrote:
or should i be doing U+V*ref_p = H?
More specifically, U + V*ref_p = H
H isn't really meaningful thing. I mean, you can define something
such that H* = H, but that's not really thermodynamics.
sorry I always have issues deciding how to talk
Your calculation seems correct. Which gmx version did you use?
The correlation between the numbers is almost 100% so there must be a
simple explanation.
gmx version is 4.5.4, and yeah the correlation is odd, in the code you
listed:
pv = vol*md-ref_p/PRESFAC;
Thanks Justin!
I've updated the values accordingly. However can I ask where you found
these? I'm curious if there is a site that I missed while searching.
Best,
Parker
On Fri, Jun 14, 2013 at 12:04 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/14/13 10:45 AM, Parker de Waal wrote:
HI
On 6/14/13 7:03 PM, Parker de Waal wrote:
Thanks Justin!
I've updated the values accordingly. However can I ask where you found
these? I'm curious if there is a site that I missed while searching.
Cutoff values are described in the primary literature for the force field of
interest.
On 2013-06-14 21:39, Jeffery Perkins wrote:
Your calculation seems correct. Which gmx version did you use?
The correlation between the numbers is almost 100% so there must be a
simple explanation.
gmx version is 4.5.4, and yeah the correlation is odd, in the code you
listed:
Then that is the
Hi, Justin,
I use Pymol to align the NMR structure and the structure after steep
minimization, find problematic areas are superposition very well, while all
the problematic areas have same character, that after steep minimization,
Amino acid will lose some H atoms connect with C
Hi, Justin,
It's seems no problem at steep energy minimization, except lose H atoms
connect with C, the superposition are very well.
When I use Pymol to align the NMR structure and the structure after cg
minimization, because cg is after steep, so same as steep, they lose H atoms
that connect
Hi Maggin,
Why do you run EM with constraints?
Cheers,
Tsjerk
On Thu, Jun 13, 2013 at 10:53 AM, maggin maggin.c...@gmail.com wrote:
Hi, Justin,
It's seems no problem at steep energy minimization, except lose H atoms
connect with C, the superposition are very well.
When I use Pymol to
Hi, Tsjerk
I want equlibration enough time, so set NVT time 10ns , but simulation
collapse at 7ns, protein have 7 fragments. Before NVT, I just do one time of
steep energy minimization.
So, I want first use constraint do steep, cg in vacuum, then add water, do
steep, cg with constraint, then
Hi GROMACS Users,
I am sorry if you are bothered by my second post about this topic. But the fact
is that I tested restarting simulations with .cpt files by GROMACS 4.6.1. and
I still cannot get binary identical results from restarted simulations with
those from continuous simulations. The
On 6/12/13 12:10 AM, maggin wrote:
Hi, Justin,
You are right, I should first fix the bad geometry.
I check 1dx0.pdb, and the problematic areas are:
atom1 atom2
1 N1+ (GLY124 N) 4 H (GLY124 HT3)
181 C (PRO137 CD)182 H
On Wed, Jun 12, 2013 at 12:42 AM, sirishkaushik kaushik.lakkar...@gmail.com
wrote:
Note that this works fine with 4.5.5.
when I installed using:
./configure CPPFLAGS=-I/home/kaushik/fftw-new/include
LDFLAGS=-L/home/kaushik/fftw-new/lib --enable-mpi --prefix
Thanks Justin and Professor Shirts. The gmxdump on the resulting tpr did
indeed solve a lot of my problems. Thanks again.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/Free-Energy-Calculations-in-Gromacs-tp5007495p5009115.html
Sent from the GROMACS Users Forum mailing
Hi,
Please see the following links:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/
http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS66.html
I think you will understand the concept of the pulling force once you go
through either of the links.
It's
On 2013-06-11 23:31, Jeffery Perkins wrote:
or should i be doing U+V*ref_p = H?
More specifically, U + V*ref_p = H
H isn't really meaningful thing. I mean, you can define something
such that H* = H, but that's not really thermodynamics.
sorry I always have issues deciding how to talk
Thank JW so much :-)
On Wed, Jun 12, 2013 at 10:30 PM, JW Gibbs hanniballecte...@gmail.comwrote:
Hi,
Please see the following links:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/
http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WCMS66.html
I think
Hi,
As Justin had already suggested, restraints will lead to nasty atomic
clashes. Looking at the gro file you have provided, it seems that the system
is very poorly equilibrated.
I had a similar issue. If the forcefield you are using is accurate enough,
follow the steps as follows:
1. Take
On 6/11/13 9:38 AM, JW Gibbs wrote:
Hi,
As Justin had already suggested, restraints will lead to nasty atomic
clashes. Looking at the gro file you have provided, it seems that the system
is very poorly equilibrated.
I had a similar issue. If the forcefield you are using is accurate enough,
Hi everybody,
Thank you so much for taking the time to read this.
I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface
tension. How else could I get a tensionless membrane?
As for the generating velocities, I completely forgot that would ruin the
equilibrium. Would you
Exactly so. I think Gromacs issues a warning when you try to initialize
velocities with Parrinello-Rahman barostat. But if you performed your
equilibration at 105K using Berendsen barostat, I think it should be okay
and you should put gen-vel = no.
--
View this message in context:
On 6/11/13 1:25 PM, Neha wrote:
Hi everybody,
Thank you so much for taking the time to read this.
I thought ref_p would need to be 0.0 and 0.0 if I wanted zero surface
tension. How else could I get a tensionless membrane?
As far as I understand, surface tension is only applied when using
Is there a reason you would like to keep it at 105K? Just curious which
forcefield are you using?
Also, for proper surface tension, there is an option called
pcoupltype = surface-tension.
I think you should check that out.
--
View this message in context:
Hi,
I am using the Martini field for those who wanted to know.
My values for the mdp file for ref_p were inspired from this paper as it
says pressure was coupled anisotropically to 0 bar in all directions.
http://www.sciencedirect.com/science/article/pii/S0005273611002045
I think I will try
that's what i thought, and what i tried to do, my pressure is a bit higher
then that, we want a Lennard-Jones liquid so it's running at 1000+ bar, and
while I agree that gromacs is giving H as Etot + pV it appears that when i
calculate pV i get a different value from what g_energy returns for it I
If you are computing enthaply in the NPT ensemble, P is constant, and
is the applied pressure.
The pressure quantity calculated from the KE and the virial is not
the pressure. It is a quantity that when averaged over time is equal
the pressure. Only the average is meaningful macroscopically.
If you are computing enthaply in the NPT ensemble, P is constant, and
is the applied pressure.
The pressure quantity calculated from the KE and the virial is not
the pressure. It is a quantity that when averaged over time is equal
the pressure. Only the average is meaningful
On 2013-06-11 21:57, Jeffery Perkins wrote:
If you are computing enthaply in the NPT ensemble, P is constant, and
is the applied pressure.
The pressure quantity calculated from the KE and the virial is not
the pressure. It is a quantity that when averaged over time is equal
the pressure.
You should not use pV from g_energy though, as Michael explained, rather
you need ref_p times V. This precludes that your system is in
equilibrium of course.
That is what I had initially thought, then take that with the U to get
H?
or should i be doing U+V*ref_p = H?
But even so I still get
or should i be doing U+V*ref_p = H?
More specifically, U + V*ref_p = H
H isn't really meaningful thing. I mean, you can define something
such that H* = H, but that's not really thermodynamics.
example system gives H = -1168 kJ/mol and i find H = -725 kJ/mol either
Interesting. What
Hi Amil,
On Mon, Jun 10, 2013 at 11:03 PM, Amil Anderson
aander...@wittenberg.edu wrote:
Szilárd,
I tried the build using a PATH without the Intel compilers and NOT including
the directives -DGMX_EXTERNAL_BLAS=OFF and -DGMX_EXTERNAL_LAPACK=OFF and it
used the FFTW 3.2 wrappers to MKL.
or should i be doing U+V*ref_p = H?
More specifically, U + V*ref_p = H
H isn't really meaningful thing. I mean, you can define something
such that H* = H, but that's not really thermodynamics.
sorry I always have issues deciding how to talk about this stuff, so thanks
for putting up
Note that this works fine with 4.5.5.
when I installed using:
./configure CPPFLAGS=-I/home/kaushik/fftw-new/include
LDFLAGS=-L/home/kaushik/fftw-new/lib --enable-mpi --prefix
/home/kaushik/gromacs_executable/gromacs-old
ldd mdrun on the 4.5.5 version correctly points to the fftw and the mpi
OK I found the problem. I had installed Surfnet the protein cavity finder a
few weeks ago, and it turns out this also has a function called genbox! so
my silly mistake.
I was wondering why centre and not center.
Thanks,
Matt
On Mon, Jun 10, 2013 at 6:23 PM, Justin Lemkul [via GROMACS]
Hi, Justin,
You are right, I should first fix the bad geometry.
I check 1dx0.pdb, and the problematic areas are:
atom1 atom2
1 N1+ (GLY124 N) 4 H (GLY124 HT3)
181 C (PRO137 CD)182 H (PRO137 HD1)
262 H
Roland,
Here is the output from the debug run with the stack trace:
[aanderson@warp2-login gmxdemo]$ gdb mdrun
GNU gdb Fedora (6.8-27.el5)
Copyright (C) 2008 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html
This is free software: you are
501 - 600 of 6386 matches
Mail list logo
