If the two end states of a system are fixed, the free energy difference is
independent of the path. I am not sure what caused the problem, but if besides
the protein, water and ions, there are some other molecules in your simulation
box (e.g., membrane or ligand), the states A and B of your
You are right, I am not expecting to get exactly the same PMF for
trajectory A --B and B --A.
But I do expect to get at least the same trend for the end states of the
trajectory.
On Thu, Nov 15, 2012 at 10:22 AM, Jianguo Li ljg...@yahoo.com.sg wrote:
If the two end states of a system are fixed,
Hi,
CHARMM22star FF is a fork of CHARMM27 ff for proteins with several changes in
some diedral parameters. It should be compatible with the others CHARMM
parameters for biomolecules.
Stephane --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
All,
I would like to parameterise the Dreiding force field for use with Gromacs. One
thing I am not sure about is how to parameterise the dihedrals
The Dreiding paper has the form;
E= 0.5k { 1 - cos[ n( phi - phi_o)]}
However I cannot find this form in the Gromacs manual. The closest I can
You could shift the reference angle by pi, which changes the sign of the cosine.
Best,
Erik
15 nov 2012 kl. 14.25 skrev Laura Leay:
All,
I would like to parameterise the Dreiding force field for use with Gromacs.
One thing I am not sure about is how to parameterise the dihedrals
The
On 11/15/12 8:41 AM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to run simulations of protein and FE(2+) atoms. I placed
them randomly around the protein, solvated the system and tried to
minimize. After grompp, I tried mdrun:
Stepsize too small, or no change in energy.
Converged to
On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 8:41 AM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to run simulations of protein and FE(2+) atoms. I placed
them randomly around the protein, solvated the system and tried to
minimize. After grompp,
On 11/15/12 9:03 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 8:41 AM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to run simulations of protein and FE(2+) atoms. I placed
them randomly around the protein, solvated the
I will. Thank you.
Steven
On Thu, Nov 15, 2012 at 2:30 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 9:03 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 8:41 AM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to
Thanks Eric,
Just to clarify (I hope this notation is in fact clear):
E=0.5k [ 1 - cos( n*phi - n*phi_o +180 ) ] = 0.5k [ 1 + cos(n*phi - n*phi_o)]
^ this whole equation is Dreiding ^this whole equation is
Dreiding converted to the form in Gromacs
This would mean that:
You'll have to find the authors of it and read what they wrote about it.
Mark
On Wed, Nov 14, 2012 at 7:38 PM, Albert mailmd2...@gmail.com wrote:
hello:
I found that there is a CHARMM22star FF in Gromacs website, it is said
was developed by Deshaw group instead of the one in Maryland. I am
On 11/15/12 9:47 AM, rama david wrote:
Hi Gromacs Friends,
I want to do the simulation of system containing the
biotin.
I know that the charge calculated by prodrg is not good.
I want to use the GROMOS96 53a6 force field or OPLS force field.
( 1st choice is GROMOS second
On 11/15/12 9:49 AM, Rajiv Gandhi wrote:
Hello gmx users,
I have created the topology file for my ligand through PRODRG, protein from
pdb2gmx. when i try to energy minimize the protein with ligand system it
gives error that
Atoms in the .top are not numbered consecutively from 1.
Could you
On 11/15/12 9:53 AM, Thomas Evangelidis wrote:
Hi Szilárd,
This is the warning message I get this time:
WARNING: Oversubscribing the available -66 logical CPU cores with 1
thread-MPI threads.
This will cause considerable performance loss!
I have also attached the md.log file.
On Thu, Nov 15, 2012 at 2:35 PM, Steven Neumann s.neuman...@gmail.com wrote:
I will. Thank you.
Steven
On Thu, Nov 15, 2012 at 2:30 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 9:03 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 9:57 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 2:35 PM, Steven Neumann s.neuman...@gmail.com wrote:
I will. Thank you.
Steven
On Thu, Nov 15, 2012 at 2:30 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 9:03 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at
Hi,
15 nov 2012 kl. 15.41 skrev Laura Leay:
Thanks Eric,
Just to clarify (I hope this notation is in fact clear):
E=0.5k [ 1 - cos( n*phi - n*phi_o +180 ) ] = 0.5k [ 1 + cos(n*phi - n*phi_o)]
^ this whole equation is Dreiding ^this whole equation is
Dreiding
:
On Thu, Nov 15, 2012 at 2:58 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 9:57 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 2:35 PM, Steven Neumann s.neuman...@gmail.com
wrote:
I will. Thank you.
Steven
On Thu, Nov 15, 2012 at 2:30 PM, Justin Lemkul
I tried both options and now different atom is responsible of this
(Oxygen from small molecule next to Fe). With nstxout = 1 I observed
the trajectory - My Fe(2+) is coming very close to the Oxygen atom
and it looks that their coordinate became equal: in VMD Oxygen absorbs
Fe(2+) and the atom
On 11/15/12 10:26 AM, Steven Neumann wrote:
I tried both options and now different atom is responsible of this
(Oxygen from small molecule next to Fe). With nstxout = 1 I observed
the trajectory - My Fe(2+) is coming very close to the Oxygen atom
and it looks that their coordinate became
Please, see final coordinates.
94LIG O1 787 0.482 5.056 3.507
94LIG FE 805 0.432 5.011 3.039
How is that possible?
On Thu, Nov 15, 2012 at 3:26 PM, Steven Neumann s.neuman...@gmail.com wrote:
I tried both options and now different atom is responsible of this
(Oxygen
On 11/15/12 10:29 AM, Steven Neumann wrote:
Please, see final coordinates.
94LIG O1 787 0.482 5.056 3.507
94LIG FE 805 0.432 5.011 3.039
How is that possible?
Please see my previous post and answer the question regarding the source of your
Fe parameters.
atomtypes.atp
FE 55.84700 ; heme iron 56
ffnonbonded
FE 9 18.9980.000 A 0.115816833358244 -0
aminoacids.rtp
[ FE ]
[ atoms ]
FE FE 2.000
H, confusing...
On Thu, Nov 15, 2012 at 3:29 PM, Steven Neumann s.neuman...@gmail.com wrote:
On 11/15/12 10:41 AM, Steven Neumann wrote:
atomtypes.atp
FE 55.84700 ; heme iron 56
ffnonbonded
FE 9 18.9980.000 A 0.115816833358244 -0
aminoacids.rtp
[ FE ]
[ atoms ]
FE FE 2.000
H, confusing...
What force field is that?
On Thu, Nov 15, 2012 at 3:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 10:41 AM, Steven Neumann wrote:
atomtypes.atp
FE 55.84700 ; heme iron 56
ffnonbonded
FE 9 18.9980.000 A 0.115816833358244 -0
aminoacids.rtp
[ FE ]
[ atoms ]
FE
On 11/15/12 10:55 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 3:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 10:41 AM, Steven Neumann wrote:
atomtypes.atp
FE 55.84700 ; heme iron 56
ffnonbonded
FE 9 18.9980.000 A 0.115816833358244 -0
On Thu, Nov 15, 2012 at 4:03 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 10:55 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 3:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 10:41 AM, Steven Neumann wrote:
atomtypes.atp
FE 55.84700 ; heme iron 56
I found something in ffnonbonded in OPLSAA ff
; These ion atomtypes are NOT part of OPLS, but since they are
; needed for some proteins or tutorial Argon simulations we have added them.
Cu2+ Cu2+ 29 63.54600 2.000 A2.08470e-01 4.76976e+00
Fe2+ Fe2+ 26 55.84700
On 11/15/12 12:18 PM, Steven Neumann wrote:
Dear Gmx Users,
Maybe someone before was simulating Fe(2+) in water and protein system
using Charmm27 ff. I am looking for nonbonded parametrs. I found in
OPLSAA:
; These ion atomtypes are NOT part of OPLS, but since they are
; needed for some
On 11/15/12 11:34 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 4:03 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 10:55 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 3:47 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 10:41 AM, Steven Neumann wrote:
So what would you do to get those parameters asap?
On Thu, Nov 15, 2012 at 5:19 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/15/12 12:18 PM, Steven Neumann wrote:
Dear Gmx Users,
Maybe someone before was simulating Fe(2+) in water and protein system
using Charmm27 ff. I am looking for
On 11/15/12 12:47 PM, Steven Neumann wrote:
So what would you do to get those parameters asap?
Get what parameters? The ones shown below (except Cu2+) have no citation and no
one has vouched for their authenticity. As such, the decision was made to
delete them to prevent anyone from
Dear Gromacs users,
I tried g_rdf function and have obtained a strange result:
usually the RDF curve looks like relaxing oscillations around 1.0 constant
level,
but in my case it appears to be oscillation around exponent going from 0.0
at zero distance to 1.0 at large distances.
Is the RDF
Hi Justin thank you,
The ATB server link for Biotin are as follow..
http://compbio.biosci.uq.edu.au/atb/download.py?molid=5783
compbio.biosci.uq.edu.au/atb/download.py?molid=2212
Now should I need to do QM calculations, free energy simulations, and
empirical refinement.
What is your opinion on
Hi Erik,
Thank you for your answer.
I see your point now. Went and had a look in gmx_wham.c to see how things
are calculated, and that makes sense.
I was looking for an easy way of relating different parts of the resulting
PMF to my original starting frames, as a means to understand exactly
Hi Chris
Seems my confusion was that I assumed that the distances in the
profile.xvg-file should correspond to something I could measure with
g_dist. Turns out it does not.
Thank you for helping me sorting out this, I got it now :-)
About pull_pbcatom0 though. My box is 2*1.08 nm in all
Should I need to corret charge ...???
On Thu, Nov 15, 2012 at 11:51 PM, rama david ramadavidgr...@gmail.comwrote:
Hi Justin thank you,
The ATB server link for Biotin are as follow..
http://compbio.biosci.uq.edu.au/atb/download.py?molid=5783
Dear Gromacs users,
I tried g_rdf function and have obtained a strange result:
usually the RDF curve looks like relaxing oscillations around 1.0 constant
level,
but in my case it appears to be oscillation around exponent going from 0.0
at zero distance to 1.0 at large distances.
Is the
Hello:
I would like to simulate water flow over a single carbon nanotube.
The water temperature and flow speed needs to be varied independently for a
parametric study.
I presume this is a non-equilibrium MD simulation.
I am new to Molecular Dynamic Simulations. Can I use GROMACS for this
problem
On 11/15/12 2:16 PM, rama david wrote:
Should I need to corret charge ...???
Have you read the ATB paper? Does it give you confidence in the results? How
might you evaluate whether or not the topology produces reasonable dynamics?
All of these are things to consider, particularly the
On 11/15/12 2:28 PM, Dr. Vitaly Chaban wrote:
Dear Gromacs users,
I tried g_rdf function and have obtained a strange result:
usually the RDF curve looks like relaxing oscillations around 1.0 constant
level,
but in my case it appears to be oscillation around exponent going from 0.0
at zero
Hi Szilárd,
I assume I get the same segmentation fault error as Sebastian (don't
shoot if not so). I have 2 NVIDA GTX580 cards (and 4x12-core amd64
opteron 6174).
in brief :
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fffc07f8700 (LWP 32035)]
0x761de301
Hello Vitaly,
Thank you very much for your advise.
I will follow up the link you suggested.
regards,
shankar
_
Shankar Subramaniam
75 Hockanum Blvd., # 936
Vernon, CT 06066
Phone: 860-896-0104 (h)
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