On 7/10/06, [EMAIL PROTECTED] <[EMAIL PROTECTED]
> wrote:
From: "Robert fiske" <[EMAIL PROTECTED]
>Subject: [gmx-users] Energy profile with umbrella samplingWe are using umbrella sampling to observe a hydrogen transfer. And wouldlike to analyze our results by graphing the energy against the reacti
Jae Hyun Park wrote:
Thank you, Mark.
I have one more question for the confirmation. So, if there
is other asymmetries (e.g. initially the fluid is at one
side and the other side is empty, and as time goes on, it
spreads to the empty side - non-equilibrium process. In flow
direction there is
Thank you, Mark.
I have one more question for the confirmation. So, if there
is other asymmetries (e.g. initially the fluid is at one
side and the other side is empty, and as time goes on, it
spreads to the empty side - non-equilibrium process. In flow
direction there is no periodicty while pe
Dongsheng Zhang wrote:
Yang Ye,
Thank you very much!
Do you know if there is any reason for gromacs to prevent using both LJ
and Buckingham potential for nonbonded interaction between different
atoms? I have a force field which includes an attractive part of
Buckingham potential for h-bond (All
> Dear all;
>
> I have very simple question about center-of-mass removal,
> which would be very easy for the expert like you.
> When we dealing with the system whose center-of-mass is moving
> (e.g. initially the fluid is at one side, and as time goes on,
> it spreads to other direction), do we sti
Dear all;
I have very simple question about center-of-mass removal,
which would be very easy for the expert like you.
When we dealing with the system whose center-of-mass is moving
(e.g. initially the fluid is at one side, and as time goes on,
it spreads to other direction), do we still have to re
Hi,
Please avoid the use of multiple exclamation marks or capitals in
subjects. The problem may be of tremendous significance to you, but your
urgency means very little to the others of us, and you will get more
helpful feedback if you sound like you are describing your symptoms calmly
and clearly
> Hello everybody,
>
> I am quite interested by the implementation of the CHARMM27 force field
> into Gromacs. I have read few messages on the Gromacs mailing list and
> have downloaded the CHARMM conversion on this web page:
>
> http://www.gromacs.org/old/topologies/force_fields.php
I also recom
> Hello,
> I'm still working on the CHARMM ff convertion into the Gromacs standards
> and I wonder how exactly to convert kcals of CHARMM in to Gromacs'
> KJoules. I have found 3 different constants (at least?)
> - officially (SI) : 1 kcal = 4.1868 kJ
> - but often : 1 kcal = 4.184 kJ
> - in my gra
Hello,
I'm still working on the CHARMM ff convertion into the Gromacs standards
and I wonder how exactly to convert kcals of CHARMM in to Gromacs'
KJoules. I have found 3 different constants (at least?)
- officially (SI) : 1 kcal = 4.1868 kJ
- but often : 1 kcal = 4.184 kJ
- in my graduate courses
Hello Gmx users
I have recently upgraded to gromacs3.3. I was running
an MD simulation of a protein-ion complex immersed in
water, on gromacs3.2 before and it worked fine. Later
I rerun the same simulation on gromacs 3.3 but with
different starting velocity. I am getting this error
now:
Warning:
Yang Ye,
Thank you very much!
Do you know if there is any reason for gromacs to prevent using both LJ
and Buckingham potential for nonbonded interaction between different
atoms? I have a force field which includes an attractive part of
Buckingham potential for h-bond (All other nonbonded interact
Soren,
They are all independent runs, so there is no fundamental reason they
need to be the same length. And in fact you're right -- you'd expect
some simulations to be much slower to converge than others.
Incidentally, are you calculating ion hydration free energies or
something? If so, you mig
We are using umbrella sampling to observe a hydrogen transfer. And would
like to analyze our results by graphing the energy against the reaction
coordinates, in order to see the energy profile for the transition state.
Does the force constant from the umbrella sampling affect the output of
g_
Hello everybody,
I am quite interested by the implementation of the CHARMM27 force field
into Gromacs. I have read few messages on the Gromacs mailing list and
have downloaded the CHARMM conversion on this web page:
http://www.gromacs.org/old/topologies/force_fields.php
So, I have some question
Longshoremen Zhang wrote:
On Mon, 2006-07-10 at 13:58 +0800, Yang Ye wrote:
Dongsheng Zhang wrote:
Yang Ye,
Thank you very much for your help. I still have some questions:
On Mon, 2006-07-10 at 11:35 +0800, Yang Ye wrote:
Dongsheng Zhang wrote:
Dear GMX users
On Mon, 2006-07-10 at 13:58 +0800, Yang Ye wrote:
> Dongsheng Zhang wrote:
> > Yang Ye,
> >
> > Thank you very much for your help. I still have some questions:
> >
> > On Mon, 2006-07-10 at 11:35 +0800, Yang Ye wrote:
> >
> >> Dongsheng Zhang wrote:
> >>
> >>> Dear GMX users:
> >>>
> >>>
>
> I am sorry. The particle does move if I give it an initial velocity myself
> after setting comm-mode = None. However with gen_velocity = yes, It gives
> the atom a velocity of zero.
So it probably produces velocities such that the center of mass velocity
is zero... this is something that a norma
Hello,
It is a probably a pretty naive answer and you probably tested it
already but have you checked the box size?
Erwin
yes i have used gen_velocity = yes. when it did not work with this i gave
the system a velcity of my own. It did not move even then.
even after removing the restrictions oon
I am sorry. The particle does move if I give it an initial velocity
myself after setting comm-mode = None. However with gen_velocity = yes,
It gives the atom a velocity of zero.
thanks for your help.
karamyog.
___
gmx-users mailing listgmx-users@gro
yes i have used gen_velocity = yes. when it did not work with this i
gave the system a velcity of my own. It did not move even then.
even after removing the restrictions oon center of mass motion, that is
after setting comm-mode = None, the particle does not move.
any idea why?
-
karamyog.On 7/10
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