Justin A. Lemkul wrote:
Petridis, Loukas wrote:
Hi,
We are examining a system comprising of two molecules (called mol1 and
mol2) in water that are initially separated by > 1.5nm. We calculate
the surface accessible area of the first molecule ( mol1) in two ways:
(a) sasa_a: by setting both
Carsten Kutzner wrote:
On Dec 21, 2009, at 5:26 PM,
wrote:
Dear Users,
Re Introductory tutorial;
Trying to run the following:
editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2
You have to give real coordinates for the center, not
in terms of x, y, z. The coordinates are given e.
Henry Yang wrote:
Hi all,
I want to calculate the electrostatic potential of my simulated membrane
system (DMPC). I think, I need to make an index file for this purpose.
Isn't it? In that case, how could I make the selection, I mean i have to
select the whole membrane group or I have to creat
Lum Nforbi wrote:
Hi all,
Is there a way to use genconf such that it does not reproduce the
exact same coordinates over and over again (or multiples of the same
coordinates) but assigns different coordinate values to each atom in the
x, y and z directions?
Sort of. See genconf -h
Mark
--
Hi all,
Is there a way to use genconf such that it does not reproduce the exact
same coordinates over and over again (or multiples of the same coordinates)
but assigns different coordinate values to each atom in the x, y and z
directions?
Thanks,
Lum
--
gmx-users mailing listgmx-users@grom
Petridis, Loukas wrote:
Hi,
We are examining a system comprising of two molecules (called mol1 and mol2) in
water that are initially separated by > 1.5nm. We calculate the surface
accessible area of the first molecule ( mol1) in two ways:
(a) sasa_a: by setting both the output and calculati
Hi,
We are examining a system comprising of two molecules (called mol1 and mol2)
in water that are initially separated by > 1.5nm. We calculate the surface
accessible area of the first molecule ( mol1) in two ways:
(a) sasa_a: by setting both the output and calculation groups to mol 1
(b) sasa
rasoul nasiri wrote:
Hi,
Thank you for your quick reply.
Is there another CGFF for this purpose that Gromacs can read it? What is
your opinion about CG GO model?
There are several CG models out there, but I don't know much about them. The
nice thing about Gromacs is that it can use any
Hi,
Thank you for your quick reply.
Is there another CGFF for this purpose that Gromacs can read it? What is
your opinion about CG GO model?
Kind regards
Rasoul
On Mon, Dec 21, 2009 at 8:23 PM, Justin A. Lemkul wrote:
>
>
> rasoul nasiri wrote:
>
>> Dear Justin,
>> Thank you for your message.
rasoul nasiri wrote:
Dear Justin,
Thank you for your message.
I have found some experimental evidence to suggest that the secondary
structure information of protein how change during the reaction of the
unfolding. In the other hand, I have percentage of the secondary
structure information (
Dear Justin,
Thank you for your message.
I have found some experimental evidence to suggest that the secondary
structure information of protein how change during the reaction of the
unfolding. In the other hand, I have percentage of the secondary structure
information (%alpha-Helix, %beta-sheet an
On Dec 21, 2009, at 5:26 PM,
wrote:
> Dear Users,
>
>
>
> Re Introductory tutorial;
>
>
>
> Trying to run the following:
>
> editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2
You have to give real coordinates for the center, not
in terms of x, y, z. The coordinates are given e.g. a
Dear Users,
Re Introductory tutorial;
Trying to run the following:
editconf -f out.gro -o fws_ctr.gro -center x/2 y/2 z/2
I get the error message,
Fatal error:
Expected a real argument for option -center
Can anyone help,
Many Thanks,
David.
--
gmx-users mailing listgmx-user
On 12/21/09 5:32 PM, Yanmei Song wrote:
Thanks for all the helpful response. But do I have to use dispersion
correction when I use PME? I don't quite understand what dispersion
correction do. Sometime I found using dispersion correction make my
results worse for a large molecule system.
Read th
Thanks for all the helpful response. But do I have to use dispersion
correction when I use PME? I don't quite understand what dispersion
correction do. Sometime I found using dispersion correction make my results
worse for a large molecule system.
On Mon, Dec 21, 2009 at 12:48 AM, David van der Sp
Thank you Carsten for this information and for the sd/edi fix. This
actually makes a bunch of sense. I can effect the eigenvalues with
-linfix -linstep, and I see now that eigenvalues can not be sensibly
combined with -linacc in in its current incarnation.
Thank you,
Chris.
-- original mes
Hi all,
I want to calculate the electrostatic potential of my simulated membrane system
(DMPC). I think, I need to make an index file for this purpose. Isn't it? In
that case, how could I make the selection, I mean i have to select the whole
membrane group or I have to create an index file with
Hi Chris,
the segfault was due to the fact that with the sd integrator the constraints
have to be evaluated twice and in the second call there is no pointer to
the velocities present. I have fixed that in the master and release-4-0-
patches branches. The velocity correction is now only done when v
Dear Mr Tsjerk Wassenaar ：
Thank you for your help!
what you said is reasonal, but how to implement them, or detial procedure? The
2d projections can convert to a free energy landscape, and how to obtain
conformation in the minimum of energy surface?
best regards!
--- 09年12月21日，周一, Tsjerk
Arden Perkins wrote:
From what my Professor told me it is my understanding that cutoff
length is somewhat a trade-off between accuracy of the simulation and
length of time to generate the simulation. A higher cut-off indicates
more accuracy but will take longer to simulate. I use low cut-offs
From what my Professor told me it is my understanding that cutoff
length is somewhat a trade-off between accuracy of the simulation
and length of time to generate the simulation. A higher cut-off
indicates more accuracy but will take longer to simulate. I use low
cut-offs for less important
Ni hao,
Since it's a projection, there is not (in general) a single conformation for
each point in the 2D plane. On the other hand, the points you obtained are
derived from distinct (ordered) conformations, so it is trivial to retrieve
them. Each conformation (time) yields one point: find the time
Hi Chris,
the eigenvalues (-eig) are only read/used in case of flooding.
The behaviour for each eigenvector is solely controlled by its reference
(initial) projection, and the step size.
Carsten
On Dec 19, 2009, at 5:16 PM, chris.ne...@utoronto.ca wrote:
> Hello,
>
> When utilizing more tha
>From what my Professor told me it is my understanding that cutoff length is
somewhat a trade-off between accuracy of the simulation and length of time
to generate the simulation. A higher cut-off indicates more accuracy but
will take longer to simulate. I use low cut-offs for less important
simula
On Dec 21, 2009, at 9:01 AM, David van der Spoel wrote:
On 12/21/09 8:55 AM, XAvier Periole wrote:
Would it be all cut-offs: elect + vdW ? Or the increase is separate?
For your info the vdW are attractive potentials at long distances so
an increase of cutoff would result in an increase of at
On 12/21/09 8:55 AM, XAvier Periole wrote:
Would it be all cut-offs: elect + vdW ? Or the increase is separate?
For your info the vdW are attractive potentials at long distances so
an increase of cutoff would result in an increase of attraction and
therefore to an increase of density!
This is
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