rob yang wrote:
Hi list,
I have a system solvated in dodecahedron box. To visualize it, I used:
trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc whole
Version 3.3.3 gave me a cubic box with broken molecules while the previous
versions gave me the right visualization on the same
sudheer babu wrote:
Thanks Mr .Justin for your response,
I am describing answers for your questions,
1.My box size is 6.0nm in xyz dimensions.
2.The forcefield I am using "ffgmx.itp" for membrane which I downloaded
from Pieter Tieleman webiste and deprecated FF for protein.
3 .I inserted prot
Thanks Mr .Justin for your response,
I am describing answers for your questions,
1.My box size is 6.0nm in xyz dimensions.
2.The forcefield I am using "ffgmx.itp" for membrane which I downloaded
from Pieter Tieleman webiste and deprecated FF for protein.
3 .I inserted protein into membrane by usi
Jestin,I am just using the TIP5P parameter file that comes with gromacs and it
doesn't have the flexible parameters in there. I too wonder the impacts it
would have on MD, so maybe somebody else might have some insights. But my
understanding is that the important parts of the water model are th
Rob,
I wonder whether you have got the flexible water model, TIP5P. I want to run
simulations using the flexible TIP5P water model. Well, how does the results
from the MD be affected if I use rigid water models in place of a flexible one?
regards
Jestin
On Thu, 06 Mar 2008 rob yang wrote
Hi list,
I have a system solvated in dodecahedron box. To visualize it, I used:
trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc whole
Version 3.3.3 gave me a cubic box with broken molecules while the previous
versions gave me the right visualization on the same system.gro
Does
Ricardo Soares wrote:
Hi everybody,
I think this may sound rather trivial for most users, but I intend to
install gromacs 3.3.1 on a dual core machine and I want to be sure
what to do. Could anyone indicate me some online tutorial to do so (as
well some simulation examples)? Is this conside
Hi everybody,
I think this may sound rather trivial for most users, but I intend to
install gromacs 3.3.1 on a dual core machine and I want to be sure what
to do. Could anyone indicate me some online tutorial to do so (as well
some simulation examples)? Is this considered parallelization (with
Hello gmx users,
I suppose this is one of the more common subject post
going around in the mailing list. I have gone through the
list and have gathered some information on the subject.
But I have some queries and if someone can shed light on
it, it will be of great help to me.
Ethernet has very high latency, it wasn't made for this kind of thing.
Gmx 4 will be much much better, check the paper gromacs website.
On 3/6/08, Ricardo Soares <[EMAIL PROTECTED]> wrote:
>
> Diego Enry wrote:
> On Thu, Mar 6, 2008 at 1:26 PM, Ricardo Soares <[EMAIL PROTECTED]>
> wrote:
>
>
>
Diego Enry wrote:
On Thu, Mar 6, 2008 at 1:26 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote:
Hello everyone,
I have 3 available computers for my simulations; two of them are dual
core. Which is better for me: run one simulation each independently or
parallelize them all?
Mark, thank you for reply!
In the output file of genbox the 'right' box size is written:
8.8 8.8 8.8
Tobias
On Fri, 7 Mar 2008, Mark Abraham wrote:
Tobias Unruh wrote:
Hi,
I created a box (8.8 x 8.8 x 8.8 nm^3 = 681.472 nm^3) of 722 alkane
(C32H66) molecules (molecular w
On Thu, Mar 6, 2008 at 1:26 PM, Ricardo Soares <[EMAIL PROTECTED]> wrote:
> Hello everyone,
>
> I have 3 available computers for my simulations; two of them are dual
> core. Which is better for me: run one simulation each independently or
> parallelize them all?
>
In theory, if the simulations
Hello everyone,
I have 3 available computers for my simulations; two of them are dual
core. Which is better for me: run one simulation each independently or
parallelize them all?
Thanks!
Ricardo.
--
___
Ricardo Oliveira dos Santos Soa
rob yang wrote:
Thanks Mark for the pointer.
The TIP5P.itp has [settles] only, whereas TIP4P.itp (as well as spc.itp, and
TIP3P) has parameters for flexible water [FLEXIBLE] as well as rigid [settles].
This, by definition would restrict any systems using TIP5P to the SHAKE
algorithm. I am wo
Tobias Unruh wrote:
Hi,
I created a box (8.8 x 8.8 x 8.8 nm^3 = 681.472 nm^3) of 722 alkane
(C32H66) molecules (molecular weight: 450.88 g/mol). This gives a
density of 793.23 g/l. But genbox calculates 743.576 g/l. The atom
masses and numbers of atoms are ok in the input .gro file.
Some su
Thanks Mark for the pointer.
The TIP5P.itp has [settles] only, whereas TIP4P.itp (as well as spc.itp, and
TIP3P) has parameters for flexible water [FLEXIBLE] as well as rigid [settles].
This, by definition would restrict any systems using TIP5P to the SHAKE
algorithm. I am wondering:
1) are t
Hi,
I created a box (8.8 x 8.8 x 8.8 nm^3 = 681.472 nm^3) of 722 alkane (C32H66)
molecules (molecular weight: 450.88 g/mol). This gives a density of 793.23 g/l.
But genbox calculates 743.576 g/l. The atom masses and numbers of atoms are ok
in the input .gro file.
Some suggestions?
Best rega
Dear gmx-users,
Thanks for the answer, but I already saw about P atom and tried it, but didn't
work. It looks like the problem is more related to center of mass removal or
PBC (size effect). Could you please explain how to solve this problem? Details
are explained below in my previous email.
412 (+/- 0.0021) 1e-5 cm^2/s. I calculated it for each monolayer,
> > and also for bilayer, but had similar values. This big value comes from
> the
> > size effect ? Is there anyway to get a reasonable lateral D?
> >
> > 2) When I ran the bilayer simulation, did I hav
Berk Hess a écrit :
Hi,
I now realized that my fix what completely incorrect.
I wanted to multiply the margin of 0.0001 by 2, not the factor 0.5.
But my mistake means that is now given an error when the off diagonal
element is relatively more than 1 instead of more than 0.5.
This is a far too we
Quoting sudheer babu <[EMAIL PROTECTED]>:
> Hi gmx users,
> I inserted my protein into Popc Bilayer . EM is fine, when I do
> equilibration the water molecules from oneside of bilayer moving to other
> side, it looks undistribution of water , but total sturucture in cubic form.
> can you give me
Hi i have modified the src to stop harmonic potentials being put into the
graph (as was suggested to me by Berk Hess, see below for the modification
you need to make). I would be imagine this is also possible to do for
distance/orientation restraints, however i only know a small amount of
progr
Hi gmx users,
I inserted my protein into Popc Bilayer . EM is fine, when I do
equilibration the water molecules from oneside of bilayer moving to other
side, it looks undistribution of water , but total sturucture in cubic form.
can you give me detailed information regarding this problem
is it due
Look at it this way: the total energy is a double sum over all particles.
For efficiency one only computes half the matrix, i.e.
E = sum_{i=1}^N sum_{j=i+1}^N E_{ij}
however one can also compute it like this:
E = 1/2 sum_{i=1}^N sum_{j=1}^N E_{ij}
Now if you define
E_i = 1/2 sum_{j=1}^N E_
Hi,
I now realized that my fix what completely incorrect.
I wanted to multiply the margin of 0.0001 by 2, not the factor 0.5.
But my mistake means that is now given an error when the off diagonal
element is relatively more than 1 instead of more than 0.5.
This is a far too weak check.
So I would n
Xavier Periole wrote:
Still, if you want to partition the energy over molecules you have
to make some kind of division. For instance, if you calculate the
potential energy for 216 water molecules you will find that is is
roughly -9000 kJ/mol at room T, and hence you can derive the
potential en
Still, if you want to partition the energy over molecules you have to
make some kind of division. For instance, if you calculate the
potential energy for 216 water molecules you will find that is is
roughly -9000 kJ/mol at room T, and hence you can derive the potential
energy per molecule to be
Xavier Periole wrote:
On Thu, 06 Mar 2008 09:42:09 +0100
David van der Spoel <[EMAIL PROTECTED]> wrote:
Xavier Periole wrote:
On Wed, 05 Mar 2008 20:38:59 +0100 (MET)
[EMAIL PROTECTED] wrote:
Dear developers,
I would like to know the exact definition of the total potential
energy with
res
On Thu, 06 Mar 2008 09:42:09 +0100
David van der Spoel <[EMAIL PROTECTED]> wrote:
Xavier Periole wrote:
On Wed, 05 Mar 2008 20:38:59 +0100 (MET)
[EMAIL PROTECTED] wrote:
Dear developers,
I would like to know the exact definition of the total potential
energy with
respect to protein-solvent
Hi,
Which values are fluctuating?
If something is fluctuating, you can see it is running, or not?
Did you use the -v option of mdrun?
This prints the force and energy for every accepted step to stderr.
Berk.
Date: Thu, 6 Mar 2008 05:09:06 +
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.or
Dear Gromacs Users,
I'm going to simulate solution-mediated polymorphic transformation from b to
a-Glycine. From literature, I came to know that constant stress ensemble can
be used to simulate such transformation.
I'm interested to know whether I can use NPT ensemble with PR pressure
coupling f
Xavier Periole wrote:
On Wed, 05 Mar 2008 20:38:59 +0100 (MET)
[EMAIL PROTECTED] wrote:
Dear developers,
I would like to know the exact definition of the total potential
energy with
respect to protein-solvent interactions, in an explicit solvent
protein simulation.
The definition of protei
Monika,
Daniel has already given the answer. The third column gives the
standard deviation, whereas the second gives the average SAS. You
could've found this answer also by browsing the mailing list archive,
as this is one of those questions being posted every once in a
while...
Cheers,
Tsjerk
Hello All,
For reference, the output files are as:
# This file was created Thu Jan 31 17:27:21 2008
# by the following command:
# g_sas -f pro-total-21ns-300K-PT.xtc -s pro-3ns-300K-PT.tpr -o
pro-21ns-300K-g_sas-area.xvg -or pro-21ns-300K-g_sas-resarea.xvg -oa
pro-21ns-300K-g_sas-atomarea.xvg -
35 matches
Mail list logo
