Hi!
Big thanks to those of you who already participated in this survey - we got
about 100 *VERY* useful answers this far, but considering the size of the
community I think we should be able to improve that fivefold :-)
We will use the results of this survey to steer future Gromacs development,
On 27/03/2012 1:04 PM, Justin A. Lemkul wrote:
Jernej Zidar wrote:
Hi.
I'm trying to import a PDB containing the following components to
Gromacs using pdb2gmx:
- polymer (1 molecule composed of 5 residues)
- lipids (cholesterol-37 molecules and sphingomyelin-78 molecules)
- water (2297 molec
On 27/03/2012 12:57 PM, Jernej Zidar wrote:
Hi.
I'm trying to import a PDB containing the following components to
Gromacs using pdb2gmx:
- polymer (1 molecule composed of 5 residues)
- lipids (cholesterol-37 molecules and sphingomyelin-78 molecules)
- water (2297 molecules)
The problem I h
Jernej Zidar wrote:
Hi.
I'm trying to import a PDB containing the following components to
Gromacs using pdb2gmx:
- polymer (1 molecule composed of 5 residues)
- lipids (cholesterol-37 molecules and sphingomyelin-78 molecules)
- water (2297 molecules)
The problem I have is that for some str
Hi.
I'm trying to import a PDB containing the following components to
Gromacs using pdb2gmx:
- polymer (1 molecule composed of 5 residues)
- lipids (cholesterol-37 molecules and sphingomyelin-78 molecules)
- water (2297 molecules)
The problem I have is that for some strange reason pdb2gmx does
On 27/03/2012 8:23 AM, Roy Roshko wrote:
Dear gromacs users,
Aside from a scale factor, should the time dependence of the
temperature T(t) extracted from the .trr file with g_traj for a given
residue be
Using what command line? Have you read g_traj -h about -ot?
identical to the time dep
Hi,
Is there any way in gromacs to use radius of gyration of a polymer as
reaction coordinate for umbrella sampling ?
Thanks
Sanku--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/M
bipin singh wrote:
Thanks for your reply.
Yes, you are right that these topologies are self supporting and there
is no need to to call any other information. I followed your
suggestions and able to generate a biphasic system of water/octane
containing a protein molecule. But, when I tried gromp
Thanks for your reply.
Yes, you are right that these topologies are self supporting and there
is no need to to call any other information. I followed your
suggestions and able to generate a biphasic system of water/octane
containing a protein molecule. But, when I tried grompp on this
biphasic syst
Dear gromacs users,
Aside from a scale factor, should the time dependence of the temperature T(t)
extracted from the .trr file with g_traj for a given residue be identical to
the time dependence of the total kinetic energy (translational + rotational)
K(t) extracted from the .trr file with g_tr
Lara Bunte wrote:
Hi
with the -ter option I got the same errors. I read in the manual something about the termini database but I don't understand what that s about (I didn't study Chemistry...).
Well what choices did you make regarding termini? Telling us you invoked the
option doesn't
Hi
with the -ter option I got the same errors. I read in the manual something
about the termini database but I don't understand what that s about (I didn't
study Chemistry...).
I read this tutorial page but that doesn't help me :-(
Could you explain me in your words what it has to do with th
rama david wrote:
Hi Gromacs Friends,
Thank you for your reply and nice suggestion.
I read the wikipedia article
..http://en.wikipedia.org/wiki/Flying_ice_cube suggested by Mark..
as per the article..
More conservatively, the rate of velocity rescaling can be reduced, the
scale factor compu
On 26/03/2012 11:55 PM, Lara Bunte wrote:
Hi
my command was pdb2gmx -f isoalloxazin.pdb -water tip3p which worked for ISO
Isoalloxazin in the residuetypes.dat
Sure, because pdb2gmx had not been told that ISO was protein, it didn't
try to treat it as protein.
I don't get an output of this
bipin singh wrote:
Thanks for your reply.
But as far as I understood, in order to use these GAFF topology (for
e.g. to perform simulation using these topologies) with Gromacs we
have to incorporate the information from these topologies to the
existing Amber forcefields in Gromacs or Is there an
Thanks for your reply.
But as far as I understood, in order to use these GAFF topology (for
e.g. to perform simulation using these topologies) with Gromacs we
have to incorporate the information from these topologies to the
existing Amber forcefields in Gromacs or Is there anyway (Possibility
of us
Hi
my command was pdb2gmx -f isoalloxazin.pdb -water tip3p which worked for ISO
Isoalloxazin in the residuetypes.dat
I don't get an output of this command, only the fatal error I wrote and an
empty topology file.
I don't know what to do now
Greetings
Lara
- Ursprüngliche Message -
On 26/03/2012 11:21 PM, Lara Bunte wrote:
Hi
I changed in my residuetypes.dat file ISO Isoalloxazin in ISO Protein. I want
to repeat the calculations I did before by pdb2gmx it already failed. I got the
error:
Fatal error:
Atom OXT in residue ISO 1 was not found in rtp entry ISO with 32 atoms
Hi
I changed in my residuetypes.dat file ISO Isoalloxazin in ISO Protein. I want
to repeat the calculations I did before by pdb2gmx it already failed. I got the
error:
Fatal error:
Atom OXT in residue ISO 1 was not found in rtp entry ISO with 32 atoms
while sorting atoms.
I have no shortcut O
On 2012-03-26 13:55, bipin singh wrote:
Hello all,
I am using the GAFF topology provided for octan-1-ol at Gromacs liquid
database (http://virtualchemistry.org/molecules/111-87-5/index.php). I
have incorporated all the parameters
for atoms, bonds and non-bonded interaction type in the forcefield
Hello all,
I am using the GAFF topology provided for octan-1-ol at Gromacs liquid
database (http://virtualchemistry.org/molecules/111-87-5/index.php). I
have incorporated all the parameters
for atoms, bonds and non-bonded interaction type in the forcefield
(Amber99sb-ildn in Gromacs) from GAFF top
Try to use constrains = all-bonds which is the way to use Gromos force fields.
On Mar 26, 2012, at 12:30, SebastianWaltz
wrote:
> Dear Gromacs user,
>
> I try to simulate the human Villin head peace HP35 in approx. 6000 water
> molecules (spc) with the gromos ff ffG53a6. Using the 4.0.7 vers
Dear Gromacs user,
I try to simulate the human Villin head peace HP35 in approx. 6000 water
molecules (spc) with the gromos ff ffG53a6. Using the 4.0.7 version the
NPT equilibration for 5ns with position restraint protein (lincs) atoms
and a integration step of 0.002 using the leap-frog integrator
Hi Gromacs Friends,
Thank you for your reply and nice suggestion.
I read the wikipedia article
..http://en.wikipedia.org/wiki/Flying_ice_cubesuggested by Mark..
as per the article..
More conservatively, the rate of velocity rescaling can be reduced, the
scale factor computed over a time-averaged s
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