Dear All,
I've performed TMD simulation using NAMDprogram. I'd like to calculate PMF
plot based on the frames that were taken from TMD simulations by using
GROMACS.
The coordinate of reaction is RMSD of backbone.
The first step is to do Umbrella sampling. The question is how fix the
position of
Of course I read Justin's tutorial.
The reason I am asking is that I am not sure how to do it.
On Wed, Oct 17, 2012 at 11:09 AM, Arman Mahboubi Soufiani
armansoufi...@gmail.com wrote:
Hi,
I recommend you Justin's tutorial on Umbrella Sampling
On 10/17/12 5:44 AM, Netaly Khazanov wrote:
Of course I read Justin's tutorial.
The reason I am asking is that I am not sure how to do it.
As far as I am aware, there is no way to conduct umbrella sampling in this way
using Gromacs. The PMF calculations that Gromacs does are based on
Thanks.
However, I can restrain the position of backbone (x,y,z -coordinates) while
running umbrella sampling and treat it like reaction coordinate. Is it
right?
Maybe I am missing something.
pull = umbrella
pull_geometry = position
;pull_dim = Y Y Y
pull_start = yes
pull_ngroups = 1
On 10/17/12 9:17 AM, Netaly Khazanov wrote:
Thanks.
However, I can restrain the position of backbone (x,y,z -coordinates) while
running umbrella sampling and treat it like reaction coordinate. Is it
right?
Maybe I am missing something.
pull = umbrella
pull_geometry = position
;pull_dim = Y
Thank you, Peter.
Do you mean that the [atomtypes] section is not important? In other words,
Gromacs will skip them if the data have been given in [pairtypes] section,
isn't it? I have type the follow command:
/pdb2gmx -f *.pdb -o *.gro -p *.top -ss -his
grompp -v -f vac-min.mdp -c *.gro -p
On 10/17/12 9:41 AM, spin wrote:
Thank you, Peter.
Do you mean that the [atomtypes] section is not important? In other words,
Gromacs will skip them if the data have been given in [pairtypes] section,
isn't it? I have type the follow command:
/pdb2gmx -f *.pdb -o *.gro -p *.top -ss -his
Thank you, Justin.
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It seems difficult to use RMSD as the reaction coordinate to do umbrella
sampling simulations. Maybe you can try meta-dynamics in which you can
use RMSD as a collective to get the free energy. It is implemented in a
modified version of gromacs (GROMETA), or you can use PLUMED together
with
Hi,
I am trying to compute free energy of a polymer in presence of a constant
force.
If I understand correctly, I need to use two pull-option here in gromacs: one
for performing umbrella sampling and other for applying constant force. But,
as far as I know I can not specify two pull option
hello:
I am going to perform replica exchange MD with Gromacs and I found
some problems there:
1. my protein have around 290 aa with 4680 atoms. If I would like to
perform with implicite solvent with exchange probability 0.2, I found
from http://folding.bmc.uu.se/remd/ that I will have to
hello Justin:
thanks a lot for kind reply.
I've got another question: how to disable PBC? shall I simply delete
pbc=xyz from .mdp file? I found that sometimes if we delete some
parameters from .mdp, gromacs will use the default instead of disable it.
thank you very much
best
Albert
On
On 10/17/12 2:31 PM, Albert wrote:
Hello Justine:
I've got the following messages by command:
grompp -f implicit.mdp -c complex.pdb -p complex.top -o test.tpr
Setting gen_seed to 18463
Velocities were taken from a Maxwell distribution at 310 K
GB parameter(s) missing or negative for atom
IC.
I just saw your previous thread.
thanks again for kind helps.
On 10/17/2012 08:49 PM, Justin Lemkul wrote:
On 10/17/12 2:46 PM, Albert wrote:
On 10/17/2012 08:43 PM, Justin Lemkul wrote:
Here you're adding atom types, not the associated GB parameters.
Some of
these atom types
You can not have multiple reference groups or multiple types of pulling
(constraint, harmonic, etc) in any version of gromacs that I am aware of. I
have modified versions of gromacs 3.3.3 and 4.0.5 that we modified in-house to
put a loop over the pull code so that this is possible. For v3.3.3,
Dear Gromacs users,
It might seem a simple problem, however, I could not find a correct way to
define two restrained groups in my .mdp file.
If I include the following an error appears that notifies me that I am not
able to define two restraints!
define = -DPOSRES_1
define = -DPOSRES_2
Do I
On 10/17/12 5:46 PM, Arman M. Soufiani wrote:
Dear Gromacs users,
It might seem a simple problem, however, I could not find a correct way to
define two restrained groups in my .mdp file.
If I include the following an error appears that notifies me that I am not
able to define two restraints!
It depends on how the molecules are defined in the topology file.
If the coordinates of both molecules are contained in the main
part of the topology file, only one position restraint file is enough
and it should contain entries for all the non-hydrogen atoms in
both molecules. However, if the
Dear Justin,
I appreciate your rapid response.
BR
Arman
On Thu, Oct 18, 2012 at 1:25 AM, Justin Lemkul jalem...@vt.edu wrote:
On 10/17/12 5:46 PM, Arman M. Soufiani wrote:
Dear Gromacs users,
It might seem a simple problem, however, I could not find a correct way to
define two
Dear Paulo,
I greatly appreciate your kind and thorough response.
I should say that not only I got the point that I was looking for but also
I learnt much more of your explanations.
Best Wishes
Arman
On Thu, Oct 18, 2012 at 1:35 AM, Paulo Netz paulo.n...@gmail.com wrote:
It depends on how
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