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 wrote:
> It depends on how the molecules are def
Dear Justin,
I appreciate your rapid response.
BR
Arman
On Thu, Oct 18, 2012 at 1:25 AM, Justin Lemkul 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 restrained g
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 coor
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!
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 nee
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,
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 probabl
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 probably already exist within the gbsa.itp file of the force
field, judging by their names. At least one (OS) does not.
-
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 probably already exist within the gbsa.itp file of
the force field, judging by their names. At least one (OS) does not.
-Justin
thank you for kind comment
On 10/17/12 2:41 PM, Albert wrote:
On 10/17/2012 08:35 PM, Justin Lemkul wrote:
You need GB parameters for every atom type in the system. Most protein and
nucleic acid types work out of the box, but if you have a complex system with
some novel molecule in it, you have to add parameters for th
On 10/17/2012 08:35 PM, Justin Lemkul wrote:
You need GB parameters for every atom type in the system. Most
protein and nucleic acid types work out of the box, but if you have a
complex system with some novel molecule in it, you have to add
parameters for the atom types that it uses.
thank
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
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 type 'OS'
Hi,
the main remaining issue are the new (faster) group cut-off kernels.
As always any volunteers are very welcome. Remaining issues can be found at
redmine.gromacs.org and if someone wants to help but doesn't want to
program it is always nice to have help with the documentation
wiki.gromacs.org (
Hi Justin:
thank you so much for such kind and helpful comments. My system is a
protein/ligand system.
I will try it with your advices these days.
best
Albert
On 10/17/2012 07:58 PM, Justin Lemkul wrote:
On 10/17/12 1:52 PM, Albert wrote:
Hi Justin:
Thank you very much for eply.
So th
On 10/17/12 1:52 PM, Albert wrote:
Hi Justin:
Thank you very much for eply.
So the modified .mdp file (including the GBSA model setting) is the following?
Is this correct?
No. See inline comments.
title = Protein-ligand complex NVT equilibration
define = -DPOSRES ; position restrain the
Hi Justin:
Thank you very much for eply.
So the modified .mdp file (including the GBSA model setting) is the
following? Is this correct?
title = Protein-ligand complex NVT equilibration
define = -DPOSRES ; position restrain the protein and ligand
; Run parameters
integrator = sd ;
nsteps = 50
On 10/17/12 1:43 PM, Albert wrote:
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.
The
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 10/
On 10/17/12 11:01 AM, Sanku M wrote:
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
On 10/17/12 1:35 PM, Albert wrote:
thank you all the same. I saw many people use Amber for REMD and few people use
Gromacs for REMD and the parameters is not easy reachable. However, what I found
is that Amber use cutoff=999
I am just wondering, shall I also use such big value for the followin
thank you all the same. I saw many people use Amber for REMD and few
people use Gromacs for REMD and the parameters is not easy reachable.
However, what I found is that Amber use cutoff=999
I am just wondering, shall I also use such big value for the following?
rlist = 999; short-range neighbo
I am no expert in implicit solvent simulations but I think for these
simulations it is better to use stochastic dynamic integrators with no
pbc (instead of NVT) and infinite (or very large) cut-off distances because
there is no actual water molecule in your simulation box and [normally] you
do not
Hi Saber:
thanks a lot for such kind reply.
How about the second question? I don't find any tutorial for the GBSA
solvent simulation in Gromacs website and I am not sure what kind of
parameters we should use for GBSA.
thank you very much
best
Albert
On 10/17/2012 05:48 PM, saber naderi wro
Hi Albert,
Regarding you first question, your protein is relatively big and in my
opinion 28 replicas is not much for a protein made of 290 AA with the
temperature range of 280-530. One thing that you can do is to use a lower
value for exchange probability to have less replicas. By doing this the
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 g
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 in
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 curr
Thank you, Justin.
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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
gromp
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 *.to
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
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
;pull_grou
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 restr
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
>
> http://www.bevanlab.biochem.vt.edu/Pages/
Hi,
I recommend you Justin's tutorial on Umbrella Sampling
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
Regards
Arman
On Wed, Oct 17, 2012 at 10:47 AM, Netaly Khazanov wrote:
> Dear All,
>
> I've performed TMD simulation using NAMDprogram. I'd lik
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
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