In my case for second order parameter I need the angle between the unit
vector linking N- and C-termini of the ith peptide and the d (the
director) is a unit vector defining the preferred direction of alignment.
These vectors are not clear to me.. please suggest something.
Nidhi
On Sat, Jun 3
On 6/2/17 7:31 PM, Saeed Nasiri wrote:
Dear Justin
I really thanks for your useful help in the last topic.
I totally changed the method. I copy the oplsaa.ff file in the working
directory
and insert the parameters in the related files.
But I have a problem with dihedral parameters. As far as
Hi Nidhi,
In short: you are using a general-purpose software, so it does not have
tools for all specific applications any user might be interested in. Either
you have to hack/adapt existing analysis tools or you have to write your
own tools.
That being said: the director is a rather arbitrary dir
On Sat, 3 Jun 2017, nidhi sorout wrote:
Hello,
Thank you Antonio..
But my angle of interest is the angle between the molecular axis of protein
and the director. I am not able to understand here, from where I can choose
this 'director'?
In your case, what does 'director' mean exactly?
Nidh
Dear Justin
I really thanks for your useful help in the last topic.
I totally changed the method. I copy the oplsaa.ff file in the working
directory
and insert the parameters in the related files.
But I have a problem with dihedral parameters. As far as I know, the opls
force filed used
the Rycka
>
>
>>
> A pull vector can indeed not be (0, 0, 0) but that's not a pull rate.
The pull vector is exactly as set by you to N N Y, maybe the code
multiplies the vector components by the corresponding pull rates and then
checks the resulting velocity vector, I don't know, but the error is there
wit
On 6/2/17 6:40 PM, Alex wrote:
I find that surprising. Please provide the full, exact error and your
pull settings. All of the geometries should work with zero or non-zero
pull rates. But I admit, it has been many years since I used GROMACS with
the pull code.
Simply take your pull code
>
> I find that surprising. Please provide the full, exact error and your
>> pull settings. All of the geometries should work with zero or non-zero
>> pull rates. But I admit, it has been many years since I used GROMACS with
>> the pull code.
>>
>
Simply take your pull code from the tutorial and
On 6/2/17 3:13 PM, Archana Sonawani-Jagtap wrote:
Thanks for solving my error. But then do we need to remove the periodicity
of the bilayer obtained from charmm-gui?
Have you visualized the structure you got? Is there a reason you think you need
to play with trjconv yet?
-Justin
--
On 6/2/17 3:51 PM, Li, Shi wrote:
Dear Gromacs users,
I am wondering if there is a better way to randomly replace some molecules
in a system box with another type of molecule. For example, I have a system
with 1000 molecule A as the solvent and I have another molecule B as the
solute. I want t
On 6/2/17 4:17 PM, Alex wrote:
So, Justin, just to follow up here. With 'cylinder', grompp refuses to
accept a zero pulling rate. This begs a different question: in my
I find that surprising. Please provide the full, exact error and your pull
settings. All of the geometries should work wit
Hello,
Thank you Antonio..
But my angle of interest is the angle between the molecular axis of protein
and the director. I am not able to understand here, from where I can choose
this 'director'?
Nidhi
On 30 May 2017 8:55 p.m., "Antonio Baptista" wrote:
> Hi Nidhi,
>
> If I remember correctly
So, Justin, just to follow up here. With 'cylinder', grompp refuses to
accept a zero pulling rate. This begs a different question: in my
particular system, the COM position coincides with the center of the single
reactive pore at the geometric center of the membrane. Why even bother with
this setup
Thanks for replying.
I have also tried that before. If we give the whole system the same
acceleration, then it wouldn't experience any shear. That was what I was
observing also.
Is there no way/ inbuilt method which use SLLOD , like in LAMMPS ?
On Fri, Jun 2, 2017 at 4:09 PM, David van der Spoel
On 02/06/17 22:02, nishi kashyap wrote:
Hi
I have a system of PEG for which I want to find viscosity. I want to use
SLLOD equations to find viscosity for a specific shear rate. I have read
allot about different ways , even tried to use 'deform'. But I did not
understand what do you mean by "off d
Hi
I have a system of PEG for which I want to find viscosity. I want to use
SLLOD equations to find viscosity for a specific shear rate. I have read
allot about different ways , even tried to use 'deform'. But I did not
understand what do you mean by "off diagonal elements in a single array". I
am
Dear Gromacs users,
I am wondering if there is a better way to randomly replace some molecules
in a system box with another type of molecule. For example, I have a system
with 1000 molecule A as the solvent and I have another molecule B as the
solute. I want to generate a series of systems with di
Thanks for solving my error. But then do we need to remove the periodicity
of the bilayer obtained from charmm-gui?
Regards,
Archana
On Fri, Jun 2, 2017 at 2:24 AM, Justin Lemkul wrote:
>
>
> On 6/1/17 4:43 PM, Archana Sonawani-Jagtap wrote:
>
>> Hi,
>>
>> I want to perform GPCR simulation in
Yes, because if your ion diffuses laterally (or whatever constitutes
your "hole"), then you're not sampling what you think you're
sampling. That's what the cylinder geometry is for. You have a
system capable of significant lateral movement, so if you fail to
apply a bias that acts in th
Hi,
I suggest you decide what you want to observe before choosing a tool to
observe with :-) A telescope is no good for micro-organisms.
Mark
On Fri, 2 Jun 2017 17:20 Apramita Chand wrote:
> Dear All,
> I would be grateful if you could help me with links to relevant
> papers/websites/sources o
Dear All,
I would be grateful if you could help me with links to relevant
papers/websites/sources on how to interpret RMSD matrices when comparing
all frames of single trajectory to reference structure and also when
comparing two different trajectories.
I am taking the reference structure from t
Dear All,
Even after applying g_trjconv -f file.gro -s file.tpr -pbc mol -ur compact
-center -o newfile.gro,
for visualisation purposes of peptide inside the box, a portion of it still
sticks out of the box. Is it unnatural?
What might be done to sort out the problem?
yours sincerely
Apramita
--
Dear All,
I want to calculate the COM RDFs between my peptide and water for which I
have used the -com option in gromacs.(Also tried with -com and -rdf
res_com).
It generates a wierd RDF which does not look correct. I want to take the
first minimum and use the -cn option to get the coordination n
On 6/2/17 7:20 AM, Varvdekar Bhagyesh Rajendra wrote:
Dear Justin,
I would like to correct myself. Actually, the COM of the two groups - Protein
and Ligand are about 5 nm away at the end of the pulling process. But the rear
end of the ligand is just 0.6 nm away from the closest Amino acid of
Thanks, I've opened the issue at https://redmine.gromacs.org/issues/2200 .
From: Mark Abraham
Sent: Thursday, June 1, 2017 20:10
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] System volume "jumps" on exact continuati
Dear Justin,
I would like to correct myself. Actually, the COM of the two groups - Protein
and Ligand are about 5 nm away at the end of the pulling process. But the rear
end of the ligand is just 0.6 nm away from the closest Amino acid of the
Protein. Is that reasonable for the Binding affinity
On 6/2/17 4:26 AM, Saeed Nasiri wrote:
Dear *Justin*
I checked all of the parameters again and again and I try that to prepare
them similar to the opls itp files.
However, the problem does not solve. Also, when the energy minimization
has been run there is warning about 1-4 interaction. I thi
I suggest that you try to understand the parallelization option of mdrun
first. You seem to be mixing MPI and thread-MPI. The latter won't work for
multi-node runs. If you sort that out and launch with correctly set up PBS
parameters (ranks and cores/threads per ran), your runs should be fine.
htt
On 6/1/17 6:29 PM, Varvdekar Bhagyesh Rajendra wrote:
Dear Justin,
Since I have the settings pull_coord1_dim = Y Y Y, I am not sure which axis the
ligand is pulled. My initial simulation box size was 5 nm in each side. To care
of the pulling of the ligand in any direction I made the box size
On 6/1/17 6:35 PM, Alex wrote:
You have a membrane with water on either side, yes? That's a layered
system.
But frankly, at this point I don't follow at all what you're trying to do.
-
Let me try from the beginning. :)
A membrane in XY, water on both sides. At the center of the membra
Perhaps try something like:
(in your PBS Script)
-l nodes=8:ppn=28 (request for 8 nodes with all cores)
source (your source stuff here)
mpirun -n 56 -npernode 7 gmx_mpi mdrun -ntomp 4 (your run stuff here).
This should give you 7 mpi ranks per node, with each rank using 5 openMP
threads, which
What I notice is:
You don't use bond-constraints but you have set your time step to 2 fs.
What happens if you (significantly) increase simulation time per
lambda? Your variances are really large.
What is the motivation of using such a long cutoff radius for vdW?
On Fri, 26 May 2017 11:13:08 -0
>
> Dear *Justin*
>
> I checked all of the parameters again and again and I try that to prepare
> them similar to the opls itp files.
> However, the problem does not solve. Also, when the energy minimization
> has been run there is warning about 1-4 interaction. I think
> that the problem is relate
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