I thought the virtual sites can affect analysis.For example, dont they cause
incorrect calculations of SASA, RMSD or something else?
Thanks in advance
2013/2/20 Justin Lemkul
>
>
> On 2/20/13 9:18 AM, Ahmet yıldırım wrote:
>
>> Dear users,
>>
>> I have the virtual sites in reference structure a
Hello All,
I want to know how to mention a group (group2) without any temperature
coupling in mdp file. From the manual I got to know that we should mention
tau_t= -1 for no temperature coupling. And in the ref_temp section I have
mention two values, 300K for coupled part (group1) and 10k for unco
Correction on #6
6. if that doesn't help decrease your time step.
Sorry for the confusion :)
Cheers,
EB
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Anu Chandran
Sent: Thursday, 21 February 2013 3:34 PM
To: Discussion list f
Dear,
there are three waters in active site of receptor,mediating the binding of
ligand with target protein. i want to study the three waters how to affect the
binding of ligand with target protein and the contribution to the stability of
the system.
In order to avoid the three waters exc
There might be more than one reason for this kind of error.
1. check your topology file specially for the 1-4 interaction error.
2. check your coordinate file (gro/pdb file), weather it is correct or not.
3. do the minimization for more steps than you did before.
4. check which atoms are making t
Sir,
I tried using cutoff for van der Waals interactions. I got the following
error during the nvt equilibration:
"step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.040332, max 2.236585 (between atoms 24073 and 24072)
bonds that rotated more than 30 degrees:
ato
On 2/20/13 10:30 AM, vidhya sankar wrote:
Thank you justin for your Nice reply
As you Mailed Me
How Could i Check My System Is constructed efficiently or Poorly?
Can I Check Through APL?
I Have Stopped EM After Reaching APL as follows
On 2/20/13 10:31 AM, Felipe Pineda, PhD wrote:
Hi again,
my topology is non-consecutively numbered. I was looking for a tool to renumber
it, but didn't find it yet. A hint will be really appreciated. I was not sure
I doubt one exists. Many people have asked for such a thing, but no one has
On 2/20/13 11:01 AM, Yun Shi wrote:
Hi Justin,
I was not able to find relevant posts in the archive. Any special
keyword for searching?
I'm afraid I can't think of anything magical off the top of my head, no.
But I wonder if it would introduce any additional error to deltaG
calculations
On 2/20/13 1:59 PM, cdo wrote:
Hi all,
I'm new to Gromacs with a very basic question while I was reading tutorials.
Tried to search this but I couldn't narrow down to useful discussions so
far.
It's simple. I saw some pdb files in the Tutorias. (such as LYSOZYME). But
this particular pdb file
Hi,
pdb2gmx generate the connectivity from the residue and atom sequences
(the file format specs state the order in which they appear) and the
distances between atoms. This is fairly robust as long as the
coordinates aren't unusually bad. For instance, if two carbons are
located at ~1 C-C
Hi James,After doing your 2D projections with g_anaeig, determine the x-y
boundaries of your "transition state" from the plots.Your next task will be to
generate indices corresponding to the frames you want to extract. You can store
these indices in a file named frames.ndx (for example). The fil
Hi all,
I'm new to Gromacs with a very basic question while I was reading tutorials.
Tried to search this but I couldn't narrow down to useful discussions so
far.
It's simple. I saw some pdb files in the Tutorias. (such as LYSOZYME). But
this particular pdb file do not have all the connectivity i
Dear Mark,
Thank you for your reply, I was able to fix the position of ghost atom by
using "energygrp_excl " in my mdp file for energy exclusion between
ghost atom and the remaining part of the system and have removed center
of mass motion by using option comm_mode = linear .
If I o
Dear Bogdan,
Thank you for reply.
Best,
Ramesh.
On Mon, Feb 18, 2013 at 5:31 PM, Bogdan Costescu wrote:
> On Mon, Feb 18, 2013 at 12:10 PM, Mark Abraham
> wrote:
> > b) a particle needs to be at that immobile reference point - you can
> > measure a distance to a point whether or not there i
Hi Justin,
I was not able to find relevant posts in the archive. Any special
keyword for searching?
But I wonder if it would introduce any additional error to deltaG
calculations if I restrain the dissociation pathway to x axis, using
pull_vecl = 1 0 0. Would the program then forcing the velocit
Thank you justin for your Nice reply
As you Mailed Me
How Could i Check My System Is constructed efficiently or Poorly?
Can I Check Through APL?
I Have Stopped EM After Reaching APL as follows in Area.dat for DPPC
0.61064642393184 0
Hi again,
my topology is non-consecutively numbered. I was looking for a tool to
renumber it, but didn't find it yet. A hint will be really appreciated.
I was not sure either whether or not is it possible to use the xtc
generated with the original topology with the renumbered one. My main
dou
Thank you justin for your Nice reply
As you Mailed Me
How Could i Check My System Is constructed efficiently or Poorly?
Can I Check Through APL?
I Have Stopped EM After Reaching APL as follows in Area.dat for DPPC
0.61064642393184 0
On 2/20/13 9:41 AM, Felipe Pineda, PhD wrote:
Hi,
is it possible to apply g_order to a trajectory of a lipid bilayer when the
carbon atoms of the acyl chains of the lipid molecules for which the SCD should
be calculated are not numbered consecutively, i.e. the atom numbers
corresponding to C21
On 2/20/13 9:20 AM, Ahmet yıldırım wrote:
Dear users,
What is the meaning of the dummy atom in Gromacs?
Old terminology for virtual site.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
On 2/20/13 9:18 AM, Ahmet yıldırım wrote:
Dear users,
I have the virtual sites in reference structure and all trajectory. When
analyzing simulation, do I have to get rid of those(virtual sites)? If
yes/no, why?
Why do you think you need to remove them?
-Justin
--
=
On 2/20/13 9:03 AM, vidhya sankar wrote:
Dear Justin,
Thank you for your Previous reply.
I am DoingProtein- Lipid Simulation For My Assembly Of Cyclic Peptide
As you Told Me I Have Used The Restraint on water oxygen Atom Along the
Z-direction for My NVT equilibr
Hi,
is it possible to apply g_order to a trajectory of a lipid bilayer when
the carbon atoms of the acyl chains of the lipid molecules for which the
SCD should be calculated are not numbered consecutively, i.e. the atom
numbers corresponding to C21-C22-C23-... (sn-2 chain) are eg 23 22
1
Dear users,
What is the meaning of the dummy atom in Gromacs?
Regards
--
Ahmet Yıldırım
--
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/Mailing_Lists/Search before posting!
* Pl
Dear users,
I have the virtual sites in reference structure and all trajectory. When
analyzing simulation, do I have to get rid of those(virtual sites)? If
yes/no, why?
Regards
--
Ahmet Yıldırım
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-user
Dear Justin,
Thank you for your Previous reply.
I am Doing Protein- Lipid Simulation For My Assembly Of Cyclic Peptide
As you Told Me I Have Used The Restraint on water oxygen Atom Along the
Z-direction for My NVT equilibration There is No Leakage o
Thank Justin so much !
On Wed, Feb 20, 2013 at 8:15 PM, Justin Lemkul wrote:
>
>
> On 2/20/13 4:09 AM, Kieu Thu Nguyen wrote:
>
>> Dear all,
>>
>> I do not know whether there is any difference between a big bilayer and
>> the
>> other bilayer made from merging two small bilayers made before.
>>
On 2/20/13 1:14 AM, Yun Shi wrote:
Hi all,
For the purpose of calculating deltaG from umbrella sampling, I have
first pulled my ligand away from the enzyme active site along an
arbitrary direction (say x axis), setting the enzyme as pull_group0.
But I found the ligand was moving in the yz pla
On 2/20/13 4:09 AM, Kieu Thu Nguyen wrote:
Dear all,
I do not know whether there is any difference between a big bilayer and the
other bilayer made from merging two small bilayers made before.
I make a bilayer from two methods:
(1) merging two small bilayers (made before) by the below comman
On 2/20/13 12:46 AM, Hector Manuel Manzanilla Granados wrote:
Excuseme dear Dr. Tomas, forgiveme the boldness,
I'm new with this, and I dont know who to address
when I have a problem. My name is Hector, and I'm
tryng to install the gromacs software in my computer;
I follewed all the steps in t
My understanding is the following:
If you performed a simulation and then analyse it with different values
for 'nrexcl' the results will differ since a different amount of
interactions are excluded. It seems that the exclusion only helps for
'-rdf atom' and not for '-rdf mol_com'.
But the under
On Tue, Feb 19, 2013 at 8:19 PM, Tsjerk Wassenaar wrote:
> Hi Seok Yun,
>
> Duh. I meant why are you trying to determine the eigenvectors and
> eigenvalues of a 50k by 50k covariance matrix. How did you end up with
> such a matrix, and why do you think that that matrix will help you
> solve your
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