I want to add new potential function into Gromacs, and I know there is a
way to do this by using "tabulate".
But I am not sure about how to use tabulate,and how many new potential
function could be added?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/
Dear all :)
I have one extra question about Genion.
I want to neitralise my system with the qtot - 1.550002e by placing some Na
and Cl ions under the physiological concetrantion 100 mmol/l
I've performed
genion -s ions.tpr -o b2ar_ions.gro -p topol.top -pname NA -nname CL -conc
0.1 -neutral
bu
Dear Gromacs users,
i am adding new residue to the existing charmm27
force field of the gromacs and i am planning to use buckingham potential
for the non bonded interactions. for that i made following changes to the
ffnonbonded.itp file
[ atomtypes ]
;name at.num m
Many thanks, can you tell me the reason? becuase I see in the old
manual, there said "if there is fixed part in the system, then you can
not use the removal of the center of the mass."
XJ
2012/2/21, Yang Ye :
> yes. you need to and can still put System for the removal group.
>
>>
>> On Feb 21, 201
What does it look like when you visualise the coordinate file? That is how you
can answer that question, as we certainly can't.
And as you will soon find out, you cannot have a single interface in a
simulation box, you have to have two.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug
Search the literature and see what others have done to do exactly this.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
From: NG HUI WEN
Sent: Sunday, February 19, 2012 1:19 PM
To: gmx-users@gromacs.org
Subject: Distance Restraints on Protein - possible at all?
Dear gmxusers,
I have been trying to apply distance restraints on my protein but have been
unsuccessful thus far.
I have consulted the user forum
On 2012-02-21 03:41:07PM -0500, Justin A. Lemkul wrote:
>
>
> Andrew DeYoung wrote:
> > Hi,
> >
> > I am interested in doing a membrane-type simulation, in which I have
> > all-atom membrane "walls" parallel to xy plane, at z = -z_0 and z = +z_0
> > (where z_0 is a constant). I would like to ru
On 21/02/2012 19:02, "David van der Spoel" wrote:
> On 2/21/12 6:17 PM, Richard Broadbent wrote:
>> Dear All,
>>
>> I am considering conducting a simulation of a polymeric system in
>> gromacs. I would like to use the COMPASS forcefield as it has a complete
>> parameter set for my molecule.
>
On 22/02/2012 3:11 AM, mohammad agha wrote:
Dear Gromacs Specialists,
I made a box consists of water with box lengths: 6nm * 6nm * 6nm ,
then I equilibrated it with NPT ensemble, box size increased to
6.66176, then I kept the /x-/ and /y-/dimensions fixed, and double the
system size in /z
Andrew DeYoung wrote:
Hi,
I am interested in doing a membrane-type simulation, in which I have
all-atom membrane "walls" parallel to xy plane, at z = -z_0 and z = +z_0
(where z_0 is a constant). I would like to run an NPT simulation at 1 atm.
What type of pressure coupling should I use? Is
Anna Marabotti wrote:
Dear users,
I'm using g_hbond with option -contact in order to find the contacts
between my protein and a series of ligands, in a radius of 0.5 nm. I
made several calculations but I'm quite uncertain about the results,
therefore I'm asking you some questions.
The comm
Dear users,
I'm using g_hbond with option -contact in order to find the contacts between
my protein and a series of ligands, in a radius of 0.5 nm. I made several
calculations but I'm quite uncertain about the results, therefore I'm asking
you some questions.
The command I used is:
g_hbond -f my_
On 2/21/12 6:17 PM, Richard Broadbent wrote:
Dear All,
I am considering conducting a simulation of a polymeric system in
gromacs. I would like to use the COMPASS forcefield as it has a complete
parameter set for my molecule.
I believe the majority of the implementation is simple (though long an
Dear All,
I am considering conducting a simulation of a polymeric system in
gromacs. I would like to use the COMPASS forcefield as it has a complete
parameter set for my molecule.
I believe the majority of the implementation is simple (though long and
fiddly). However, it has Bond-Dihedral and An
Hi,
I am interested in doing a membrane-type simulation, in which I have
all-atom membrane "walls" parallel to xy plane, at z = -z_0 and z = +z_0
(where z_0 is a constant). I would like to run an NPT simulation at 1 atm.
What type of pressure coupling should I use? Isotropic pressure coupling
Dear all,
>I have done the clustering analysis using g_cluster, I got the 11 clusters i
>have used the cutoff of 0.4 nm, now i want to see how well the
>structure distributed in each clusters. I have got the middle structure of
>each clusters, Here i have given the cutoff of 0.4 nm, due to which
Dear Gromacs Specialists,
I made a box consists of water with box lengths: 6nm * 6nm * 6nm , then I
equilibrated it with NPT ensemble, box size increased to 6.66176, then I kept
the x- and y-dimensions fixed, and double the system size in z as following:
editconf -f pr1.gro -o newbox1.gro -bo
Hi GMX-users!
If someone else get the same problem. I will present how I could
recover the edr files:
1. Calculate the number of bytes for header consisted of in single and
double precision, respectively.
run some short test runs to calculate this
2. Calculate the number of bytes for each fram
Hi
I'm trying to set to zero the charges of my ligand group (MOL) using
tpbconv:
tpbconv_d -s md.tpr -f md.trr -n -o md_lig_zero.tpr -zeroq
then I select the MOL group and I get the following message:
Selected 14: 'MOL'
Segmentation fault (core dumped)
Any explanation to why this may have happ
Hi
I ran a md simulation for a system with two groups: Surrounding , LIG.
I wish to set the charges of the surrounding group to zero and to
recalculate the Coulomb interactions between the groups.
For this purpose I used tpbconv with the -zeroq option:
tpbconv_d -s md_prev.tpr -f md_prev.trr -n
yes. you need to and can still put System for the removal group.
>
> On Feb 21, 2012 5:51 PM, "xiaojing gong" wrote:
>>
>> Dear all,
>> I used the GMX 4.5.5 to run a simulation with a fixed plane and
water.
>> I wonder to know if I fix the plane, shall I use the command of
>> the remov
lina wrote:
Hi,
I don't know how to extract the position like the x y z with t or r with t.
g_traj prints coordinates from a trajectory.
-Justin
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemist
shahid nayeem wrote:
Initially I used g_wham -if pullf-files.dat -it tpr-files.dat -unit Kcal
-histo. But now as suggested by you I added -b 1000 -e 1 leaving
1ns for equilibriation. The new profile.xvg is attached. How can I
further improve it.
I don't know. You've never even state
Hi,
I don't know how to extract the position like the x y z with t or r with t.
Thanks for any suggestions,
Best regards,
--
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_L
Hi Ariel,
If it works, it's good :)
It really only affects the visualization... It doesn't change the system.
Cheers,
Tsjerk
On Tue, Feb 21, 2012 at 10:33 AM, Siew Wen Leong
wrote:
> Dear all,
>
> Have anyone tried using CHARMM36 equilibrated POPE bilayer by Dr.Klauda
> http://terpconnect.umd.
Dear all,
I used the GMX 4.5.5 to run a simulation with a fixed plane and water.
I wonder to know if I fix the plane, shall I use the command of
the removal of the center of mass for water? I will appreciate it if
you will share your opion.
Many thanks
XJ
--
gmx-users mailing list
Dear all,
Have anyone tried using CHARMM36 equilibrated POPE bilayer by Dr.Klauda
http://terpconnect.umd.edu/~jbklauda/research/download.html?
I am planning to use the membrane patch for a transmembrane protein
simulation. At first visualization, the membrane patch consists of a
bilayer with a si
Dear Gromacs Specialists,
I want to make a system consists of one box of solvent (for example water) that
there is 100 surfactant molecules in it and water is in contact with air in
surface as same as we do in laboratory in beaker. But I don't know how should I
define this air-water interface f
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