Dear Gromacs users,
I am planing to simulate a polymeric crystal in
gromacs, which is of monoclinic unit cell with cell parameters a = 0.805 nm
b = 1.304 nm and c = 1.948 nm and beta = 125.4 deg. my crystal is of 424
type i.e 4 unit cells along 'a' direction '2' unit c
Hi Justin ,
Thank you , You are right .
Problem get solved by change in spacing in PDB file.
have a nice day.
With Best Wishes,
R.David
On Fri, Apr 6, 2012 at 6:36 PM, Justin A. Lemkul wrote:
>
>
> rama david wrote:
>
>> HI all ,
>> sorry for above incomplete information ,
>> I change CH3 of
On 2012-04-06 06:41:57PM -0700, Acoot Brett wrote:
> Dear All,
>
> Can I remove all the H from the PDB file and then input it to the pdb2gmx so
> that pdb2gmx can produce all the correct protonation state of the protein
> residues including HIS?
>
> Cheers,
>
> Acoot
It will not do what
Acoot Brett wrote:
Dear All,
Can I remove all the H from the PDB file and then input it to the
pdb2gmx so that pdb2gmx can produce all the correct protonation state of
the protein residues including HIS?
This question has already been answered several times in different forms, for
exam
On 2012-04-06 08:04:56PM -0500, ffavela wrote:
> Dear gmx-users,
>
> I'm trying to do a minimization of a popc bilayer created with the VMD
> membrane builder plugin. I've followed some of the recommendations of
> Justin Lemkul to build the topology for my system, i.e., running pdb2gmx
> for one l
Dear All,
Can I remove all the H from the PDB file and then input it to the pdb2gmx so
that pdb2gmx can produce all the correct protonation state of the protein
residues including HIS?
Cheers,
Acoot --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listi
bipin singh wrote:
Thanks for your comments
I have a very crude question which may not be even logical to ask here
but I just want to know your opinion on this:
If I will perform two simulations in following two ways :
*RUN:1*
(1) Did NVT with POSRES on protein and
gen_vel=yes
gen
ffavela wrote:
Dear gmx-users,
I'm trying to do a minimization of a popc bilayer created with the VMD
membrane builder plugin. I've followed some of the recommendations of
Justin Lemkul to build the topology for my system, i.e., running pdb2gmx
for one lipid (choosing the charmm36 force field
Dear gmx-users,
I'm trying to do a minimization of a popc bilayer created with the VMD
membrane builder plugin. I've followed some of the recommendations of
Justin Lemkul to build the topology for my system, i.e., running pdb2gmx
for one lipid (choosing the charmm36 force field I've downloaded fro
Thanks for your comments
I have a very crude question which may not be even logical to ask here but
I just want to know your opinion on this:
If I will perform two simulations in following two ways :
*RUN:1*
(1) Did NVT with POSRES on protein and
gen_vel=yes
gen_temp= 350
(2) Did NPT w
pitheve...@free.fr wrote:
Dear gmx users,
I try to use gmx to make some minimization. Unfortunatly, I have some SS
bonds which are not formed in my PDB because the S-S atoms are too far away
to connect to each other. I saw at that page :
http://www.gromacs.org/Documentation/How-tos/Making_Disu
Dear gmx users,
I try to use gmx to make some minimization. Unfortunatly, I have some SS bonds
which are not formed in my PDB because the S-S atoms are too far away to
connect to each other. I saw at that page :
http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds that it is
pos
On 7/04/2012 12:37 AM, Justin A. Lemkul wrote:
bipin singh wrote:
Thanks for your comments.
One more question.
Does Gromacs saves velocities in pdb files, when we use gen_vel=yes
option in mdp and save the output(-c) of mdrun as pdb file instead of
gro file.
No. Velocities are only save
bipin singh wrote:
Thanks for your comments.
One more question.
Does Gromacs saves velocities in pdb files, when we use gen_vel=yes
option in mdp and save the output(-c) of mdrun as pdb file instead of
gro file.
No. Velocities are only saved in the .trr and/or .cpt files. There is no pl
Thanks for your comments.
One more question.
Does Gromacs saves velocities in pdb files, when we use gen_vel=yes option
in mdp and save the output(-c) of mdrun as pdb file instead of gro file.
On Fri, Apr 6, 2012 at 19:48, Mark Abraham wrote:
> On 7/04/2012 12:15 AM, bipin singh wrote:
>
> When
On 7/04/2012 12:15 AM, bipin singh wrote:
When we mention
gen_vel=no ;And provide pdb as input with no velocities
As mentioned in the manual:
"The velocities are set to zero when there are no velocities in the
input structure file"
Please elaborate what does this sentence mean.
Each atom mu
When we mention
gen_vel=no ;And provide pdb as input with no velocities
As mentioned in the manual:
"The velocities are set to zero when there are no velocities in the input
structure file"
Please elaborate what does this sentence mean.
On Fri, Apr 6, 2012 at 19:10, Justin A. Lemkul wrote:
>
>
bipin singh wrote:
Also, if we give continuation=yes in mdp file and use input as pdb file
as input instead of gro file, grompp never complainsI don't no how
it reads velocities from pdb file (as no velocities are present in pdb
files). Ideally it should complain that no velocities found
Also, if we give continuation=yes in mdp file and use input as pdb file as
input instead of gro file, grompp never complainsI don't no how it
reads velocities from pdb file (as no velocities are present in pdb files).
Ideally it should complain that no velocities found in input file
On Fri
rama david wrote:
HI all ,
sorry for above incomplete information ,
I change CH3 of ACE residue of my pdb file to CA .
The formatting of a .pdb file requires fixed spacing. By turning CH3 into CA
(which is correct), you deleted a space such that instead of finding 'ACE' as
the residue n
Dear GROMACS community,
I would like to do a simulation with an oscillating electric field, using a
frequency of 14 GHz. Can anyone help me on what parameters(ver.4.5.3) I set
in E_X, E_Y, E_Z, E_Xt, E_Yt, E_Zt?
Thank you very much.
regards Roberto
--
View this message in context:
http://gr
Dear GROMACS community,
I would like to do a simulation with an oscillating electric field, using a
frequency of 14 GHz. Can anyone help me on what parameters(ver.4.5.3) I set
in E_X, E_Y, E_Z, E_Xt, E_Yt, E_Zt?
Thank you very much.
regards Roberto
--
View this message in context:
http://gr
HI all ,
sorry for above incomplete information ,
I change CH3 of ACE residue of my pdb file to CA .
Thank you in advance
On Fri, Apr 6, 2012 at 5:34 PM, rama david wrote:
> Hi GROMACS Friends and Mark..
>
> Thank you for reply ...
> My command line is
> pdb2gmx -f pdb -o p.pdb -p p.top -
Hi GROMACS Friends and Mark..
Thank you for reply ...
My command line is
pdb2gmx -f pdb -o p.pdb -p p.top -ignh -ter
I choose the G96 53a6 ff , along with spc water model.
Select start terminus type for ACE-1
0: NH3+
1: NH2
2: None
2
Start terminus ACE-1: None
Select end terminus
0: COO-
On 6/04/2012 9:05 PM, Mark Abraham wrote:
On 6/04/2012 8:27 PM, rama david wrote:
Hi Gromacs Friends and Justin ,
Thank you for reply and suggestion.
These is short part of my PDB .
ATOM 1 1H ACE 1 0.000 0.000 0.000
ATOM 2 CH3 ACE 1 0.000 1.090 0.000
A
On 6/04/2012 8:27 PM, rama david wrote:
Hi Gromacs Friends and Justin ,
Thank you for reply and suggestion.
These is short part of my PDB .
ATOM 1 1H ACE 1 0.000 0.000 0.000
ATOM 2 CH3 ACE 1 0.000 1.090 0.000
ATOM 3 2H ACE 1 1.028 1.4
Acoot Brett wrote:
Dear All,
For low resolution structure PDB, the protonation state of histidine is
niot clear. Then how does pdb2gmx treat the protonation state of HS?
Even for high resolution structure of protein, the protonation state of
HIS is usallly unclear or unspefified.
In t
Dear All,
For low resolution structure PDB, the protonation state of histidine is niot
clear. Then how does pdb2gmx treat the protonation state of HS?
Even for high resolution structure of protein, the protonation state of HIS is
usallly unclear or unspefified.
In the manual og gromacs,
Hi Gromacs Friends and Justin ,
Thank you for reply and suggestion.
These is short part of my PDB .
ATOM 1 1H ACE 1 0.000 0.000 0.000
ATOM 2 CH3 ACE 1 0.000 1.090 0.000
ATOM 3 2H ACE 1 1.028 1.453 -0.000
ATOM 4 3H ACE 1
Dear Tsjerk,
Thank you very much from your response.
How do I consider this in my analysis, Please?
Best Regards
Dina
From: Tsjerk Wassenaar
To: dina dusti ; Discussion list for GROMACS users
Sent: Friday, April 6, 2012 12:53 PM
Subject: Re: [gmx-users] vo
Thank you very much! Sorry , solid wall for me is distance between the solute
and the box!
Best wishes!
At 2012-04-06 16:42:02,"David van der Spoel" wrote:
Op 6 apr 2012 om 10:30 heeft "Xianwei Wang" het
volgende geschreven:
Thank you for your answer! But if electric field was screened by
Op 6 apr 2012 om 10:30 heeft "Xianwei Wang" het
volgende geschreven:
> Thank you for your answer! But if electric field was screened by the outside
> water in the box ,how I decide the size of electric field in the protein when
> I used "E_x = 1.0 0.71e-2 0" and solute wall distance of 1 nm?
Thank you for your answer! But if electric field was screened by the outside
water in the box ,how I decide the size of electric field in the protein when I
used "E_x = 1.0 0.71e-2 0" and solute wall distance of 1 nm?
Best wishes!
yours Xianwei Wang
At 2012-04-06 14:53:58,"David van der Spoel"
Hi Dina,
In your experiments your volume doesn't change (significantly). But if you
were to carve out a very small cube around a micelle, and track the
molecules in there (neglecting diffusion), you'd see that the molecules
sometimes expand and sometimes contract. That's what's happening on a
micr
Dear GROMACS Specialists,
May I ask you to answer my question, Please?
I have several systems consist of water and different molecules (surfactant
and etc. with same molecule number in all of them except water) that
equilibrated them in NPT ensemble, I wanted to have all of systems with same
Dear Gromacs users,
I am trying to simulate a polymer crystal in gromacs,
which is of monoclinic unit cell with cell parameters a = 0.805 nm, b =
1.304 nm, c = 1.948 nm, beta = 125.4 deg. my crystal consists of 4 unit
cells along 'a' , 2 unit cells along 'b' and 4 unit ce
On 2012-04-06 11:05:51AM +0400, James Starlight wrote:
> Dear Gromacs users!
>
>
> I have small question about order of the runs and input data.
>
> Ussually I do 2 equilibration phases and subsequent productive phase in the
> conditions wich are equal to the last equilibration phase ( e.g often
Dear Gromacs users!
I have small question about order of the runs and input data.
Ussually I do 2 equilibration phases and subsequent productive phase in the
conditions wich are equal to the last equilibration phase ( e.g often this
is npt ).
In the second equil.mdp and md.mdp there is option
On 6/04/2012 4:57 PM, Acoot Brett wrote:
Dear All,
Before and after extention we have 2 trajectorty files, and by trjcat
we got we, then we can do the g_rms
g_rms -s *.tpr -f *_noPBC.xtc -o rmsd.xvg -tu ns
But here for the g_rms command I find no matter whether we use the
*.tpr of the initiat
Because if all you did to generate the 2nd tpr file was tpbconv -extend, then
both tpr files are same *except* for the simulation time.
(gmxdump should prove it)
On 2012-04-05 11:57:41PM -0700, Acoot Brett wrote:
> Dear All,
>
> Before and after extention we have 2 trajectorty files, and by trjc
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