Hello. How could the martini CG-force-field could be used?You need to insert
some input files or you can find somewhere this forcefield and insert it in
the gromacs already excisted force-field list?Thank you!___
gmx-users mailing list
On Sun, 2009-02-01 at 23:34 -0300, Rafael Real Guerra wrote:
Hi
Well, let’s start saying that I’m new at Linux and I’m trying to start
on Gromacs as well.
I’ve been trying to install Gromacs 4.0 in my computer (laptop ACER
Aspire 4530, AMD Athlon 64X2) running Mandriva 2009 and I
Hi Nahren,
Gromacs does not include a tool for generation of porcupine plots. But
if you're offered a means to do it through a webservice, all you
really need is to take the extreme projections (two frames: g_anaeig
-extr) and submit them. In a sense, you'll get the same thing if you
load the
Check the VMD list, you should find the script there.
On Feb 1, 2009, at 9:28 PM, Mark Abraham wrote:
nahren manuel wrote:
Dear Gromacs Users,
I have done PCA of my MD , I want to visually represent the motions
in terms of porcupine plots. I came across Dynamite (web server)
for this
Hi Shirin,
The sed-solution is:
sed -ne '/^MODEL/,/^ENDMDL/{/^MODEL/{x;d};H}' -e '${x;p}' traj.pdb
Which might come in handy as an alias (csh-style:)
alias lastmodel sed -ne /^MODEL/,/^ENDMDL/{/^MODEL/{x;d};H} -e ${x;p} \!*'
Hope it helps,
Tsjerk
On Mon, Feb 2, 2009 at 8:03 AM, nahren
Hi,
pbc=full is replaced by the mdp option periodic_molecules,
which works both with pbc=xyz and pbc=xy.
Berk
Date: Sun, 1 Feb 2009 17:45:13 +0100
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] infinite polymer crystals at gromacs 4.x.x
Claus Valka wrote:
Hi all users,
I am wondering how to get the original pdb file for CG DNA model. I have looked
for this file in the website but no pdb file. Can anyone of you give me some
suggestions how to get such file ?
Thank you in advance.
Yang
___
gmx-users
Good afternoon,
The reason of this email is to ask:
is it possible to combine Martini's force field with the opls force field?
The system is conformed by dopc membrane [Modeled by Martini's force field]
with a small molecule of about 50 atoms [Modeled with opls. With all its
hydrogens].
if
Have you tried a web search? There are a number of sites that have
databases of structures. Plus you could contact people that have
published simulations using those molecules. What about the Protein
Data Bank?
Catch ya,
Dallas Warren
A polar bear is a Cartesian bear that has undergone a
On Feb 2, 2009, at 10:19 PM, DAVID RINCON wrote:
Good afternoon,
The reason of this email is to ask:
is it possible to combine Martini's force field with the opls force
field?
The system is conformed by dopc membrane [Modeled by Martini's force
field] with a small molecule of about 50
Hi, Justin
I remove the del command. But I still got an error.
make_ndx -f a.pdb -o a.ndx make_ndx.input
make_ndx.input:
chain A and B !a H*
chain C !a H*
q
checking input for internal consistency...
Opening library file /export/apps/share/gromacs/top//ffG53a6.itp
Opening library file
Alright, so how about the other comment I made? Are you using the right
coordinate file? I recall you got this error when you used the non-pdb2gmx
processed .pdb file as input into grompp. You must use the coordinate file that
corresponds to your topology.
-Justin
Liu Shiyong wrote:
Dear Dr. Tsjerk,
thanks for your reply. I got the clue from your reply and i did the same via
VMD. But can you please be little more speicific about Pymol. I am not quite
used to that software.
regards,
nahren
--- On Mon, 2/2/09, Tsjerk Wassenaar tsje...@gmail.com wrote:
From: Tsjerk
Hello, users. Can Gromacs do protein crystallization simulations? I tried
looking for some information about it on mailings but failed. Would anyone
give me some advice how to do it? Thanks.
Best,
william
___
gmx-users mailing list
doty alexiou wrote:
well.. it seems that there is a problem in the page for downloading
files from http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html.
It appears to be working now.
As to your original question, I would say learn to walk before you run. I have
used MARTINI only
Santan William wrote:
Hello, users. Can Gromacs do protein crystallization simulations? I
tried looking for some information about it on mailings but failed.
Would anyone give me some advice how to do it? Thanks.
Well, Gromacs can technically simulate galaxies, so I guess anything is
Hi Berk,
Could you please post the relevant cvs diff here? While my energies are now output consistently for zero-step mdruns while separating
my energygrps, I am still seeing some very aberrant behaviour when I apply the free-energy code during a 2-10 ns MD run,
even with lambda=0.0. I get
pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p
r-l_365130_G53a6.minim_traj_withH_0.6.top -i
r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o
r-l_365130_G53a6.minim_traj_withH_0.6.gro
r-l_365130_G53a6.minim_traj_withH_0.6.output.pdb2gmx 21
Hi, Justin
grompp read the
Liu Shiyong wrote:
pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p
r-l_365130_G53a6.minim_traj_withH_0.6.top -i
r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o
r-l_365130_G53a6.minim_traj_withH_0.6.gro
r-l_365130_G53a6.minim_traj_withH_0.6.output.pdb2gmx 21
Hi Nahren,
If you're used to VMD and got what you wanted, why would you want to
use Pymol for doing the same? Not that Pymol's not worth knowing :) In
Pymol, check the help for the 'align' command: 'help align'
Cheers,
Tsjerk
On Mon, Feb 2, 2009 at 11:51 AM, nahren manuel meetnah...@yahoo.com
On Mon, Feb 2, 2009 at 5:26 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Liu Shiyong wrote:
pdb2gmx -ignh -ff G53a6 -f r-l_365130_G53a6.minim_traj_withH.pdb -p
r-l_365130_G53a6.minim_traj_withH_0.6.top -i
r-l_365130_G53a6.minim_traj_withH_0.6.posre.itp -o
Liu Shiyong wrote:
Here is my command.
pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o
a6.gro
pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
Why are you running pdb2gmx twice? Unless you have multiple
proteins, and need multiple
command:
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
+ editconf -f a6.gro -o a6.gro -d 20.0
+ make_ndx -f a.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
b.pdb
ATOM 1 N ASP
Hi, Justin:
I saw in the manual that by g_energy -vis the viscosity of the system
can be calculated. But when I perform the command i got this:
@title Bulk Viscosity
@xaxis label Time (ps)
@yaxis label \8h\4 (cp)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@
Yanmei Song wrote:
Hi, Justin:
I saw in the manual that by g_energy -vis the viscosity of the system
can be calculated. But when I perform the command i got this:
@title Bulk Viscosity
@xaxis label Time (ps)
@yaxis label \8h\4 (cp)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@
Alright, none of this looks like it will cause a problem. Can you post your
em.mdp file?
-Justin
Liu Shiyong wrote:
command:
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
+ editconf -f a6.gro -o a6.gro -d 20.0
+ make_ndx
Liu Shiyong wrote:
command:
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
+ editconf -f a6.gro -o a6.gro -d 20.0
+ make_ndx -f a.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
I
On Feb 2, 2009, at 12:26 AM, Mark Abraham wrote:
No, I've no idea since I don't simulate DNA.
In that case, thank you the help that much more!
So I'm now attempting to add restraints for the base-pair H-
bonds, but I'm having trouble. It seems like no matter what I
try, my system reliably
Hi, Mark,
I tried your suggestion.
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb
+ editconf -f a6.pdb -o a6.gro -d 20.0
+ make_ndx -f a6.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
title = b
cpp
Liu Shiyong wrote:
Hi, Mark,
I tried your suggestion.
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb
+ editconf -f a6.pdb -o a6.gro -d 20.0
+ make_ndx -f a6.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
title
Liu Shiyong wrote:
Hi, Mark,
I tried your suggestion.
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb
+ editconf -f a6.pdb -o a6.gro -d 20.0
+ make_ndx -f a6.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
title =
Joshua Ballanco wrote:
On Feb 2, 2009, at 12:26 AM, Mark Abraham wrote:
No, I've no idea since I don't simulate DNA.
In that case, thank you the help that much more!
So I'm now attempting to add restraints for the base-pair
H-bonds, but I'm having trouble. It seems like no matter what I
Hi,
I have added the #include drg.itp statement under the title, ; Include
forcefield parameters in the .top file. Thr drg.itp is saved in the current
directory.
Still showing the sanme error as previous.
including a part of the top file.Please check this.
Ms. Aswathy S wrote:
Hi,
I have added the #include drg.itp statement under the title, ; Include
forcefield parameters in the .top file. Thr drg.itp is saved in the current directory.
This is the incorrect order. You've inserted the drg.itp moleculetype
information before your protein,
Ms. Aswathy S wrote:
Hi,
I have added the #include drg.itp statement under the title, ; Include
forcefield parameters in the .top file. Thr drg.itp is saved in the current directory.
Still showing the sanme error as previous.
including a part of the top file.Please check this.
Justin A. Lemkul wrote:
Ms. Aswathy S wrote:
Hi,
I have added the #include drg.itp statement under the title, ;
Include forcefield parameters in the .top file. Thr drg.itp is saved
in the current directory.
This is the incorrect order. You've inserted the drg.itp moleculetype
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