Tandia, Adama wrote:
Dears,
I'm generating a box filled with NO3 molecules using Gromacs 3.3:
Any particular reason you're using software that is five years old? Unless
you've got a particular reason (i.e. continuity with older work), I'd strongly
recommend upgrading to version 4.0.7 for
Dears,
I'm generating a box filled with NO3 molecules using Gromacs 3.3:
genbox -ci molecule.gro -p molecule.top -o bigbox.gro -box 4.0 4.0 4.0
-nmol 800 -vdwd 0.2
The file bigbox.gro is generated but molecules are entangled. This makes
the geometry optimization to remove close contact impossib
What happened when you tried that command?
If you ran the command, tried it, and check the output to see if it is
what you want, you would be a long way head of waiting hours or more for
someone on the emailing list to reply with a response.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry
I tried the -Sg and it worked. Thanks.
But, I used -Sgsl for a spatial profile and it looks like that it is not
a valid option. I tried the following:
g_order_d_mpi -f Ih0001_54_62_102.xtc -n wateroxygens.ndx -s
Ih0001_54_62_102.tpr -os Ih0001_54_62_102-sg -sl 100 -d z
but I ran into the previou
Hi,
Gromacs 4.5-beta3 explicitly include the CHARMM c27 force field but not the
c36 force field. Have anyone done any work to transfer the CHARMM c36 force
field to Gromacs? Dr. Mark James Abraham has written a perl script to do the
charmm_to_gromacs transfer, however that only works for the c27 w
Alex,
If you do decide to continue along with the method that I suggested,
I'll join back in. To this point, I see no indication that you have
tried to relate the force to the position for the water runs, which is
my standing suggestion to you.
Chris.
Quoting alexander yakovenko :
sure.
On 2010-08-31 21.19, Paymon Pirzadeh wrote:
Here is the command:
g_order_d_mpi -f 265K_50_50_50_2-pbcfixed.xtc -n wateroxygens.ndx -s
265K_50_50_50_2.tpr -o Sg265K
You need to replace -o by one of
-Sg sg-ang.xvg Output, Opt. xvgr/xmgr file
-Sksk-dist.xvg Output, Opt. xvgr/xmgr file
Here is the command:
g_order_d_mpi -f 265K_50_50_50_2-pbcfixed.xtc -n wateroxygens.ndx -s
265K_50_50_50_2.tpr -o Sg265K
On Tue, 2010-08-31 at 21:15 +0200, David van der Spoel wrote:
> On 2010-08-31 21.10, Paymon Pirzadeh wrote:
> > Yes,
> > I tried it, but I run into segmentation fault. Here is
On 2010-08-31 21.10, Paymon Pirzadeh wrote:
Yes,
I tried it, but I run into segmentation fault. Here is part of the error
message:
WARNING: distance between atoms 4869 and 0> 0.3 nm (3.515866). Index
file might be corrupt.
WARNING: distance between atoms 4870 and 0> 0.3 nm (3.580329). Index
fi
Yes,
I tried it, but I run into segmentation fault. Here is part of the error
message:
WARNING: distance between atoms 4869 and 0 > 0.3 nm (3.515866). Index
file might be corrupt.
WARNING: distance between atoms 4870 and 0 > 0.3 nm (3.580329). Index
file might be corrupt.
WARNING: distance between
Hi,
On 08/31/2010 12:53 PM, Christian Mücksch wrote:
Dear all,
I am using Gromacs-4.5-beta4 and compiled the GPU-Version. So far only
Amber-FF are working in the GPU-version.
Gromacs-GPU supports only AMBER and CHARMM forcefields. By default,
pdb2gmx enables the -cmap option, and cmap dih
Can you post a snip of your pullx and pullf files from the water box
simulation where you pulled on 2 waters?
Quoting alexander yakovenko :
Yep, my case is b :(... Gromacs do writes pullx as ref COM global
coords and pull COM displacement. And I still don't realize what is
force value i
Yep, my case is b :(... Gromacs do writes pullx as ref COM global coords and
pull COM displacement. And I still don't realize what is force value in pullf
but it gives identical results for both -if and -ix options of g_wham. And
g_wham do works OK at least for 2 waters separation in 0.3-1nm sc
On 2010-08-31 20.26, Paymon Pirzadeh wrote:
Hello,
It is said in the mannual that g_order compute the order parameter per
atom for carbon tails. Can it also calculate order (degree of
tetrahedrality) for water molecules if only water oxygens are selected
in index file? The reference paper is for
Hello,
It is said in the mannual that g_order compute the order parameter per
atom for carbon tails. Can it also calculate order (degree of
tetrahedrality) for water molecules if only water oxygens are selected
in index file? The reference paper is for water molecules though. Also,
does it calculat
Hi all,
I am simulating drugs in water/lipid bilayer environment.
And I have noticed that when I put drug into the middle of the box, it is
moving rather quickly around until it finds a x or y boundary. Then it stays
there moving not much on both sides of the box.
In the first time it looked fine t
Hello,
I am trying to simulate N-methylglycine amide. I selected 'none'
for the termini using oplsaa forcefield. I got the topology but I got
the error saying:
ERROR 1 [file topol.top, line 126]:
No default Ryckaert-Bell. types
I checked the line 126 in my topol file and it is the di
On 2010-08-31 16.23, WJ Evans wrote:
> Hello,
> We are trying to create a model of a carbon nanotube with simple
> carbon-like chains attached around the entrance and exit of the
> nanotube. The problem is we need nrexcl set to 3 in nanotube but wnat
> nrexcl=1 in the chains. We have searched th
Hello,
We are trying to create a model of a carbon nanotube with simple carbon-like
chains attached around the entrance and exit of the nanotube. The problem is we
need nrexcl set to 3 in nanotube but wnat nrexcl=1 in the chains. We have
searched the GROMACS manual and user list extensively and
Dear Erik Marklund
thabks for your attention
I want only have water molecules being in 1.5 nm of solute in final frame
(2 ps)
I used following command: trjorder -f *.xtc -s *.tpr -n *.ndx -o *.gro
-r 1.5 -b 2
is it true?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gr
Dear Gromacs users,
I am quite new in gromacs, so maybe I am missing something obvious.
Is there any standard option/function to calculate different impacts into the
pressure tensor (i.e. due to VdW interactions, due to bonded interaction, due
to electrostatics etc.) ?
Thanks a lot in advance,
You can use trjorder to do this
Cheers
Tom
leila karami wrote:
Dear gromacs users
I did simulation of protein-dna complex in a box with size 7,7,7. There
are 5000 water molecule in this box. After full md simulation, I need a
pdb or gro file containing only water molecules being exactly
leila karami skrev 2010-08-31 14.48:
Dear gromacs users
I did simulation of protein-dna complex in a box with size 7,7,7.
There are 5000 water molecule in this box. After full md simulation, I
need a pdb or gro file containing only water molecules being exactly
environment of pr-dna complex
Dear gromacs users
I did simulation of protein-dna complex in a box with size 7,7,7. There are
5000 water molecule in this box. After full md simulation, I need a pdb or
gro file containing only water molecules being exactly environment of pr-dna
complex and not water molecules being in edges or
Justin A. Lemkul skrev 2010-08-31 12.35:
Nilesh Dhumal wrote:
THanks.
I have one more system dioxin + water molecules. There is possiblity of
C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water.
I want to calculate the number of hydrogen bonds.
I used the following command
It's a messy solution, but you could
1. run trjconv so that your cylinder is in the unit cell
2. convert your trajectory to .gro files
3. massively expand the x and y dimensions of each .gro
4. join the .gros to a .xtc
5. g_rdf
You could also use template.c to write a program that does this
di
Dear gromacs users
I have surface groups anchored on a cylindrical pore wall (similar to
a carbon nanotube). The pore runs along the z direction. I am trying
to determine to what extent my surface groups are clustered together
and was thinking of using g_mindist and/or g_rdf for this analy
Sorry Alex, but there is no good substitute what I have already
suggested. I helped you find a lead and I suggested a way to simplify
your system to discover what is going on. Now it's up to you to do
that work.
It might end up being a bug, but I doubt it. I have done things
similar to wh
Dear all,
I am using Gromacs-4.5-beta4 and compiled the GPU-Version. So far only
Amber-FF are working in the GPU-version. When I want to use the GBSA
implicit water-model I have to use cut-off for the electrostatic
interactions due to this error-message:
ERROR 1 [file PR.mdp]:
With GBSA,
Hi Mark,
I've just tried the link you mentioned and it seems to work. Could you
try again?
Cheers,
--
Szilárd
On Tue, Aug 31, 2010 at 9:53 AM, Mark Cheeseman
wrote:
> Hello,
>
> I am trying to download Version 4.0.5 but the FTP server keeps timing out.
> Is there a problem?
>
> Thanks,
> Mark
Nilesh Dhumal wrote:
THanks.
I have one more system dioxin + water molecules. There is possiblity of
C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water.
I want to calculate the number of hydrogen bonds.
I used the following command
g_hbond -f dix-bdmp.trr -s dix-bdmp.tpr -n
- Original Message -
From: zhongjin
Date: Tuesday, August 31, 2010 18:23
Subject: [gmx-users] Fatal error when using do_dssp
To: gmx-users@gromacs.org
---
| > Hi, > I have installed the dsspcmbi, and then add " export
DSSP=/home
- Original Message -
From: tekle...@ualberta.ca
Date: Tuesday, August 31, 2010 17:50
Subject: [gmx-users] Post processing in Gromacs code
To: Discussion list for GROMACS users
> Dear Gromacs users,
>
> Where Can I find the code for the post processing functions in
> Gromacs. I want to
Hi,
I have installed the dsspcmbi, and then add " export
DSSP=/home/hzj1000/dssp",I can use dsspcmbi.But when I use do_dssp, came across
the following error:
Failed to execute command: /usr/local/bin/dssp -na ddS7CWeR dd48KVro
> /dev/null 2> /dev/null
Please help me, thanks !
Zhongjin He
Hi,
The distance component along the O-C bond is the distance between O and the COM
of CH3.
The distance component perpendicular to the O-C bond is such that the intertia
(sum m r^2)
of the two masses matches that of the 3 H's.
I can mail you an awk script that automatically determines this fr
Hi,
massA and massB in mdatoms are only set when doing free-energy calculations.
massT gives the mass of a particle.
Unfortunately there is a serious lack of documentation in the data type include
files
(and in most other parts of the code).
Berk
> Date: Tue, 31 Aug 2010 10:46:51 +0300
> From:
Hello,
I am trying to download Version 4.0.5 but the FTP server keeps timing out.
Is there a problem?
Thanks,
Mark
--
Mark Patrick Cheeseman
Computational Scientist
KSL (KAUST Supercomputing Laboratory)
Building 1, Office #126
King Abdullah University of Science & Technology
Thuwal 23955-6900
Dear Gromacs users,
Where Can I find the code for the post processing functions in
Gromacs. I want to modify the code like for the g_dist and other
functions. I tried on the bin in gromacs but cannot open it and view
the code inside there.
Can you please tell me on that.
Rob
--
gmx-users
Good morning!
I'm having C trouble with something which should be simple enough:
GROMACS uses a struct called mdatoms which, amongst other things, houses
the atom masses during the simulation. I'm trying to access this data
(an array of the masses of all atoms). I've tried to consult internet
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