Xavier Periole wrote:
Dear Monika,
the setup of a REMD simulation is actually quite straightforward.
In the following I describe steps that would lead you to have a
REMD simulation running on a given system. The "success" of the
simulation will depend entirely on the problem you are addressing
Check out the gromacs examples in the ../share/gromacs/top for the
format.
spc.itp water parameters
spc216.growater coordinates
methanol.itp methanol parameters
Best wishes,
Art
On Dec 4, 2007, at 5:32 PM, Dallas B. Warren wrote:
So this means that f
Fiona Reid wrote:
Dear Anupam,
I also obtained a similar error to you when trying to install GROMACS on
Blue Gene. I posted a message to the list on Monday but have since
found a solution.
`/home/phd/04/mbuanjha/soft/gromacs-3.3.2/src/gmxlib/nonbonded/nb_kernel'
rm -f kernel-stamp
./mknb -
Hello,
I would like to simulate the glucose polymer dextran (~5-10 subunits)
and I am wondering what is the best way to do go about doing this. In
looking at ffgmx.rtp I see GLCA/B which seem to be the glucose parameter
files. If my numbering scheme is correct, to produce a linear dextran
mo
> > So this means that for me it's impossible to run the simulation of a
phenol
> > in a box of chloroform with ffamber99?
>
> No, it just means that you need to derive the parameters for these
molecules
> yourself according to the methods used in deriving the initial force
fields.
Or find the fi
>the last lines gives 0.000 0.000 0. in my file and in the examples
it is not.
>I assume it is the dimension of the box, isn' it?
That is correct. So that full explains what you see occuring.
>I built up the gro file using editconf -f *.pdb file.
You need to specify the size of the box wit
> Dear gmx users:
>
> I asked my question days ago, but no body answers me. So I think I
> should
> make my question compacter.
I'd suggest using gcc, or a gcc-compatibility mode of your compiler, if it
exists.
Mark
___
gmx-users mailing list
> I had trouble compiling gromacs-3.3.1 parallel (but not serial) on
> itanium2 until I found the following post:
>
> http://www.gromacs.org/pipermail/gmx-users/2004-February/009171.html
>
> And that solution was good... I now have a functional executable.
>
> To clarify, the solution was to do thi
> Hi,
>
> I installed a serial version of GMX, and am trying to install an mpi
> version. I did a make distclean, and followed standard procedures, and
> am getting the following errors during make mdrun:
>
> Any suggestions ? Thank you !
Something's badly wrong. In the absence of knowing exactly
> Respected all,
> I am currently involved in a project which aims to simulate pressure
> driven
> nanochannel fluid flow through a wall made of hydrophobic and hydrophilic
> patches using GROMACS . I have been able to successfully run the
> simulation
> and have been able to obtain most of the plo
> hi, all
> My protein has 16 subunits. After I use trjconv '-pbc nojump' to remove
> the jump in the whole protein, there are no jump to each subunits.
> However, when i check pdb file of the first frame, it is shown that the
> subunits are not in right position. The area of interface between som
>
> Dear users
> I was tyring to run an npt simulation of membrane. My mdp is:
> As advised in a recent workshop on http://www.csc.fi/chem/course/gmx2007/
> i am using Parrinello-Rahman instead of berendsen. The problem is that the
> box size is getting reduced to 9.99448 9.99448 9.25077 from 10.0
> Dear all,
>
> I am trying to simulate a ligand at the cavity of CB receptor with the
> dmso environment. Even if I used very large number of steps for the
> geometry optimization before simulation, I have some LINCS problem for the
> solvent, I changed the solvent from dmso to water, but it didn'
> Dear all
> I want to put restraint on peptide bond and analyse in both cis and trans
> form.
>
> But hor to put these restraints??
Do be aware that constraints and restraints are different things in
GROMACS. Please see Chapter 5 for information on both.
Mark
_
I would like to set up two peptide simulations (with different peptide
conformations) that have the same number of water molecules in truncated
octahedral boxes with periodic boundary conditions. Can anyone suggest a
good way to specify that the same number of waters be added for each of
these
Dear Gromacs users,
I would like to set up two peptide simulations (with different peptide
conformations) that have the same number of water molecules in truncated
octahedral boxes with periodic boundary conditions. Can anyone suggest a
good way to specify that the same number of waters be added
Quoting Mauro Puppett <[EMAIL PROTECTED]>:
>
> So this means that for me it's impossible to run the simulation of a phenol
> in a box of chloroform with ffamber99?
No, it just means that you need to derive the parameters for these molecules
yourself according to the methods used in deriving the i
So this means that for me it's impossible to run the simulation of a phenol in
a box of chloroform with ffamber99?
> Date: Tue, 4 Dec 2007 12:01:01 -0500
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] ffamber_chcl3.gro
>
> Quoting Mauro Puppett <[EMAIL PROTECTE
Quoting Mauro Puppett <[EMAIL PROTECTED]>:
>
> Hi all,
> I have to run a simulation in a box of chloroform.
> I've found a chcl3.itp and a chcl3_box.gro files but I'm using ffamber99
> forcefield.
> Is it possible to modify someway the two files above? Where can I find the
> informations to do tha
Hi all,
I have to run a simulation in a box of chloroform.
I've found a chcl3.itp and a chcl3_box.gro files but I'm using ffamber99
forcefield.
Is it possible to modify someway the two files above? Where can I find the
informations to do that?
Thanks in advance
Respected all,
I am currently involved in a project which aims to simulate pressure driven
nanochannel fluid flow through a wall made of hydrophobic and hydrophilic
patches using GROMACS . I have been able to successfully run the simulation
and have been able to obtain most of the plots necessary t
hi, all
My protein has 16 subunits. After I use trjconv '-pbc nojump' to remove
the jump in the whole protein, there are no jump to each subunits.
However, when i check pdb file of the first frame, it is shown that the
subunits are not in right position. The area of interface between some
subunits
Dear all,
I am trying to simulate a ligand at the cavity of CB receptor with the dmso
environment. Even if I used very large number of steps for the geometry
optimization before simulation, I have some LINCS problem for the solvent, I
changed the solvent from dmso to water, but it didn't help
Dear all
I want to put restraint on peptide bond and analyse in both cis and trans form.
But hor to put these restraints??
regards
nur
-
Did you know? You can CHAT without downloading messenger. Click here__
From: "Adrien Leygue" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users
To: "Discussion list for GROMACS users"
Subject: [gmx-users] tabulated potential and long range pressure correction
Date: Mon, 3 Dec 2007 18:17:56 +0200
Dear Gromacs users,
I am using Gromacs on a system
Hi Jestin,
As I said, the last line in the .gro file codes for the box. So, you have a
singular box! You probably did something wrong with editconf. Did you give
it box dimensions at all (-box/-d). Have a look at the help: editconf -h
Besides that, do have a look at the procedure you used to obta
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