Payman Pirzadeh wrote:
You were right! The dimensions of the box are zero in the .gro file. Should
I change them to the values I have?
Set them using editconf
Mark
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On Behalf Of Justin A. Lemkul
Sent: July 16, 2009 11:42 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Hello,
Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the
rvdw cutoff to 10A, but problem was still there.
No
Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> But, I am using a .pdb file as the input of the gromacs. Does the
> preparation of pdb file differ from software to software?
>
It shouldn't, and I'm not 100% sure on how Gromacs handles
gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 16, 2009 11:42 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Hello,
Previously, my box was 27.154*31.354*103.386 (all in A) and
g]
On Behalf Of Justin A. Lemkul
Sent: July 16, 2009 11:42 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Hello,
Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the
rvdw cutoff to 10A, but problem was still there.
Now I m
: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Hello,
> Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the
> rvdw cutoff to 10A, but problem was still there.
> Now I made my box bigger by using a visualization
ion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Thanks Justin.
Unfortunately, I realized that after I sent the e-mail. Anyways, I
started
running to models: SPCE and TIP4P to check the energies of these systems
to
figure out where the proble
box size or reduce the rvdw.
Payman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 15, 2009 7:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman
users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Thanks Justin.
Unfortunately, I realized that after I sent the e-mail. Anyways, I started
running to models: SPCE and TIP4P to check the energies of these systems
to
figure out where the problem with my own system (six
OMACS users'
Subject: [gmx-users] making a box of water
Hello,
I have an .pdb file from another simulation. I want to make the appropriate
input files to run a simulations. I have used grompp to produce the .tpr
file, but I get the usual ERROR:
ERROR: The cut-off length is longer than half th
-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: July 15, 2009 12:23 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Thanks Justin.
> Unfortunately, I realized that after I sent the e-mail. Anyways, I started
> r
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 15, 2009 11:38 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Hi again,
I have a question about
15, 2009 11:38 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Hi again,
> I have a question about the .itp files. When e.g. TIP4P.itp the atomtypes
in
> the [atoms ]are specifies as opls_???, doesn't grompp check the
ssage-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: July 15, 2009 10:14 AM
To: jalem...@vt.edu; 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] making a box of water
OK!
I changed my .top file to
;Thi
ayman
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: July 15, 2009 10:14 AM
To: jalem...@vt.edu; 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] making a box of water
OK!
I changed my .top fil
o: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Will #include "ffgmx.itp" solve my problem? Would it be a general solution
> or in each case I should specify (if I add other solutes such as
proteins)?
>
Well, ffgmx is dep
n...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 14, 2009 7:07 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
You need to #include an appropriate force field that contains the
[defaults],
[atomtypes], etc. before you can define a [moleculetype].
-Just
emkul
Sent: July 14, 2009 7:07 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
You need to #include an appropriate force field that contains the
[defaults],
[atomtypes], etc. before you can define a [moleculetype].
-Justin
Payman Pirzadeh wrote:
> Here is my .to
: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Hello,
I am trying to make a box of water from three different water models. I
can make one from my own water model, but when I want to test TIP4P and
SPCE, as soon as it comes to energy minimization step and using grompp,
users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 14, 2009 6:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
> Hello,
>
> I am trying to make a box of water from three different water models. I
> ca
Payman Pirzadeh wrote:
Hello,
I am trying to make a box of water from three different water models. I
can make one from my own water model, but when I want to test TIP4P and
SPCE, as soon as it comes to energy minimization step and using grompp,
I get the following error message:
Prog
Hello,
I am trying to make a box of water from three different water models. I can
make one from my own water model, but when I want to test TIP4P and SPCE, as
soon as it comes to energy minimization step and using grompp, I get the
following error message:
Program grompp, VERSION 4.0.4
Sourc
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