Hello Gromacs users,
I ran gmxcheck on a trr file I got from running energy minimization,
Gmxcheck's output is:
-
Checking file 4PLMYWOrg01_em_tim.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time0.000
# Atoms 55986
Reading f
Shay Amram wrote:
Hello Gromacs users,
I ran gmxcheck on a trr file I got from running energy minimization,
Gmxcheck’s output is:
-
*/ Checking file 4PLMYWOrg01_em_tim.trr /*
*/ trn version: GMX_trn_file (single precision) /*
*/ Reading /* */ frame
Hi Jeroen
Thank you for your reply. I just wanted to know whether the correction
term for the 'uniform background charge' is included in the code; I didn't
meant to to take it out.
Another thing is about the dipole correction that is applied for conducting
boundary conditions. Is it switched
I thought as much but wanted to make sure.
Thank you for your quick reply.
-Shay
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of David van der Spoel
Sent: Wednesday, September 19, 2007 11:38
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Mm
Georgios Patargias wrote:
Hi Jeroen
Thank you for your reply. I just wanted to know whether the correction
term for the 'uniform background charge' is included in the code; I didn't
meant to to take it out.
Another thing is about the dipole correction that is applied for conducting
boundar
Hi George,
Sorry, I got a bit carried away. Actually, I once thought of somehow
taking it out myself, so probably that's why. ;-)
About the dipole correction: I haven't experimented with it myself, but
I'm pretty sure it's switched off when epsilon_surface is 0. That's also
what the manual says (
Hi Jeroen
Thanks once again for your reply.
Best wishes
George
-Original Message-
From: [EMAIL PROTECTED] on behalf of van Bemmelen
Sent: Wed 9/19/2007 11:16 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] RE: Neutralising charge distribution
Hi George,
Sorry, I got a bit carried
parichita parichita wrote:
Thaks for your suggesion...
I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the
problem I encounter is that the pdb2gmx produces the topologies where hydrogens
sitting on carbons are condensed on carbon atoms they sit on. I need them expl
Thaks for your suggesion...
I want to use Gromacs for MD on my disaccharides in explicit water box.Now, the
problem I encounter is that the pdb2gmx produces the topologies where hydrogens
sitting on carbons are condensed on carbon atoms they sit on. I need them
explicitly
since I would like
Hi
Somer,
I want to simulate my Alpha d-mannopyranosyl (1-6) alpha d-mannopyranose
explicitly using my NOE restrain.
I am new to MD using GROMACS .
Please,give some thought .
Thanks in advance
parichita
Parichita Mazumder
Junior Research Fello
Actually, I'd say they're not incorrect, but incomplete (well, for many
systems). There's no mention of the correction terms George was asking
about, only the self correction term is taken into account in those
equations. But they're in the code allright, and a lot can be induced
from the mdp param
thanks for reply.I want to perform simulation of popc membrane.
Steps which i have done are as follows:
1. download popc128a.pdb, popc.it,lipids.itp
(http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
2. download ffgmx_lipids files
3.convert POPC of .top & popc.itp i
Quoting Moutusi Manna <[EMAIL PROTECTED]>:
> thanks for reply.I want to perform simulation of popc membrane.
> Steps which i have done are as follows:
> 1. download popc128a.pdb, popc.it,lipids.itp
> (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
> 2. download ff
Hello David:
Yes, you are right. the value equals to the square of the distance,
approximately. In fact, the force field I used was GROMOS96 43a1 force
field. I have also tried the other kind of force fields, such as
OPLS-AA/L all-atom force field, the same warning was reported, but the
"sh
Hello, David
I have download the CVS version 3.3.2. it works well.
Thank you very much for your hard work in gromacs.
YuDaqi
在 2007-09-19三的 11:45 [EMAIL PROTECTED]
> Re: Atomic distances problems using gmxcheck (David van der Spoel)
___
Hello everyone,
Eventually I want to pull a carbon nanotube through water at a
constant rate. Before I get to this, I'm pulling a nanotube in vacuum
just to make sure I'm using the pull code correctly.
My system consists of a carbon nanotube aligned along the z axis and a
single dummy atom fixed o
Hi All,
Does anyone know what the default vdw type if none is specified?
Is the value in brackets in the manual the default? If so, there is
none listed for VWD type.
Additionally, if PME is selected as the coulombtype, do the cutoffs
matter? I am a bit confused in this regard.
Thanks i
Hi GXM Users,
I'm trying to execute some AFM Pulling. I followed the pull code tutorial
from GMX WORKSHOP 2007, and I found there is no specific to com motion in
mdp, so the default is "comm-mode=Linear" and "comm-grps=System". I was
confused about it as I believed we should not stopcm when
18 matches
Mail list logo