Hello list,
does g_mdmat ouput the standard deviation that goes along with the mean.xpm
file? Thank you.
-Rob
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> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] g_hbond angle def
>
> rob yang wrote:
> > At the risk of exposing my density in triangle geometry here, why does
> > 180-DHA = ADH?
> > H
> >/ \
> > D - A
>
>
At the risk of exposing my density in triangle geometry here, why does 180-DHA
= ADH?
H
/ \
D - A
Thank you.
-Rob
> Obviously the DHA angle in a linear Hbond is
> 180, so it should either be 180-DHA or ADH. The ADH angle is what's
> implemented in gromacs > 3.2.1, however in
Hi list,
What's the geometric relation b/w the commonly used Donor-H-Acceptor angle and
the gromacs implementation of Acceptor-Donor-H angle? I guess I don't quite
follow why it's valid to define the ADH cutoff as 30 degrees, the same angle
most commonly used to define DHA, which suggests ADH==
Okay, my mistake. Here's what each option gave me (all with -ur compact):
-pbc whole: broken protein, rectangular box
-pbc mol: intact protein, rectangular box, part of protein sticking outside the
box
-pbc atom: intact protein, dodecahedron box
> but -pbc mol -ur compact should give you a dod
trjconv
> Date: Fri, 7 Mar 2008 15:54:11 +
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] .gro files generation for a certain time-step interval
> in a simulation
>
> Hi All,
>
> I wonder if anyone knows what is the command to u
Dave,
I am using it for visualization for now. -pbc mol gave me the same output as
-pbc whole, which was a cubic box with broken protein. -pbc atom gave the
dodecahedron box and intact protein. But since the functionality of -pbc mol
has changed, and may not be applicable to visualization purpo
> Subject: Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous
> versions
>
> rob yang wrote:
>> Hi list,
>> I have a system solvated in dodecahedron box. To visualize it, I used:
>> trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc who
TED]: Re: RE: [gmx-users] TIP5P and cg minimization Rob,I wonder
whether you have got the flexible water model, TIP5P. I want to run simulations
using the flexible TIP5P water model. Well, how does the results from the MD be
affected if I use rigid water models in place of a flexible one?regards
Hi list,
I have a system solvated in dodecahedron box. To visualize it, I used:
trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc whole
Version 3.3.3 gave me a cubic box with broken molecules while the previous
versions gave me the right visualization on the same system.gro
Does
Thanks Mark for the pointer.
The TIP5P.itp has [settles] only, whereas TIP4P.itp (as well as spc.itp, and
TIP3P) has parameters for flexible water [FLEXIBLE] as well as rigid [settles].
This, by definition would restrict any systems using TIP5P to the SHAKE
algorithm. I am wondering:
1) are t
Hi list,
I have solvated my protein in TIP5P box that's provided by 3.3.3. However, when
I try to run an energy minimization using cg (at the grompp stage), I get:
ERROR: can not do Conjugate Gradients with constraints (218328)
I don't have any problem using the same em.mdp file on TIP4P, so I
Hi Ken,
#define gd_9 0.000 3.14 2
0.000 = phase shift. it takes on values of 0 or 180.
3.14 = force constant in KJ/mol
2 = multiplicity of the torsion term
the torsion equation is: Sum of {(Force constant)/2*(1+cos(phase
shift)*cos(multiplicity * your angle))}
it can the
Hi list,
Just wondering if anybody have gromacs-formatted oplsaa2005 parameters?
Thank you.
Rob
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7:26:43.0416 (UTC)
FILETIME=[CCC10580:01C64467]
It can be possibly done as you said... =) You may have your difficulty in
this but not specified in the mail.
Use nstep=1 to calculate the energy.
Yang Ye
rob yang wrote:
Hi list,
is there a way to calculate the energy of a given molecule wi
Hi list,
is there a way to calculate the energy of a given molecule without having to
put it in a periodic box?.. thanks
Rob
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X-OriginalArrivalTime: 04 Mar 2006 05:16:52.0925 (UTC)
FILETIME=[D91BDED0:01C63F4A]
rob yang wrote:
hi list,
i am comparing the relative energy differences between different
conformat
o/gmx-users>,<mailto:[EMAIL PROTECTED]>
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rob yang wrote:
hi list,
i am comparing the relative energy differences between different
conformat
alTime: 04 Mar 2006 01:15:18.0051 (UTC)
FILETIME=[197D9F30:01C63F29]
rob yang wrote:
hi list,
i am comparing the relative energy differences between different
conformations of a same molecule in vaccuum. i am using both gromacs and
another software to compare the results. the forcefield for b
alTime: 04 Mar 2006 01:15:18.0051 (UTC)
FILETIME=[197D9F30:01C63F29]
rob yang wrote:
hi list,
i am comparing the relative energy differences between different
conformations of a same molecule in vaccuum. i am using both gromacs and
another software to compare the results. the forcefield for b
hi list,
i am comparing the relative energy differences between different
conformations of a same molecule in vaccuum. i am using both gromacs and
another software to compare the results. the forcefield for both softwares
is oplsaa (2001), and i've manually verified that they are indeed the sam
hi list,
i am comparing the relative energy differences between different
conformations of a same molecule in vaccuum. i am using both gromacs and
another software to compare the results. the forcefield for both softwares
is oplsaa (2001), and i've manually verified that they are indeed the sam
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