sarbani chattopadhyay wrote:
hi,
I want to select two groups in the index file, one group consisting
of only the aromatic
ring of phenylalanine and the other group consisting of only the alpha
carbon.
I want to know the way to use the make_ndx command for this.
After entering
Thanks Mark,
I could do it following your suggestion.
Sarbani
On Wed, 24 Oct 2007 Mark Abraham wrote :
sarbani chattopadhyay wrote:
hi,
I want to select two groups in the index
From: Martin Höfling [EMAIL PROTECTED]
Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org
To: Discussion list for GROMACS users gmx-users@gromacs.org
Subject: [gmx-users] missing Ryckaert-Bell in 3.3.2 is now considered
asERROR?
Date: Wed, 24 Oct 2007 00:14:55 +0200
Hi all,
Hi all,
I use the option #Surf*SurfTens in g_engery to calculate the surface
tension, but I find that I really do not know how it works after I get some
inconsistent results compared with the calculation using the formula gamma
= 0.5*(Pzz - (Pxx+Pyy)/2) * Lz ( there are two surfaces here and
Bo Zhou wrote:
Hi all,
I use the option “#Surf*SurfTens” in g_engery to calculate the
surface tension, but I find that I really do not know how it works after
I get some inconsistent results compared with the calculation using the
formula “gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz” ( there
I tried trjconv -pbc nojump to the whole protein and then calculated
the rmsf of the subunits. This method seems good to some separate
subunits, but other separate subunits still have strange high rmsf
values. I try trjconv -pbc mol too, and i have got same results. In
this simulation,the
Does anyone know the reference for the parameters for urea in the urea.itp file
(found in the top directory)?
Thanks,
Ronen
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Hi Sarbani,
If I understand correctly your problem, you want to know hydrogen bond between
center of the aromatic ring and CA hydrogen atom with time, you can do this in
two steps (if you are not considering angle criteria).
1) first create the index files which should have two extra groups
Hello Maria,
You can do it by two different methods.
1) You can increase the default VdW radii of the lipid atoms in
/usr/local/gromacs/share/top/vdwradii.dat file (path might be different from
your system), say 0.5 for carbon, so genbox will not add the water inside the
bilayer. but you
[EMAIL PROTECTED] wrote:
Does anyone know the reference for the parameters for urea in the urea.itp file
(found in the top directory)?
Please don't use it as is. Check literature for better models.
Thanks,
Ronen
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Thanks. I am looking at other models as well, but was wondering how the numbers
in urea.itp were obtained. What type of properties they were parametrized for?
Ronen
-- Original message --
From: David van der Spoel [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
[EMAIL PROTECTED] wrote:
Thanks. I am looking at other models as well, but was wondering how the numbers
in urea.itp were obtained. What type of properties they were parametrized for?
none. just copied from the gromos 87 ff.
Ronen
-- Original message --
From:
Dear friends:
when my MD was finished and I want to analyse the bond energy of the protein
,but g_energy did not show bond entry: the first entry is angle? When energy
miniumzation finished,g_energy did show G96 bond. why?
Please help me!
Thank you!
Dear friends:
when my MD was finished and I want to analyse the bond energy of the
protein ,but g_energy did not show bond entry: the first entry is angle?
When energy miniumzation finished,g_energy did show G96 bond. why?
So, when did you use bond length constraints? What effect would
Yes, I use bond constraints!
Mark Abraham [EMAIL PROTECTED] 写道: Dear friends:
when my MD was finished and I want to analyse the bond energy of the
protein ,but g_energy did not show bond entry: the first entry is angle?
When energy miniumzation finished,g_energy did show G96 bond. why?
So,
You can do it by two different methods.
1) You can increase the default VdW radii of the lipid atoms in /usr/local/
gromacs/share/top/vdwradii.dat file (path might be different from
your system), say 0.5 for carbon, so genbox will not add the water
inside the bilayer.
Cleaner method is
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