munuswamy baskar wrote:
Sir/Mam,
please tell me what program in Gromacs have I to use to know how many
water molecules reacting on the surface of the solute molecule in the
cubic box about 3.0A unit distance from the surface of the solute.
I don't understand what you are trying to do, but i
s lal badshah wrote:
Dear Experts,
Hi ! I am doing MD simulation on two computer, on one when I want to
start the EM and do the mdrun command the following error results:
linux:~/project # mdrun -v -s em.tpr -c em.pdb
mdadm: /dev/md-v not identified in config file.
linux:~/project # mdrun -v
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---
weixin wants to stay in better to
Dear Mark,
When I enter from root account the following is the result:
linux:~ # which mdrun
/sbin/mdrun
linux:~ # which grompp
/usr/bin/grompp
linux:~ #
But from user account the
which mdrun
usr/bin/mdrun
and also the
which grompp
/usr/bin/grompp
occured.
Actually I have very little experi
s lal badshah wrote:
Dear Mark,
When I enter from root account the following is the result:
linux:~ # which mdrun
/sbin/mdrun
linux:~ # which grompp
/usr/bin/grompp
linux:~ #
But from user account the
which mdrun
usr/bin/mdrun
and also the
which grompp
/usr/bin/grompp
occured.
Actually I hav
Hello everyone,
Here i want to caculate the binding free energy between an ligand and its
receptor. Should I set free_energy as "yes" in Free Energy Perturbation Part
or use g_lie by doing recepto-ligand-solvate md and ligand-solvate md
separately?
If run a md by set free_energy as "yes", how s
Quoting shuai lu <[EMAIL PROTECTED]>:
> Hello everyone,
>
> Here i want to caculate the binding free energy between an ligand and its
> receptor. Should I set free_energy as "yes" in Free Energy Perturbation Part
Yes, among other things. Read the manual regarding all the free energy options.
Si
Send me please your files, I would like to have a look at them
Alex--- On Fri, 4/18/08, Wei, Xiupeng <[EMAIL PROTECTED]> wrote:
From: Wei, Xiupeng <[EMAIL PROTECTED]>Subject: [gmx-users] water can't freezeTo: "gmx-users@gromacs.org" Date: Friday, April 18, 2008, 8:41 PMHi gmx users,
I'm
Dear Xiupeng,
What you're seeing is the difference between freezing water and overcooling it.
If you want your water to crystallize, you'll actually have to make it -
e.g., by putting it in contact with ice. Normally, pure water doesn't freeze
on its own, you can easily verify this experimentally
Dear Justin,
Thank you very much for helping me again!
Best wishes!
2008/4/20, [EMAIL PROTECTED] <[EMAIL PROTECTED]>:
>
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dear sir/madam
I am doing MD ap peptide with gromacs.this peptide( 13 residue) has a NH2 in
c terminal.I change it from heteroatom to atom but it take a error.and it
say :I acnnot find C alpha for residue 14 NH2 WHILE COMBINING tdb and
rtp.what do i do ?
best
--
sh-karbalaee
__
shahrbanoo karbalaee wrote:
dear sir/madam
I am doing MD ap peptide with gromacs.this peptide( 13 residue) has a
NH2 in c terminal.I change it from heteroatom to atom but it take a
error.and it say :I acnnot find C alpha for residue 14 NH2 WHILE
COMBINING tdb and rtp.what do i do ?
This is
shahrbanoo karbalaee wrote:
dear sir/madam
I am doing MD ap peptide with gromacs.this peptide( 13 residue) has a
NH2 in c terminal.I change it from heteroatom to atom but it take a
error.and it say :I acnnot find C alpha for residue 14 NH2 WHILE
COMBINING tdb and rtp.what do i do ?
-ter
b
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