Sorry for the multiple emails but everytime I tried to send the mail I
obtained a message like this:
The message's content type was not explicitly allowed. Please send
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So I tried as long as no message has been
Tsjerk Wassenaar wrote
Hi John,
Check where the unsettling water molecule is placed. If it's in the
protein. that may be the cause of the problem. Otherwise, it's some of
the other stuff you're doing, but rule out the simple things first.
Thank you Tsjerk.
I posted a reply several
Hi everybody,
I want to add protonation states to my protein with pdb2gmx.
I now that there are the options:
-lys -arg -asp -glu -his
to do this.
But was is about the cystein. How can I protonate this one?
Is there also an option for it which I haven't seen?
Thank you ,
Eva
--
gmx-users
On 7/19/12 5:00 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to add protonation states to my protein with pdb2gmx.
I now that there are the options:
-lys -arg -asp -glu -his
to do this.
But was is about the cystein. How can I protonate this one?
Is there also
Hi Justin,
thank you for your answer.
I already tried the -ss command but nothing happens. The program just
writes the topology file but it does not ask me anything. My command was:
pdb2gmx -f protOnly.pdb -o 3m71.gro -p 3m71.top -ss -water tip3p -ff amber03
is there something wrong with this
On 7/19/12 6:17 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
thank you for your answer.
I already tried the -ss command but nothing happens. The program just
writes the topology file but it does not ask me anything. My command was:
pdb2gmx -f protOnly.pdb -o 3m71.gro -p
There is only one Cystein:
ATOM 1797 N CYS A 211 10.568 1.888 4.891 1.00 1.00
ATOM 1798 CA CYS A 211 11.782 1.312 5.391 1.00 1.00
ATOM 1799 CB CYS A 211 12.968 1.606 4.452 1.00 1.00
ATOM 1800 SG CYS A 211 14.599 1.282 5.172 1.00 1.00
On 7/19/12 6:28 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
There is only one Cystein:
ATOM 1797 N CYS A 211 10.568 1.888 4.891 1.00 1.00
ATOM 1798 CA CYS A 211 11.782 1.312 5.391 1.00 1.00
ATOM 1799 CB CYS A 211 12.968 1.606 4.452
Dear Gromacs Users,
I have several questions about g_clustsize, Please help me.
I have several micelles in my system and I want to calculate: the number of
monomers in micelles and cluster number and monomer number during the time of
simulation, I used from this command as is follows:
Dear Gromacs Users,
I have several questions about g_clustsize, Please help me.
I have several micelles in my system and I want to calculate: the number of
monomers in micelles and cluster number and monomer number during the time of
simulation, I used from this command as is follows:
On 7/19/12 8:06 AM, mohammad agha wrote:
Dear Gromacs Users,
I have several questions about g_clustsize, Please help me.
I have several micelles in my system and I want to calculate: the number of
monomers in micelles and cluster number and monomer number during the time of
simulation,
On 19/07/2012 6:52 PM, Ladasky wrote:
Tsjerk Wassenaar wrote
Hi John,
Check where the unsettling water molecule is placed. If it's in the
protein. that may be the cause of the problem. Otherwise, it's some of
the other stuff you're doing, but rule out the simple things first.
Thank you
Dear Justin,
Thank you very much from your response.
according you said I should set -cut with less than 0.7, but this doesn't
answer me!
for 0.6:
0.00e+00 115
6.00e+01 107
1.20e+02 114
1.80e+02 105
2.40e+02 100
3.00e+02
On 7/19/12 9:42 AM, mohammad agha wrote:
Dear Justin,
Thank you very much from your response.
according you said I should set -cut with less than 0.7, but this doesn't
answer me!
I didn't say that, but your results are completely consistent with what I said
about how g_clustsize is
Dear Justin,
Thank you very much from your help.
I think that I should work more on this command and will ask you next.
I don't know why does it bother me for it's .xvg and -tu !!!
Thank you very much again.
Best Regards
Sara
On 7/19/12 9:42 AM, mohammad agha wrote:
Dear Justin,
Thank
Dear users,
I'm currently doing some experiments with the implicit solvation
model running on GPUs with GROMACS.
I can make simple (conventional MD) simulations using the GPUs,
allowing great acceleration by using 1 GPU. However, I was wondering
about how to make Replica
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