Dear gromacs users
I have prepared a complex system consists of a protein and carbohydrate in
lipid membrane using the
KALP-membrane tutorial. After concatenating the three coordinate files, I
visualized
using VMD, but around 18 lipid atoms and more than 25 water molecules are
joined with my
I used the command g_fg2cg to convert a coarse grained structure into
corresponding fine strcture, and i found that the water molecues can be
transformed correctly, but there is a big mess in the protien , and i could
not get correct protein strcture, can anyone give me some suggestion?
Hi,
I suggest contacting people in Johan Åqvist's lab. I'm sure they know exactly
what pitfalls there may be with regards to the choice of LIE parameters and
what has been done for different types of molecules.
Erik
On 26 Mar 2013, at 02:42, Vishwambhar Bhandare vishway...@gmail.com wrote:
Hi Dear Justin
First of all, I request you that not to shout at me! I am so sorry to ask you
questions about position restraints again!
I
know I have sent you such emails before, and you suggested me to read
include file mechanism in web site. I did this and also read some emails
in forum.
On 3/26/13 7:01 AM, Shima Arasteh wrote:
Hi Dear Justin
First of all, I request you that not to shout at me! I am so sorry to ask you
questions about position restraints again!
I haven't done any shouting, but statements like this seem to imply that I have.
The point of this forum is
On 3/26/13 5:17 AM, Shine Devaraj wrote:
Dear gromacs users
I have prepared a complex system consists of a protein and carbohydrate in
lipid membrane using the
KALP-membrane tutorial. After concatenating the three coordinate files, I
visualized
using VMD, but around 18 lipid atoms and more
No, You have not shouted at me, never! But sometimes I think that I deserve to
be shouted !!
I deeply appreciate your patience and attention. Thanks for your time and your
replies.
In my protein, chains A and B are identical.
Sincerely,
Shima
- Original Message -
From: Justin
Dear Justin Thank you for your Previous reply,
I want to calculate Variation of deuterium order Parameter With respect
to Time for Entire Trajectory and Hydration Number of Phosphate oxygen For My
Entire
On 3/26/13 8:39 AM, Shima Arasteh wrote:
No, You have not shouted at me, never! But sometimes I think that I deserve to
be shouted !!
I deeply appreciate your patience and attention. Thanks for your time and your
replies.
In my protein, chains A and B are identical.
If they are
On 3/26/13 11:24 AM, vidhya sankar wrote:
Dear Justin Thank you for your Previous reply,
I want to calculate Variation of deuterium order Parameter With respect
to Time for Entire Trajectory and
On Tue, Mar 26, 2013 at 1:01 PM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
Have a look at processed topology file here please; I see that position
restraints are brought after chain_A but not brought after chain_B.
With these settings:
; Include chain topologies
#ifdef POSRES
Dear Groetnis,
Thank you very much for your nice suggestion.
BW
Fugui
At 2013-03-26 17:34:08,Djurre de Jong-Bruinink djurredej...@yahoo.com wrote:
I used the command g_fg2cg to convert a coarse grained structure into
corresponding fine strcture, and i found that the water molecues can be
The inclusion part was edited again in original top file. I dont know why I had
written that! Sorry.
But about last itp files, which you mentioned that they are created
incorrectly, 1) I 'd like to know what itp file should be created? In my own, I
just included the chain_B.itp file with the
On Tue, Mar 26, 2013 at 2:20 PM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
The inclusion part was edited again in original top file. I dont know why
I had written that! Sorry.
But about last itp files, which you mentioned that they are created
incorrectly, 1) I 'd like to know what itp
Thanks for all your explanations.
What I get as a conclusion is this:
itp files are dependent to the numbering of aoms in molecule type directive and
not any other things! Each posre.itp file created by genrestr should be in
consistent with the molculetype numbering!
Sincerely,
Shima
On Tue, Mar 26, 2013 at 2:33 PM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
Thanks for all your explanations.
What I get as a conclusion is this:
itp files are dependent to the numbering of aoms in molecule type
directive and not any other things! Each posre.itp file created by genrestr
Dear users,
Sorry for an off-topic question..
What is the distance cut-off considered for
hydrophobic contact in protein?
Some paper states 4-8Ang, while some other
considers only till 5Ang. It is reported that this
is a long range interaction.
Any information clarifying this doubt will be very
Dear Users:
A cluster that I use went down today with a chiller failure. I lost all 16 jobs
(running gromacs 4.6.1). For 13 of these jobs, not only is the .cpt file
truncated, but also the _prev.cpt file is truncated, meaning that I am going to
have to go back through the files, extract a
The standard approach in cases like this, assuming that you have some contacts
at some point in your trajectory, is to use your trajectory to construct a
radial distribution function (RDF) and then to define a contact as any
interaction up to the minimum following the first maximum of the RDF.
Dear Chris,
While it's always possible that GROMACS can be improved (or debugged), this
smells more like a system-level problem. The corrupt checkpoint files are
precisely 1MiB or 2MiB, which suggests strongly either 1) GROMACS was in
the middle of a buffer flush when it was killed (but the
Dear Matthew:
Thank you for noticing the file size. This is a very good lead.
I had not noticed that this was special. Indeed, here is the complete listing
for truncated/corrupt .cpt files:
-rw-r- 1 cneale cneale 1048576 Mar 26 18:53 md3.cpt
-rw-r- 1 cneale cneale 1048576 Mar 26 18:54
Hai
I have done 10ns simulation for a protein to this i want to
calculate DCCM map.can you please suggest me how to calculate this map.
Thank You.
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Dear Gromacs Users!
Could someone provide me with the tutorial example with the algoritm
of ussing Nose-Hover chains thermostat. In particular It's not quite
understood for me how I should define number of chains in the mdp file
and how that number would affect on simulation performance (E.g In
Dear Gromacs users!
I'd like to perform MD simulation of the membrane protein parametrized
in Amber99sb force field. Could you tell me what cut-off patterns
should I use for such simulation ?
James
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