Dear gromacs user
I have one protein with 254 residues. I would like to simulate this protein
in solvent system. For that first we need to define box by editconf. My
question is how does we define box size?
Surya
Graduate student
India.
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Dear all, I have recently posted a question on how generate data that allows me to plot a droplet profile as a function of z-direction.https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg08966.htmlKnowing that this procedure requires the use of g_select, I am able to look up s
Thank you for getting back to me. I understand the limited precision of the
.gro file but it cannot explain such a large jump in the temperature. Other
than the fact that I am starting a new simulation, the parameters in the .mdp
file are the same as the ones that equilibrated and produced the .
On 12/31/14 12:18 PM, Nizar Masbukhin wrote:
the directory where i execute the command is in desktop. i think that
folder doesnt need write/read permission. i even have used sudo -s mode,
still the problem exist.
Disk space, maybe? In any case, this is a file management/permission/space
iss
On 12/31/14 3:05 PM, Dan Sponseller wrote:
Hello.
Every time I start a new simulation from a conformation that has been well
equilibrated, there is a jump in the temperature. For example, starting from a
.gro file with velocities that was a well equilibrated system at 400K has
initial tempe
Hello.
Every time I start a new simulation from a conformation that has been well
equilibrated, there is a jump in the temperature. For example, starting from a
.gro file with velocities that was a well equilibrated system at 400K has
initial temperature about 440K.
I am not generating new vel
the directory where i execute the command is in desktop. i think that
folder doesnt need write/read permission. i even have used sudo -s mode,
still the problem exist.
On Dec 31, 2014 11:39 PM, "Justin Lemkul" wrote:
>
>
> On 12/31/14 10:53 AM, Nizar Masbukhin wrote:
>
>> hi gromacs user,
>>
>> w
Hi Justin,
Yes, you are right!
I think I know what to do now. Thank you very much!
Regards,
Mah
On Wed, Dec 31, 2014 at 12:44 PM, mah maz wrote:
> Hi Justin,
>
> Thank you!
> but what are the old and new box? I have defined only one box with
> editconf command.
> Regards,
> Mah
>
> On Tue, Dec
On 12/31/14 10:53 AM, Nizar Masbukhin wrote:
hi gromacs user,
when i try to compute secondary structure using do_dssp program, the error
message appear:
"Program do_dssp_mpi, VERSION 5.0.2
Source code file: /home/user/gromacs-5.0.2/src/gromacs/fileio/futil.cpp,
line: 863
Fatal error:
Permiss
On 12/31/14 10:46 AM, Carlos Navarro Retamal wrote:
Dear everyone,
In order to check if my workstation were able to work with bigger systems, i
ran a md simulation of a system of 265175 atoms, but sadly this was it
performance with one GPU:
P P - P M E L O A D B A L A N C I
On 12/31/14 10:46 AM, Shima Arasteh wrote:
Hi,
Dear users,
I am trying to define a new group for the ligand in a ligand-protein
system. According to the protein-ligand complex tutorial existed in
documentation, I made my ligand.itp file, also I included it in top
file:
Ligand.itp contains:
[ m
On 12/31/14 6:48 AM, Kester Wong wrote:
Dear Justin and all,
I am stoked by what g_select can do (after reading the gmx-users list) and there
is no one-size-fits-all.
However, as I wanted to look for more resources on g_select, I was met with no
further information, for example:
g_select_m
On 12/31/14 4:14 AM, mah maz wrote:
Hi Justin,
Thank you!
but what are the old and new box? I have defined only one box with editconf
command.
I don't know; you said you got a fatal error, but then you made the box larger.
I assumed you would know what you had done to piece together the so
On 12/31/14 2:35 AM, elham tazikeh wrote:
Dear Justin
thanks for your replys
one of my most important problem is choosing correct pdb
in RCSB , there is not any pdb that consist of *Aspirin *+ HSA...and in
literature, using of *2i30* as pdb
my question is; should we use *docking software* for
hi gromacs user,
when i try to compute secondary structure using do_dssp program, the error
message appear:
"Program do_dssp_mpi, VERSION 5.0.2
Source code file: /home/user/gromacs-5.0.2/src/gromacs/fileio/futil.cpp,
line: 863
Fatal error:
Permission denied for opening ddhCTh1r
For more informat
Dear everyone,
In order to check if my workstation were able to work with bigger systems, i
ran a md simulation of a system of 265175 atoms, but sadly this was it
performance with one GPU:
>P P - P M E L O A D B A L A N C I N G
>
> PP/PME load balancing changed the cut-off and
Hi,
Dear users,
I am trying to define a new group for the ligand in a ligand-protein
system. According to the protein-ligand complex tutorial existed in
documentation, I made my ligand.itp file, also I included it in top
file:
Ligand.itp contains:
[ moleculetype ]
; Namenrexcl
HH3
Dear Justin and all,I am stoked by what g_select can do (after reading the gmx-users list) and there is no one-size-fits-all.However, as I wanted to look for more resources on g_select, I was met with no further information, for example: g_select_mpi -select 'help position' OR g_select_mpi -select
Hi Justin,
Thank you!
but what are the old and new box? I have defined only one box with editconf
command.
Regards,
Mah
On Tue, Dec 30, 2014 at 1:58 PM, mah maz wrote:
> Dear all,
>
> I have calculated the size of the box required for my system. however,
> when applying the g_x2top command with
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