On 10/29/13 12:02 PM, shahab shariati wrote:
Dear Mark
Very thanks for your reply
To make this clear, center the trajectory on the water and watch the
time evolution in some visualization program.
I did your suggestion (center the trajectory on the water). Again, drug
molecule is in region
On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati
wrote:
> Dear Mark
>
> Very thanks for your reply
>
> > To make this clear, center the trajectory on the water and watch the
> > time evolution in some visualization program.
>
> I did your suggestion (center the trajectory on the water). Again, dru
To make this clear, center the trajectory on the water and watch the time
evolution in some visualization program.
Mark
On Sun, Oct 27, 2013 at 5:08 PM, Justin Lemkul wrote:
>
>
> On 10/27/13 12:05 PM, shahab shariati wrote:
>
>> Dear Tsjerk Wassenaar
>>
>> Very very thanks for your reply.
>>
On 10/27/13 12:05 PM, shahab shariati wrote:
Dear Tsjerk Wassenaar
Very very thanks for your reply.
I used trjconv -pbc mol.
pbc problem was solved only for lipid molecules.
When I see new trajectory by vmd, there are some problesm about drug
molecule.
https://www.dropbox.com/s/xq4s6az17bu
Hi Shahab,
What about running trjconv -pbc mol with a .tpr as input file?
Cheers,
Tsjerk
On Sun, Oct 27, 2013 at 3:24 PM, shahab shariati
wrote:
> Dear Justin
>
> I attached images related to before (em2.gro) and after equilibration.
>
>
> https://www.dropbox.com/s/yjkyj5ycshvp20u/images.docx
On 10/27/13 8:16 AM, shahab shariati wrote:
Dear Justin
I want to study translocation of drug molecule in lipid bilayer.
My gro file after minimization is em2.gro.
After NPT-MD simulation, I obtained npt.gro and 0.xtc files.
When I see trajectory by vmd, there are some things abnormal.
I g
As Justin said, there is no actual division between region 1 and 4.
Apparently you got the free diffusion you asked for! :-)
Mark
On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati
wrote:
> Dear Mark
>
> Thank for your reply.
>
> If I show my system as 4 regions, my system before equilibration is
On 10/24/13 10:57 AM, shahab shariati wrote:
Dear Mark
Thank for your reply.
If I show my system as 4 regions, my system before equilibration is as fallows:
region (1): water + drug
region (2): top leaflet of bilayer
region (3): bottom leaflet of bilayer
region (4): water
After equilibratio
On Oct 24, 2013 8:10 AM, "shahab shariati"
wrote:
>
> Dear jkrieger
>
> I used 2 times trjconv tool:
>
> 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump
>
> 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol
-center
>
>
> Dear Mark
>
> I selected all lipid at
Center on a particular lipid? Or head group?
Mark
On Oct 23, 2013 6:13 PM, "shahab shariati"
wrote:
> Dear gromacs users
>
> My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
> rectangular box.
>
> I put drug molecule in 2 position: a) drug in the center of bilayer
> membrane,
I usually use -pbc nojump for my protein simulations and this works every
time.
> Dear gromacs users
>
> My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a
> rectangular box.
>
> I put drug molecule in 2 position: a) drug in the center of bilayer
> membrane, b) drug inside water
Hi Yutian Yang,
Yes. That is, if the chain is interacting with itself. If it remains curled
up, then it won't be a problem.
Cheers,
Tsjerk
On Thu, Jun 27, 2013 at 10:10 PM, Yutian Yang wrote:
> Hi all,
>
> I have a question about PBC. If I have a polymer chain that is longer than
> the box l
On 4/14/13 11:21 PM, Kieu Thu Nguyen wrote:
Thank Justin !
I used the command "editconf -center" and i saw my membrane was in center
of the box. I am stupid in that how putting the bilayer in a periodic image
(instead between two periodic images as it was).
Can you give me some instructions ?
M
Thank Justin !
I used the command "editconf -center" and i saw my membrane was in center
of the box. I am stupid in that how putting the bilayer in a periodic image
(instead between two periodic images as it was).
Can you give me some instructions ?
Many thanks !
On Fri, Apr 12, 2013 at 6:52 PM,
On Fri, Apr 12, 2013 at 7:48 AM, Kieu Thu Nguyen wrote:
> Dear All,
>
> I made a POPC bilayer and carried out embedding a protein into this
> membrane. But the fatal error has appeared :
> Fatal error:
> Something is wrong with your membrane. Max and min z values are 12.342000
> and 0.016000. Mayb
> hi, all
> My protein has 16 subunits. After I use trjconv '-pbc nojump' to remove
> the jump in the whole protein, there are no jump to each subunits.
> However, when i check pdb file of the first frame, it is shown that the
> subunits are not in right position. The area of interface between som
On 10/16/2007 2:31 AM, tangxuan wrote:
Dear all,
If pbc is full or xyz in mdp file, do i need to use the "trjconv -pbc
nojump" to remove the jump when the protein is separate in the box after
simulation and I want to calculate the rmsd of the protein?
IT is not necessary to use trjconv -pbc be
Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 4:41 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem
Hi Yuguang,
Gromacs should automatically fix the box to meet the requirements
during an mdrun
el: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 12:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users]
://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tsjerk Wassenaar
Sent: Wednesday, May 16, 2007 12:49 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PBC problem
Hi Yuguang,
> Warning: Triclinic box
Hi Yuguang,
Warning: Triclinic box is too skewed.
Box (3x3):
Box[0]={ 6.46530e+00, 0.0e+00, 0.0e+00}
Box[1]={ 2.14552e+00, 6.10274e+00, 0.0e+00}
Box[2]={-2.14464e+00, 3.05200e+00, 5.24664e+00}
This is not a rhombic dode
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