Thank you very much. I got it sorted out by following your advice.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Dec 31, 2012, at 10:23 PM, Justin Lemkul wrote:
>
>
> On 12/31/12 9:41 PM, Xu Dong Huang wrote:
>> Dear Advanced Gr
On 12/31/12 9:41 PM, Xu Dong Huang wrote:
Dear Advanced Gromacs users,
I'm trying to generate a solvated system with >1 solute (In my case 3). I do
genbox -cp polymer.gro -nmol 2 -ci polymer.gro -cs water.gro -o polymer_solv.gro
-p polymer.top
My polymer molecule contains 201 atoms. box siz
Dear Advanced Gromacs users,
I'm trying to generate a solvated system with >1 solute (In my case 3). I do
genbox -cp polymer.gro -nmol 2 -ci polymer.gro -cs water.gro -o
polymer_solv.gro -p polymer.top
My polymer molecule contains 201 atoms. box size 45x45x45
and it generates a system with th
On 12/31/12 5:50 PM, Xu Dong Huang wrote:
Dear Justin,
I'm pretty sure my .gro file is valid, here is a direct copy and paste of the
format of my .gro in the beginning:
star polymer
201
1starO41 0.000 0.000 0.000
1star O12 0.430 0.000 0.000
1s
Ok I sent it.
Let me know if you did not receive them.
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Dec 31, 2012, at 5:54 PM, Justin Lemkul wrote:
>
>
> On 12/31/12 5:50 PM, Xu Dong Huang wrote:
>> Dear Justin,
>>
>> I'm prett
On 12/31/12 5:50 PM, Xu Dong Huang wrote:
Dear Justin,
I'm pretty sure my .gro file is valid, here is a direct copy and paste of the
format of my .gro in the beginning:
star polymer
201
1starO41 0.000 0.000 0.000
1star O12 0.430 0.000 0.000
1s
Dear Justin,
I'm pretty sure my .gro file is valid, here is a direct copy and paste of the
format of my .gro in the beginning:
star polymer
201
1starO41 0.000 0.000 0.000
1starO12 0.430 0.000 0.000
1starO13 0.860 0.000 0.000
On 12/31/12 5:40 PM, Xu Dong Huang wrote:
Dear Justin,
(here is the picture of the molecule after editconf, note the negative x and
negative y axis is missing the rest of the beads that is suppose to be like the
positive x and positive y)
http://i1284.photobucket.com/albums/a571/X_huang1/Scr
Dear Justin,
(here is the picture of the molecule after editconf, note the negative x and
negative y axis is missing the rest of the beads that is suppose to be like the
positive x and positive y)
http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2012-12-31at53618PM_zpse5f421f1.png
*
On 12/31/12 4:53 PM, Xu Dong Huang wrote:
Dear advanced gromacs users,
I have created an arbitrary molecule .gro file containing coordinates of my
martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x
and -y) forming like a cross. (Each bead with distance 0.43). Howev
Dear advanced gromacs users,
I have created an arbitrary molecule .gro file containing coordinates of my
martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x
and -y) forming like a cross. (Each bead with distance 0.43). However, when I
try to use editconf on my .gro fil
A good minded advice Shima: think more for your self; science is not easy, or
if it's not possible, ask ur adviser, or look for a new job.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Shima Arasteh [shima_arasteh2...@ya
On 12/31/12 11:58 AM, Shima Arasteh wrote:
These are the last line of my gro file:
5SOLHW299818 7.429 8.372 11.524
5CL CL99819 0.485 3.864 11.451
5CL CL99820 5.689 6.730 9.692
9.21490 8.92980 12.40750
Here, I brought you the output of make_n
These are the last line of my gro file:
5SOL HW299818 7.429 8.372 11.524
5CL CL99819 0.485 3.864 11.451
5CL CL99820 5.689 6.730 9.692
9.21490 8.92980 12.40750
Here, I brought you the output of make_ndx command. As you see CL ions are not
recognized
On 12/31/12 11:45 AM, Shima Arasteh wrote:
It is 4.5.5.
I need to say that I had a pdb file which was produced by VMD, May it be the
reason of problem?
Without seeing the aforementioned information (substituting make_ndx screen
output for editconf command, which is not relevant), it's i
It is 4.5.5.
I need to say that I had a pdb file which was produced by VMD, May it be the
reason of problem?
Sincerely,
Shima
From: Justin Lemkul
To: Discussion list for GROMACS users
Sent: Monday, December 31, 2012 7:54 PM
Subject: Re: [gmx-users] Index
On 12/31/12 11:20 AM, Shima Arasteh wrote:
No, I see CL ions in gro file after using editconf, but when I want to make an
index file, there is not CL option to choose!
What Gromacs version is this? I cannot reproduce this problem with 4.5.5 or the
development 4.6 version. Anything I have
No, I see CL ions in gro file after using editconf, but when I want to make an
index file, there is not CL option to choose!
Sincerely,
Shima
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Monday, December 31, 2012 6:02 PM
On 12/31/12 3:17 AM, Shima Arasteh wrote:
I know that I can use pdb and build my index file. But I want to know the
problem. What's the problem?
It sounds rather unbelievable that editconf would mysteriously delete atoms.
There is no way for anyone to say what is going on given the curr
I know that I can use pdb and build my index file. But I want to know the
problem. What's the problem?
Sincerely,
Shima
From: Chandan Choudhury
To: Shima Arasteh ; Discussion list for GROMACS
users
Sent: Monday, December 31, 2012 11:08 AM
Subject: Re: [gmx
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