Hi,
I've written the Gromacs Mail list before, but I did not get the answer that
I wanted. I am new user Gromacs.
*1. I installed fftw-3.2.2 as following*
a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2
a...@ab-desktop:~/Masaüstü/fftw-3.2.2
a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure
Dear Gmxers,
Does anyone have an idea about what time the Gmx 4.5.2 will be released?And in
4.5.2, would the modified tip5p.itp in charmm27 force field be the same as that
in current git version?
Thanks,
Yao
--
gmx-users mailing listgmx-users@gromacs.org
Hi,
I think you are looking at the wrong issue.
Unless your concentration is ridiculously high, the dispersion heterogeneity
will be irrelevant.
Furthermore, at distances were the correction works, the distribution will be
close to homogenous.
But you do have an issue with dispersion
No, there's no ability to do this. I think there should be, though, and seem to
recall discussion of it on one or other mailing list or the web page.
Mark
- Original Message -
From: Anupam Nath Jha anu...@mbu.iisc.ernet.in
Date: Saturday, October 2, 2010 21:32
Subject: [gmx-users]
Yes, giving you a set of commands would be the simplest thing for you :-)
However I can't give you a set of commands for an arbitrary such operation,
because there's a whole set of conditions you haven't stated. Moreover,
figuring out the fine detail would take time that I don't have available.
Berk,
Thank you very much for the answer. It was not clear from my post (sorry for
that) but my main concern was indeed related to the inhomogeneity near the
surfaces. I am not targeting complete quantitative agreement, but I would like
to be save from hidden undesired qualitative effects. As
sorry for the incomplete post before, believe it or not my cat was to blame.
I want to write out only the final frames from a set of trr trajectories. This
was discussed here with apparently only a workaround:
http://www.mail-archive.com/gmx-users@gromacs.org/msg19545.html
however intuitively
Hi,
A few days ago I had posted a request regarding help with Polyethylene
surface generation. I had earlier taken help of an older thread to create a gmx
file for
Hey Floris,
Here's a python script to write out the last frame from a .trr file:
#PYTHON
#!/usr/bin/env python
import sys
# Read a 32 bit unsigned int
def i(x): return sum([ord(x[j])(24-j*8) for j in range(4)])
# Open the file, find the end and go back
f = open(sys.argv[1],'rb')
f.seek(0,2)
- Original Message -
From: ahmet yıldırım ahmedo...@gmail.com
Date: Monday, October 4, 2010 18:41
Subject: [gmx-users] resolved pdm2gmx
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi,
I've written the Gromacs Mail list before, but I did not get the answer that
I
On 2010-10-03 23.16, ahmet yıldırım wrote:
Dear Prof. Spoel,
I am a Ph.D. student, Department of Physics, Harran University, Turkey.
I've written the Gromacs Mail list before, but I did not get the answer
that I wanted. I am new user Gromacs. I need your helps.
*1. I installed fftw-3.2.2 as
On 10/2/10 Oct 2,10:51 PM, Петр Попов wrote:
Hello, dears gmx-users!
I posted a message, but didn't get a response, it was my first one, so
may be I did something wrong. Anyway, here it is:
I've already run md and got pmf and it's correct. But I want to get
not just a pmf of total force,
Hi,
I want to write out only the final frames from a set of trr trajectories. This
was discussed here:
however intuitively it seems trjconv should do this with the -dump option
documented like this:
-dumptime -1 Dump frame nearest specified time (ps)
if I give e.g. -dump
hi Mark
After deleting half the molecules of decane from the box and if i use genbox
to add water then i will only get a mixture where as i want an interface to
be formed.that will be more useful to me.
Regards
Vinoth
On Mon, Oct 4, 2010 at 4:44 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Dear Zhongjin:
First, I see no reason why you would not expect your g_dist values to
be negative. If you want the positive distances, then reverse the
order of the groups as you pass then to g_dist. Also, what type of
values do you get directly out of mdrun and into the pull_x.xvg file?
Hi Anupam,
I recently wrote a small python script to convert gromacs .xpm files
to numbers. Maybe it'll be of some use to you:
Cheers,
Tsjerk
###
#!/usr/bin/env python
import sys
def unquote(s):
return s[1+s.find(''):s.rfind('')]
def uncomment(s):
return
Date: Fri, 1 Oct 2010 16:27:29 +0100
From: Thomas Piggot t.pig...@soton.ac.uk
Subject: Re: [gmx-users] charmm c36 lipids
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4ca5fde1.8050...@soton.ac.uk
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
For a
- Original Message -
From: Yash Gandhi ydgan...@gmail.com
Date: Monday, October 4, 2010 20:32
Subject: [gmx-users] Polyethylene Surface generation
To: gmx-users@gromacs.org
Hi,
A few days ago I had posted a request regarding help with Polyethylene
surface generation. I had earlier
Hi,
The frame time has to be within 0.5*frame spacing of the wanted frame.
If you have checkpoint files, you can use those.
Berk
Date: Mon, 4 Oct 2010 02:24:57 -0700
From: floris_buel...@yahoo.com
To: gmx-users@gromacs.org
Subject: [gmx-users] last frame in trr
Hi,
I want to write
right. I also came to see one of them but with no result.
and since it was done some time back so I thought if some one has come up with
some method to get that.
right now I wanted the matrix information obtained from command g_mdmat.
can you suggest some way to get that.
thanks
anupam
Hi all,
I have done a simulation about pulling a K+ throug a (9,9)CNT. The results
may be strange.
The length of the CNT is 1.477nm,the box is 5*5*5nm.I use the Umbrella
Sampling to calculate PMF ,following the tutorial by Justin A. Lemkul. I have
pulled (along Z direction) a K+
- Original Message -
From: vinothkumar mohanakrishnan kmvin...@gmail.com
Date: Monday, October 4, 2010 22:35
Subject: Re: [gmx-users] Reg: Putting molecules on one side of the box
To: Discussion list for GROMACS users gmx-users@gromacs.org
hi Mark
After deleting half the molecules
can you tell this with the help of the command that will be more useful
Regards
Vinoth
On Fri, Sep 24, 2010 at 12:58 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
Use genconf to replicate some suitable smaller box of decane to the full
size, delete the second half of the decane
Hi Vinoth !!
Try genbox with increasing the vander Waal's radii.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Oct 4, 2010 at 5:03 PM, vinothkumar mohanakrishnan
kmvin...@gmail.com wrote:
hi Mark
After deleting half the molecules of decane from the box and if i use
genbox
Hi,
When I tried to pack different proteins around the lipids (this protein I put
it in the position which was nearly going to jump out of the lipids, so it's
not exactly inserted into it, just very shallow into it), I used the vmd to see
the system.gro, which without being inflated first, I
#ZHAO LINA# wrote:
Hi,
When I tried to pack different proteins around the lipids (this protein
I put it in the position which was nearly going to jump out of the
lipids, so it's not exactly inserted into it, just very shallow into
it), I used the vmd to see the system.gro, which without
Thanks for your answering. I will check those further later.
The unclear question was that, to the final .gro. How can I tell it that one
(protein embedded in membrane) is okay or nice, so I can continue.
based on area per lipids, or after EM ... are there some criteria?
Thanks and best
Dear All:
I am trying to do trajectory analysis on-the-fly and encountered some
difficulty.
What did I do:
I inserted a small piece of code into md.c to READ the position of
atoms and do some simple analysis. In the GMX3.2, my code works fine.
The problem:
In GMX4.5.1, my code works only if I
Hi Tsjerk
It's very useful in my problem also.
thanks again.
regards
anupam
Hi Anupam,
I recently wrote a small python script to convert gromacs .xpm files
to numbers. Maybe it'll be of some use to you:
Cheers,
Tsjerk
###
#!/usr/bin/env python
import sys
def unquote(s):
#ZHAO LINA# wrote:
Thanks for your answering. I will check those further later.
The unclear question was that, to the final .gro. How can I tell it that one
(protein embedded in membrane) is okay or nice, so I can continue.
based on area per lipids, or after EM ... are there some criteria?
---BeginMessage---
Dear Gmxers,
Does anyone have an idea about what time the Gmx 4.5.2 will be released?And in
4.5.2, would the modified tip5p.itp in charmm27 force field be the same as that
in current git version?
Thanks,
Yao
---End Message---
--
gmx-users mailing list
- Original Message -
From: 吴鹏 geroge...@gmail.com
Date: Tuesday, October 5, 2010 3:24
Subject: [gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with
multi-threading enabled?
To: Discussion list for GROMACS users gmx-users@gromacs.org
Dear All:
I am trying to do
Dear Gromacs Community,
as I understand the MDP option continuation is the new name for the
option unconstrained_start.
I think the 4.5 series manual should be updated to mention that fact,
since it still only mentions unconstrained_start
(at least the html version of gromacs 4.5.1 :
Dear Chris,
牋營 use g_wham to calculate PMF.g_wham -if
pullf-files.dat -it tpr-files.dat -b 500 -unit kT -temp 300
-o -hist
g_dist -f pull.xtc -s pull.tpr -n
index.ndx -o dist.xvg,first I select the reference
group,then pull group
Zhongjin He
attachment: umbrella
Dear Chris,
鐗嬬嚐 use g_wham to calculate PMF.g_wham -if
pullf-files.dat -it tpr-files.dat -b 500 -unit kT
-temp 300
-o -hist
聽聽聽g_dist -f pull.xtc -s pull.tpr -n
index.ndx -o dist.xvg,first I select the reference
group,then pull group
Zhongjin He
attachment: umbrella
--- 10年10月5日，周二, zhongjin zhongjin1...@yahoo.com.cn 写道：
发件人: zhongjin zhongjin1...@yahoo.com.cn
主题: about COM pulling and g_dist
收件人: gmx-users@gromacs.org
日期: 2010年10月5日,周二,上午9:51
Dear Chris,
I use g_wham to calculate PMF.g_wham -if
pullf-files.dat -it tpr-files.dat -b 500 -unit kT
Agreed. Both are equivalent and legal, but I've updated mdp_opt.html, from
which the manual is generated.
Mark
- Original Message -
From: Oliver Stueker ostue...@gmail.com
Date: Tuesday, October 5, 2010 10:58
Subject: [gmx-users] unconstrained_start vs. continuation in Gromacs 4.5.x
--- 10年10月5日，周二, zhongjin zhongjin1...@yahoo.com.cn 写道：
发件人: zhongjin zhongjin1...@yahoo.com.cn
主题: about COM pulling and g_dist
收件人: gmx-users@gromacs.org
日期: 2010年10月5日,周二,上午9:53
Dear Chris,
Snap7.jpg shows distance in one umbrella sampling window.
Zhongjin He
Hi all
I want to generate a topology file for say decane from prodrg for oplsaa
force field. is it possible?. i get a topology file from prodrg for
gromos96.1 force field and i am able to process it further. when i use the
topology file generated for gromos96.1(from prodrg) for oplsaa i get the
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