date:20101004

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 
Date: Saturday, October 2, 2010 21:32
Subject: [gmx-users] numerical matrix from xpm file
To: gmx-users@gromacs.org

> 
> Hi all
> 
> Is it possible to obtain the matrix in numeric form from xpm 
> (obtained from
> gromacs analysis) files.
> 
> because it's not coming in options for ourput files.
> 
> thanks with regards
> anupam
> 
> -- 
> 
> 
> -- 
> This message has been scanned for viruses and
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> 
> -- 
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Re: [gmx-users] Reg: Putting molecules on one side of the box

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. 
Finally, you wouldn't learn how to do solve such problems for yourself, and 
would remain dependent, instead of developing a set of skills that is useful 
for your work :-)

Be sure to read the documentation for each of the tools I have mentioned, and 
please do ask a focussed question on the list if you run into problems.

Good luck!

Mark

- Original Message -
From: vinothkumar mohanakrishnan 
Date: Monday, October 4, 2010 21:58
Subject: Re: [gmx-users] Reg: Putting molecules on one side of the box
To: Discussion list for GROMACS users 

> 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  
> wrote:
 > Use genconf to replicate some suitable smaller box of decane to the full 
 > size, delete the second half of the decane molecules, then use genbox to 
 > fill the rest with water. Cunning use of genconf should allow you to select 
 > where the division lies.
 > 
> Mark> 
> 
> - Original Message -
> From: vinothkumar mohanakrishnan 
> Date: Friday, September 24, 2010 17:22
>  Subject: [gmx-users] Reg: Putting molecules on one side of the box
> To: Discussion list for GROMACS users 
> 
> > Hi all
 > > 
> > I have a triclinic box of length of 8*3*3 nm. i want to put water on one 
> > side of the box and say decane on the other side of the box. How to 
> > generate .gro for the water-decane mixture such that they form two distinct 
> > parts of the box.
  > > 
> > Regards
 > > Vinoth
>  > -- 
> > gmx-users mailing listgmx-users@gromacs.org
>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: RE: [gmx-users] Dispersion correction in a heterogeneous

2010-10-04 Thread Mikhail Stukan

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 far as I know, the 
dispersion correction contributes something like 2-5% to the surface tension 
value (depending on the cut-off). If I consider different salt concentrations 
then the inhomogeneity near the surface will be of different order (compare to 
the bulk). So taking into account your recommendation, long cut-off with no 
dispersion correction looks like a better option.

Thanks and regards,
Mikhail


>Message: 5
>Date: Mon, 4 Oct 2010 10:16:35 +0200
>From: Berk Hess 
>Subject: RE: [gmx-users] Dispersion correction in a heterogeneous
system
>To: Discussion list for GROMACS users 
>Message-ID: 
>Content-Type: text/plain; charset="iso-8859-1"


>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 correction because of strong spatial 
>inhomogeneity because
>of the interface. The dispersion correction will have no direct effect on the 
>surface tension.

>What is the best way to proceed depends very much on the questions you want to 
>answer.
>The surface tension of many water models is off by 30%, so you probably won't 
>get quantitatively
>correct results anyhow. (note that also many "standard" combinations of Na and 
>Cl parameters are very bad)
>If you want an accurate number, given the force field limitations, you need to 
>use a long LJ cut-off,
>possibly with twin-range settings for efficiency. But force fields often have 
>not been parametrized with this.
>And finally, ion C6 parameters do not give realistic dispersion strengths in 
>most cases, but as  I said,
>this effect will be negligible in normal concentration ranges.

>Berk

>>From: mstu...@slb.com
>>To: gmx-users@gromacs.org
>>Date: Sat, 2 Oct 2010 12:40:23 +
>>Subject: [gmx-users] Dispersion correction in a heterogeneous system


>>Dear gmx-users,



>>Although  this task has been already discussed few
>>years ago 
>>(http://lists.gromacs.org/pipermail/gmx-users/2007-January/025668.html)
>>the full summary is not clear to me. So I would really appreciate if somebody
>>could give me advice on the following subject.



>>I am trying to simulate an aqueous solution of NaCl. One of
>>the properties I am interested in is surface tension, which means that
>>correction to the pressure could be quite important.  But the system is
>>heterogeneous: values of C_6 differs from 0.0003 (for Na-Na) to 0.0180 (for
>>Cl-Cl), so they are not comparable. Is it worth to use dispersion correction 
>>in
>>such a system? Or such results will have no real meaning and the proper way 
>>would
>>be to switch off the dispersion correction and just increase cut-off (or
>>perform rerun with higher cut-off)?



>>Thanks you very much in advance,

>>Mikhail



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[gmx-users] Fw: last frame in trr

2010-10-04 Thread Floris Buelens

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 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 99 trjconv doesn't do what the description led me to 
believe but falls off the end with "WARNING no output". Wouldn't it make more 
sense for trjconv to write out the last frame?
Thanks,

Floris




- Forwarded Message 
From: Floris Buelens 
To: gmx-users@gromacs.org
Sent: Mon, 4 October, 2010 11:24:57
Subject: last frame in trr

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 99 trjconv doesn't do what the description led me to 
believe



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[gmx-users] Polyethylene Surface generation

2010-10-04 Thread Yash Gandhi

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 
PE.
I also did the modifications in rtp and hdb files as mentioned in the link.
After a few thoughts I tried to create a pdb file using some logic. It's as
follows:

HETATM1  C1   EtB1  -4.243   0.027  -1.420
HETATM2  C2   EtB  1  -2.975  -0.719  -0.982
HETATM3  C1   Eth  2  -1.840   0.252  -0.620
HETATM4  C2   Eth  2  -0.566  -0.487  -0.180
HETATM5  C1   Eth  3   0.567   0.487   0.181
HETATM6  C2   Eth  3   1.841  -0.252   0.621
HETATM7  C1   EtE  4   2.976   0.719   0.983
HETATM8  C2   EtE  4   4.244  -0.026   1.420
HETATM9  H11  EtB  1  -5.058  -0.688  -1.680
HETATM   10  H12  EtB  1  -4.048   0.659  -2.317
HETATM   11  H13  EtB  1  -4.620   0.690  -0.609
HETATM   12  H21  EtB  1  -2.642  -1.393  -1.807
HETATM   13  H22  EtB  1  -3.213  -1.362  -0.102
HETATM   14  H11  Eth  2  -2.179   0.926   0.202
HETATM   15  H12  Eth  2  -1.609   0.895  -1.503
HETATM   16  H21  Eth  2  -0.227  -1.161  -1.003
HETATM   17  H22  Eth  2  -0.797  -1.130   0.702
HETATM   18  H11  Eth  3   0.228   1.161   1.003
HETATM   19  H12  Eth  3   0.798   1.129  -0.702
HETATM   20  H21  Eth  3   2.180  -0.926  -0.202
HETATM   21  H22  Eth  3   1.610  -0.895   1.504
HETATM   22  H11  EtE  4   2.643   1.393   1.807
HETATM   23  H12  EtE  4   3.213   1.362   0.102
HETATM   24  H21  EtE  4   5.059   0.688   1.679
HETATM   25  H22  EtE  4   4.621  -0.690   0.608
HETATM   26  H23  EtE  4   4.050  -0.658   2.317
CONECT12
CONECT213
CONECT324
CONECT43
END

after running pdb2gmx command and taking OPLSAA Force field with the
additional residues as mentioned in the link, I am getting the same error
always and I am not able to get the reason why
*
Fatal error:
Atom C1 in residue EtOH 1 not found in rtp entry with 9 atoms
 while sorting atoms*

Please help me urgently as I am not able to know why is the EtOH residue
being used.

Thanking you
-- 
Yash Gandhi,
4th Year, BE (Hons) Chemical,
Birla Institute of Technology & Science, Pilani, India
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Re: [gmx-users] Fw: last frame in trr

2010-10-04 Thread Tsjerk Wassenaar

Hey Floris,

Here's a python script to write out the last frame from a .trr file:

#

#!/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)
eof = f.tell()
f.seek(0)

# Have to read frame by frame since a TRR may have differently sized frames
start = 0
while True:
tag  = f.read(12)
tag  = tag + f.read(i(tag[-4:]))
num  = f.read(40)
size = sum( [ i(num[j:j+4]) for j in range(0,40,4) ] ) + 20
if (f.tell() + size >= eof):
break # May be an incomplete frame
f.seek(size,1)
start = f.tell()

# Go back to the start of the last good frame
f.seek(start)
# Open the output file
if len(sys.argv) > 2:
o = sys.argv[2]
else:
o = sys.argv[1][:-4]+"-last.trr"
open(o,"w").write(f.read())

#

Hope it helps,

Tsjerk

On Mon, Oct 4, 2010 at 11:31 AM, Floris Buelens
 wrote:
> 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 it seems trjconv should do this with the -dump option
> documented like this:
>
> -dump        time   -1      Dump frame nearest specified time (ps)
>
> if I give e.g. -dump 99 trjconv doesn't do what the description led me to
> believe but falls off the end with "WARNING no output". Wouldn't it make more
> sense for trjconv to write out the last frame?
> Thanks,
>
> Floris
>
>
>
>
> - Forwarded Message 
> From: Floris Buelens 
> To: gmx-users@gromacs.org
> Sent: Mon, 4 October, 2010 11:24:57
> Subject: last frame in trr
>
> 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:
>
> -dump        time   -1      Dump frame nearest specified time (ps)
>
> if I give e.g. -dump 99 trjconv doesn't do what the description led me to
> believe
>
>
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] resolved pdm2gmx



- Original Message -
From: ahmet yıldırım 
Date: Monday, October 4, 2010 18:41
Subject: [gmx-users] resolved pdm2gmx
To: Discussion list for GROMACS users 

> 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 --enable-threads 
> --enable-float
> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make
> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install
 
> 2. I installedgromacs-4.5.1 as folowing   
>   > a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 
> ./configure 
> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make
> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 sudo make install
This set of instructions will not use the above FFTW in GROMACS. The configure 
command is inappropriate. Please see the installation guide for the proper 
approach.



> "You need to either add the location  of your Gromacs installation to your 
> PATH (in whatever shell  configuration file, likely .bashrc) or source GMXRC 
> every time you log  in to a new terminal.  Once your Gromacs installation is 
> recognized by  your shell environment you can run all the commands."  
> I have read the installation instructions several times.
> I do not know how to apply what is said.

This is a fairly basic UNIX issue, and has nothing specific to do with GROMACS. 
You need to have an appreciation of what the UNIX environment is, and how you 
can "source" a file to adjust that environment. Please look around the web for 
some UNIX tutorial material - you'll need some experience and knowledge here 
before you can do anything at all. Once you understand the need to adjust the 
environment, you can see how "sourcing" GMXRC will solve some of your problems.

 > I have 1.pdb file. I want to convert 1.gro and 1.top this file using pdb2gmx 
 > command.
> After this, what should I do? can you show me on the command?
   > pdb2gmx –f 1.pdb –o 1.gro –p 1.top

That's not really the purpose of pdb2gmx. It tries to generate a topology from 
a set of coordinates. Perhaps working through some GROMACS tutorial material is 
a good idea to get the beginnings of an understanding of the workflows work.

A file in specifically .gro format is not necessary at any point - see 
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file

Mark

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[gmx-users] Re: pdb2gmx problem

2010-10-04 Thread David van der Spoel


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 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 --enable-threads
--enable-float
a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make
a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install

*
2. I installed  gromacs-4.5.1 as folowing*

a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 ./configure
a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make
a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 sudo make install


/"*You need to either add the location of your Gromacs installation to
your PATH (in whatever shell configuration file, likely .bashrc) or
source GMXRC every time you log in to a new terminal.  Once your Gromacs
installation is recognized by your shell environment you can run all the
commands.*"/
I do not know how to apply what is said.

Put the following line in your .chsrc or .bash_profile files:

source /usr/local/bin/GMXRC




I have 1.pdb file. I want to convert 1.gro and 1.top this file using
pdb2gmx command.
a...@ab-desktop:~/usr/bin$ How do I go the following command from here?
After this, what should I do? can you show me on the command?
*pdb2gmx –f 1.pdb –o 1.gro –p 1.top*


Thanks in advance. Please, don't be angry with me.

--
Ahmet YILDIRIM



--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Split pmf

2010-10-04 Thread Jochen Hub


 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, but several profiles each of which 
corresponds to the different components. For example, one pmf - 
protein-protein interactions, another - protein-solvent interactions. 
Or another, one pmf corresponds to electrostatic, another to VdW etc.
Should I change a program's code? If so, tell me please in what 
exactly program?
Or may be gromacs have similar functions? Or is the another way to 
split pmf?
Hi, what we did some years ago (Hub and de Groot, Does CO2 permeate 
through aquaporin-1, Biophys J 91, 842-848 (2006)), we used the energy 
file to decompose the potential (that is the enthalpic contribution to 
the PMF) into solute-water, solute-protein interactions, etc. You would 
have to make a tpr file with different energy groups and then do a 
rerun. Note that we do not decompose the mean force with that procedure 
though.


I hope this helps.

Cheers,

Jochen




Thank you for your attention!





--
---
Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell&  Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
http://xray.bmc.uu.se/~jochen/index.html
---

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Re: [gmx-users] an example to test mdrun-gpu x mdrun

2010-10-04 Thread Szilárd Páll

> If using Tcoupl and Pcoupl = no and then I can compare mdrun x mdrun-gpu,
> being my gpu ~2 times slower than only one core. Well, I definitely don't
> intended to use mdrun-gpu but I am surprised that it performed that bad (OK,
> I am using a low-end GPU, but sander_openmm seems to work fine and very fast
> on my mbp).

Just for my curiosity, do you mean that sander_openmm is very fast
compared to mdrun/mdrun-gpu, or compared to sander?

--
Szilárd
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[gmx-users] last frame in trr

2010-10-04 Thread Floris Buelens

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 99 trjconv doesn't do what the description led me to 
believe



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Re: [gmx-users] Reg: Putting molecules on one side of the box

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 wrote:

> 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.
> Finally, you wouldn't learn how to do solve such problems for yourself, and
> would remain dependent, instead of developing a set of skills that is useful
> for your work :-)
>
> Be sure to read the documentation for each of the tools I have mentioned,
> and please do ask a focussed question on the list if you run into problems.
>
> Good luck!
>
>
> Mark
>
> - Original Message -
> From: vinothkumar mohanakrishnan 
> Date: Monday, October 4, 2010 21:58
> Subject: Re: [gmx-users] Reg: Putting molecules on one side of the box
> To: Discussion list for GROMACS users 
>
> > 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 
> > wrote:
>
>> > Use genconf to replicate some suitable smaller box of decane to the
>> full size, delete the second half of the decane molecules, then use genbox
>> to fill the rest with water. Cunning use of genconf should allow you to
>> select where the division lies.
>> >
>> > Mark
>> >
>> >
>> > - Original Message -
>> > From: vinothkumar mohanakrishnan 
>> > Date: Friday, September 24, 2010 17:22
>> > Subject: [gmx-users] Reg: Putting molecules on one side of the box
>> > To: Discussion list for GROMACS users 
>> >
>> > > Hi all
>> > >
>> > > I have a triclinic box of length of 8*3*3 nm. i want to put water on
>> one side of the box and say decane on the other side of the box. How to
>> generate .gro for the water-decane mixture such that they form two distinct
>> parts of the box.
>> > >
>> > > Regards
>> > > Vinoth
>> > > --
>> > > gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] about COM pulling and g_dist

2010-10-04 Thread chris . neale


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?


Second, how did you go from values to a PMF? did you use wham? If so,  
and if you gave a succession of increasing value positive numbers to  
note restraint positions and then your values you passed were  
increasingly negative, then you will certainly get the wrong PMF.


Third, your lack of symmetry may just be a lack of convergence. Have  
you done and convergence tests?


If this doesn't solve it and you want more help, please post your  
g_dist commands and post an image of your pmf online.


Chris.

-- original message --

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+ (pulling group)frome  
one end (reference group ) of the CNT to another end to generate  
Configurations for Umbrella Sampling,both ends of CNT were fixed. Then  
I use g_dist to calculate the COM distance between K+ and the  
reference group,the result is strange,the Z direction component -dz is  
negative,it should be positive,because the Z coordinate of K+ is lager  
than that of reference in the .xtc output file. I don't know why. the  
pulling distance is not larger than half of the box size.the Z  
direction component -dz  is also negative in Umbrella Sampling windows.
   Then do Umbrella Sampling,the pulling group and reference group is  
as in COM pulling step.pull_geometry = distance,pull_rate = 0. The PMF  
is negative and not symmetry about the middle of the CNT.I think it is  
wrong.May be it is because the dz is negative,or the choice of  
reference is not proper, it should be the middle the CNT as the  
reference.Anybody could help? Thanks a lot!

; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry= distance
; Select components for the pull vector. default: Y Y Y
pull_dim = N N Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1  = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0  = 1
pull_constr_tol  = 1e-06
pull_start   = yes
pull_nstxout = 500
pull_nstfout = 500
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),  
kJ/(mol*nm^2)

pull_group0  = refer
pull_weights0=
pull_pbcatom0= 0
pull_group1  = K
pull_weights1=
pull_pbcatom1= 0
pull_vec1= 0 0 0
pull_init1   = 0
pull_rate1   = 0.0
pull_k1  = 1000

Zhongjin He






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Re: [gmx-users] numerical matrix from xpm file

2010-10-04 Thread Tsjerk Wassenaar

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 s[2+s.find('/*'):s.rfind('*/')]

def col(c):
color = c.split('/*')
value = unquote(color[1])
color = unquote(color[0]).split()
sys.stderr.write("%s: %s %s %s\n"%(c.strip(),color[0], color[1], value))
return color[0], value

# Open the xpm file for reading
xpm = open(sys.argv[1])

# Read in lines until we fidn the start of the array
meta = [xpm.readline()]
while not meta[-1].startswith("static char *gromacs_xpm[]"):
meta.append(xpm.readline())

# The next line will contain the dimensions of the array
dim = xpm.readline()
# There are four integers surrounded by quotes
nx, ny, nc, nb = [int(i) for i in unquote(dim).split()]

# The next dim[2] lines contain the color definitions
# Each pixel is encoded by dim[3] bytes, and a comment
# at the end of the line contains the corresponding value
colors = dict([col(xpm.readline()) for i in range(nc)])

for i in xpm:
if i.startswith("/*"):
continue
j = unquote(i)
z = [colors[j[k:k+nb]] for k in range(0,nx,nb)]
sys.stdout.write(" ".join(z)+"\n")

###

On Mon, Oct 4, 2010 at 12:33 PM, Anupam Nath Jha
 wrote:
>
> 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
>
>
>> 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 
>> Date: Saturday, October 2, 2010 21:32
>> Subject: [gmx-users] numerical matrix from xpm file
>> To: gmx-users@gromacs.org
>>
>>>
>>> Hi all
>>>
>>> Is it possible to obtain the matrix in numeric form from xpm
>>> (obtained from
>>> gromacs analysis) files.
>>>
>>> because it's not coming in options for ourput files.
>>>
>>> thanks with regards
>>> anupam
>>>
>>> --
>>>
>>>
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by MailScanner, and is
>>> believed to be clean.
>>>
>>> --
>>> gmx-users mailing list    gmx-us...@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>> --
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>
>
> --
> Science is facts; just as houses are made of stone, so is science is made of
> facts; but a pile of stones is not a house, and  a collection of facts is not
> necessarily science.
>
> Anupam Nath Jha
> Ph. D. Student
> Saraswathi Vishveshwara Lab
> Molecular Biophysics Unit
> IISc,Bangalore-560012
> Karnataka
> Ph. no.-22932611
>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] charmm c36 lipids

2010-10-04 Thread Pär Bjelkmar



> Date: Fri, 1 Oct 2010 16:27:29 +0100
> From: Thomas Piggot 
> Subject: Re: [gmx-users] charmm c36 lipids
> To: Discussion list for GROMACS users 
> Message-ID: <4ca5fde1.8050...@soton.ac.uk>
> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed

> For a POPC bilayer then both your and my files produce the same tpr's 
> (checked both with gmxcheck and gmxdump). This is pleasing as I not only 
> scripted the conversions but did some parts by hand! I shall check the 
> other lipids to make sure that there are no discrepancies in these.
Good!

> 
> Also for my files I have included the bonded and non-bonded parameters 
> with parameters from CHARMM27 so as to allow simulations in water and 
> with proteins. I want to re-check these before contributing the 
> forcefield to the website, so it will probably be next week before I 
> upload it. Just to let you know I will use your lipids.rtp as it has the 
> atoms in separate charge groups so as to avoid having to use 
> -nochargegrp with pdb2gmx, whilst mine doesn't. I hope this is fine with 
> you.
For sure it is but you should be aware (and I think you are, since you were 
involved in the September discussion about this) that GROMACS does not treat 
charge groups as CHARMM does. See messages with subject "ARG Charmm gmx 4.5.1" 
(seems like the gmx-mailing list db is down so cannot provide you with a direct 
link). 

/Pär



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Re: [gmx-users] Polyethylene Surface generation



- Original Message -
From: Yash Gandhi 
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 taken help of an older thread to create a 
> gmx file for PE. I also did the modifications in rtp and hdb files as 
> mentioned in the link. After a few thoughts I tried to create a pdb file 
> using some logic. It's as follows:
 > 
> HETATM1  C1   EtB1  -4.243   0.027  -1.420 
> HETATM2  C2   EtB  1  -2.975  -0.719  -0.982 
> HETATM3  C1   Eth  2  -1.840   0.252  -0.620 
> HETATM4  C2   Eth  2  -0.566  -0.487  -0.180 
> HETATM5  C1   Eth  3   0.567   0.487   0.181 
> HETATM6  C2   Eth  3   1.841  -0.252   0.621 
> HETATM7  C1   EtE  4   2.976   0.719   0.983 
> HETATM8  C2   EtE  4   4.244  -0.026   1.420 
> HETATM9  H11  EtB  1  -5.058  -0.688  -1.680 
> HETATM   10  H12  EtB  1  -4.048   0.659  -2.317 
> HETATM   11  H13  EtB  1  -4.620   0.690  -0.609 
> HETATM   12  H21  EtB  1  -2.642  -1.393  -1.807 
> HETATM   13  H22  EtB  1  -3.213  -1.362  -0.102 
> HETATM   14  H11  Eth  2  -2.179   0.926   0.202 
> HETATM   15  H12  Eth  2  -1.609   0.895  -1.503 
> HETATM   16  H21  Eth  2  -0.227  -1.161  -1.003 
> HETATM   17  H22  Eth  2  -0.797  -1.130   0.702 
> HETATM   18  H11  Eth  3   0.228   1.161   1.003 
> HETATM   19  H12  Eth  3   0.798   1.129  -0.702 
> HETATM   20  H21  Eth  3   2.180  -0.926  -0.202 
> HETATM   21  H22  Eth  3   1.610  -0.895   1.504 
> HETATM   22  H11  EtE  4   2.643   1.393   1.807 
> HETATM   23  H12  EtE  4   3.213   1.362   0.102 
> HETATM   24  H21  EtE  4   5.059   0.688   1.679 
> HETATM   25  H22  EtE  4   4.621  -0.690   0.608 
> HETATM   26  H23  EtE  4   4.050  -0.658   2.317 
> CONECT12 
> CONECT213 
> CONECT324 
> CONECT43 
> END
> 
> after running pdb2gmx command and taking OPLSAA Force field with the 
> additional residues as mentioned in the link, I am getting the same error 
> always and I am not able to get the reason why
> 
> Fatal error:
>  Atom C1 in residue EtOH 1 not found in rtp entry with 9 atoms
>  while sorting atoms
> 
> Please help me urgently as I am not able to know why is the EtOH residue 
> being used.

EtOH for ethanol is defined in standard OPLS/AA force field files. pdb2gmx is 
trying to match what you've given it to that, rather than your ethylene .rtp 
entries. What are your .rtp entries? Have you got your PDB columns correct? 
Also, perhaps keeping atoms from the same residue adjacent will be a good idea.

Mark

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RE: [gmx-users] last frame in trr

2010-10-04 Thread Berk Hess


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 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 99 trjconv doesn't do what the description led me to 
> believe
> 
> 
>   
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] numerical matrix from xpm file

2010-10-04 Thread Anupam Nath Jha


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


> 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 
> Date: Saturday, October 2, 2010 21:32
> Subject: [gmx-users] numerical matrix from xpm file
> To: gmx-users@gromacs.org
>
>>
>> Hi all
>>
>> Is it possible to obtain the matrix in numeric form from xpm
>> (obtained from
>> gromacs analysis) files.
>>
>> because it's not coming in options for ourput files.
>>
>> thanks with regards
>> anupam
>>
>> --
>>
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
> --
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> Please search the archive at 
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--
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily science.

Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611



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[gmx-users] about COM pulling and g_dist

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+ (pulling group)frome one end (reference group ) 
of the CNT to another end to generate Configurations for Umbrella Sampling,both 
ends of CNT were fixed. Then I use g_dist to calculate the COM distance between 
K+ and the reference group,the result is strange,the Z direction component -dz 
is negative,it should be positive,because the Z coordinate of K+ is lager than 
that of reference in the .xtc output file. I don't know why. the pulling 
distance is not larger than half of the box size.the Z direction component -dz  
is also negative in Umbrella Sampling windows.
   Then do Umbrella Sampling,the pulling group and reference group is as in COM 
pulling step.pull_geometry = distance,pull_rate = 0. The PMF is negative and 
not symmetry about the middle of the CNT.I think it is wrong.May be it is 
because the dz is negative,or the choice of reference is not proper, it should 
be the middle the CNT as the reference.Anybody could help? Thanks a lot!
; COM PULLING  
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry= distance 
; Select components for the pull vector. default: Y Y Y
pull_dim = N N Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1  = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0  = 1
pull_constr_tol  = 1e-06
pull_start   = yes
pull_nstxout = 500
pull_nstfout = 500
; Number of pull groups 
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)
pull_group0  = refer
pull_weights0= 
pull_pbcatom0= 0
pull_group1  = K
pull_weights1= 
pull_pbcatom1= 0
pull_vec1= 0 0 0
pull_init1   = 0 
pull_rate1   = 0.0
pull_k1  = 1000

Zhongjin He




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Re: [gmx-users] Reg: Putting molecules on one side of the box



- Original Message -
From: vinothkumar mohanakrishnan 
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 

> 
> 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.

That is true only if the molecules in the smaller decane boxes that genconf 
replicated were distributed randomly in the file for the box. They aren't. If, 
say, you make genconf replicate two copies of a box in a given direction, then 
delete the second half of the molecules, you will get a decane-vacuum 
interface. Then solvate that.

Mark

> 
> Regards
>  Vinoth
> 
> 
> On Mon, Oct 4, 2010 at 4:44 PM, Mark Abraham  wrote:
>  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. 
> Finally, you wouldn't learn how to do solve such problems for yourself, and 
> would remain dependent, instead of developing a set of skills that is useful 
> for your work :-)
 > 
> Be sure to read the documentation for each of the tools I have mentioned, and 
> please do ask a focussed question on the list if you run into problems.
> 
> Good luck!
> 
> Mark
> 
> - Original Message -
>  From: vinothkumar mohanakrishnan 
> Date: Monday, October 4, 2010 21:58
> Subject: Re: [gmx-users] Reg: Putting molecules on one side of the box
>  To: Discussion list for GROMACS users 
> 
> > 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  
 > > wrote:
  > > Use genconf to replicate some suitable smaller box of decane to the full 
size, delete the second half of the decane molecules, then use genbox to fill 
the rest with water. Cunning use of genconf should allow you to select where 
the division lies.
  > > 
> > Mark > > 
> > 
 > > - Original Message -
> > From: vinothkumar mohanakrishnan 
 > > Date: Friday, September 24, 2010 17:22
> >  Subject: [gmx-users] Reg: Putting molecules on one side of the box
 > > To: Discussion list for GROMACS users 
> > 
 > > > Hi all
  > > > 
 > > > I have a triclinic box of length of 8*3*3 nm. i want to put water on one 
 > > > side of the box and say decane on the other side of the box. How to 
 > > > generate .gro for the water-decane mixture such that they form two 
 > > > distinct parts of the box.
   > > > 
 > > > Regards
  > > > Vinoth
 > >  > -- 
> > > gmx-users mailing listgmx-users@gromacs.org
 > >  > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > > > Please search the archive at 
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Re: [gmx-users] Reg: Putting molecules on one side of the box

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 wrote:

> Use genconf to replicate some suitable smaller box of decane to the full
> size, delete the second half of the decane molecules, then use genbox to
> fill the rest with water. Cunning use of genconf should allow you to select
> where the division lies.
>
> Mark
>
>
> - Original Message -
> From: vinothkumar mohanakrishnan 
> Date: Friday, September 24, 2010 17:22
> Subject: [gmx-users] Reg: Putting molecules on one side of the box
> To: Discussion list for GROMACS users 
>
> > Hi all
> >
> > I have a triclinic box of length of 8*3*3 nm. i want to put water on one
> side of the box and say decane on the other side of the box. How to generate
> .gro for the water-decane mixture such that they form two distinct parts of
> the box.
> >
> > Regards
> > Vinoth
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] Reg: Putting molecules on one side of the box

2010-10-04 Thread Chandan Choudhury

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 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 wrote:
>
>> 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.
>> Finally, you wouldn't learn how to do solve such problems for yourself, and
>> would remain dependent, instead of developing a set of skills that is useful
>> for your work :-)
>>
>> Be sure to read the documentation for each of the tools I have mentioned,
>> and please do ask a focussed question on the list if you run into problems.
>>
>> Good luck!
>>
>>
>> Mark
>>
>> - Original Message -
>> From: vinothkumar mohanakrishnan 
>> Date: Monday, October 4, 2010 21:58
>> Subject: Re: [gmx-users] Reg: Putting molecules on one side of the box
>> To: Discussion list for GROMACS users 
>>
>> > 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 > > wrote:
>>
>>> > Use genconf to replicate some suitable smaller box of decane to the
>>> full size, delete the second half of the decane molecules, then use genbox
>>> to fill the rest with water. Cunning use of genconf should allow you to
>>> select where the division lies.
>>> >
>>> > Mark
>>> >
>>> >
>>> > - Original Message -
>>> > From: vinothkumar mohanakrishnan 
>>> > Date: Friday, September 24, 2010 17:22
>>> > Subject: [gmx-users] Reg: Putting molecules on one side of the box
>>> > To: Discussion list for GROMACS users 
>>> >
>>> > > Hi all
>>> > >
>>> > > I have a triclinic box of length of 8*3*3 nm. i want to put water on
>>> one side of the box and say decane on the other side of the box. How to
>>> generate .gro for the water-decane mixture such that they form two distinct
>>> parts of the box.
>>> > >
>>> > > Regards
>>> > > Vinoth
>>> > > --
>>> > > gmx-users mailing listgmx-users@gromacs.org
>>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> > > Please search the archive at
>>> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> > > Please don't post (un)subscribe requests to the list. Use the
>>> > > www interface or send it to gmx-users-requ...@gromacs.org.
>>> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> > --
>>> > gmx-users mailing listgmx-users@gromacs.org
>>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> > Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>> > www interface or send it to gmx-users-requ...@gromacs.org.
>>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>> >
>> > --
>> > gmx-users mailing listgmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
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>
>
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[gmx-users] protein embedded into membrane.

2010-10-04 Thread #ZHAO LINA#

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 noticed
some warnings like this:

Warning) Unusual bond between residues: 40 (protein) and 491 (none)
Warning) Unusual bond between residues: 40 (protein) and 491 (none)
Warning) Unusual bond between residues: 40 (protein) and 491 (none)

when I removed those residues such as 491 (none), not protein ones, those
warning disappeared.

I noticed on Justine's tutorial, there were 26 iterations of scaling down. I
did those iterations step by step manually before and cost me nearly 40
mind-not-running minutes to finish, but later I spent crazy 2 hours or more to
write a short and clumsy script to save mine 40 mins work in the future. This
is not the point. The point was that, are there some shortcuts? I wonder
whether I could avoid doing those inflategro first, and then shrink and energy
minimization also being avoided by simply removed those lipids (I know I still
need a final EM).
or,
Can we locally inflated those membrane and then locally packed them together.
Very local, or maybe just simply removed those lipids.

How could I make sure the removal ones are going to be nice, from which sides I
should check.

Thanks and best regards,

lina

p.s To avoid a very trivial description, I put some background information
below, thanks for your time.

from Tieleman's website
http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis

and Justine's webpage
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html

I tried pack the lipids around the protein, no doubt followed perfectly based
on the tutorial before.

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Re: [gmx-users] protein embedded into membrane.

2010-10-04 Thread Justin A. Lemkul

#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 being inflated
first, I noticed

some warnings like this:

when I removed those residues such as 491 (none), not protein ones,
those warning disappeared.

VMD is detecting close contacts, not actual bonds, but since its heuristic
algorithm tells it there are bonds, then you get these warnings. Perhaps a
simple EM will resolve them, but maybe not.

I noticed on Justine's tutorial, there were 26 iterations of scaling
down. I did those iterations step by step manually before and cost me
nearly 40 mind-not-running minutes to finish, but later I spent crazy 2
hours or more to write a short and clumsy script to save mine 40 mins
work in the future. This is not the point. The point was that, are
there some shortcuts? I wonder whether I could avoid doing those
inflategro first, and then shrink and energy minimization also being
avoided by simply removed those lipids (I know I still need a final EM).

or,

What is presented in the tutorial is simply one way to build a membrane protein
system. If you have an easier case, then as long as you can justify your
methods, do what you see fit. Perhaps the iterations of InflateGRO are, in your
case, unnecessary. There is also a new tool called g_membed that might be
useful. It is far more automated than InflateGRO, but I have never used it myself.

Can we locally inflated those membrane and then locally packed them
together. Very local, or maybe just simply removed those lipids.

Not to my knowledge, unless you write this program yourself.

How could I make sure the removal ones are going to be nice, from which
sides I should check.

I don't understand what you're asking for here.

-Justin

Thanks and best regards,

lina

p.s To avoid a very trivial description, I put some background
information below, thanks for your time.

from Tieleman's website
http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis

and Justine's webpage
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html

I tried pack the lipids around the protein, no doubt followed perfectly
based on the tutorial before.

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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RE: [gmx-users] protein embedded into membrane.

2010-10-04 Thread #ZHAO LINA#

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 regards,

lina 

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, October 04, 2010 11:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] protein embedded into membrane.

#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 being inflated
> first, I noticed
> some warnings like this:
>
> Warning) Unusual bond between residues:  40 (protein) and 491 (none)
> Warning) Unusual bond between residues:  40 (protein) and 491 (none)
> Warning) Unusual bond between residues:  40 (protein) and 491 (none)
>
> when I removed those residues such as 491 (none), not protein ones,
> those warning disappeared.
>

VMD is detecting close contacts, not actual bonds, but since its heuristic
algorithm tells it there are bonds, then you get these warnings.  Perhaps a
simple EM will resolve them, but maybe not.

> I noticed on Justine's tutorial, there were 26 iterations of scaling
> down. I did those iterations step by step manually before and cost me
> nearly 40 mind-not-running minutes to finish, but later I spent crazy 2
> hours or more to write a short and clumsy script to save mine 40 mins
> work in the future. This is not the point.  The point was that, are
> there some shortcuts? I wonder whether I could avoid doing those
> inflategro first, and then shrink and energy minimization also being
> avoided by simply removed those lipids (I know I still need a final EM).
> or,

What is presented in the tutorial is simply one way to build a membrane protein
system.  If you have an easier case, then as long as you can justify your
methods, do what you see fit.  Perhaps the iterations of InflateGRO are, in your
case, unnecessary.  There is also a new tool called g_membed that might be
useful.  It is far more automated than InflateGRO, but I have never used it 
myself.

> Can we locally inflated those membrane and then locally packed them
> together. Very local, or maybe just simply removed those lipids.
>

Not to my knowledge, unless you write this program yourself.

> How could I make sure the removal ones are going to be nice, from which
> sides I should check.
>

I don't understand what you're asking for here.

-Justin

> Thanks and best regards,
>
> lina
>
> p.s  To avoid a very trivial description, I put some background
> information below, thanks for your time.
>
> from Tieleman's website
> http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis
>
> and Justine's webpage
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
>
>  I tried pack the lipids around the protein, no doubt followed perfectly
> based on the tutorial before.
>
>

--

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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[gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled?

2010-10-04 Thread 吴鹏

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 set mdrun -nt to 1, i.e. force GMX
to use one thread. Otherwise, mdrun reports segmentation fault.

Questions:
1. I speculate that the segmentation fault is caused by thread
conflict, i.e., I somehow break parallelization in Gromacs - is this
right?
2. Is it possible to perform on-fly analysis or other types of
customization of Gromacs when multi-threading is enabled?
3. If answer to 2 is yes, where can I find the documentations for
doing so, and how difficult is it to write multi-threading code using
Gromacs's own library?

Thank you very much for your time.

Best regards,

Peng
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Re: [gmx-users] numerical matrix from xpm file

2010-10-04 Thread Anupam Nath Jha


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):
> return s[1+s.find('"'):s.rfind('"')]
>
> def uncomment(s):
> return s[2+s.find('/*'):s.rfind('*/')]
>
> def col(c):
> color = c.split('/*')
> value = unquote(color[1])
> color = unquote(color[0]).split()
> sys.stderr.write("%s: %s %s %s\n"%(c.strip(),color[0], color[1], value))
> return color[0], value
>
> # Open the xpm file for reading
> xpm = open(sys.argv[1])
>
> # Read in lines until we fidn the start of the array
> meta = [xpm.readline()]
> while not meta[-1].startswith("static char *gromacs_xpm[]"):
> meta.append(xpm.readline())
>
> # The next line will contain the dimensions of the array
> dim = xpm.readline()
> # There are four integers surrounded by quotes
> nx, ny, nc, nb = [int(i) for i in unquote(dim).split()]
>
> # The next dim[2] lines contain the color definitions
> # Each pixel is encoded by dim[3] bytes, and a comment
> # at the end of the line contains the corresponding value
> colors = dict([col(xpm.readline()) for i in range(nc)])
>
> for i in xpm:
> if i.startswith("/*"):
> continue
> j = unquote(i)
> z = [colors[j[k:k+nb]] for k in range(0,nx,nb)]
> sys.stdout.write(" ".join(z)+"\n")
>
> ###
>
> On Mon, Oct 4, 2010 at 12:33 PM, Anupam Nath Jha
>  wrote:
>>
>> 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
>>
>>
>>> 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 
>>> Date: Saturday, October 2, 2010 21:32
>>> Subject: [gmx-users] numerical matrix from xpm file
>>> To: gmx-users@gromacs.org
>>>

 Hi all

 Is it possible to obtain the matrix in numeric form from xpm
 (obtained from
 gromacs analysis) files.

 because it's not coming in options for ourput files.

 thanks with regards
 anupam

 --


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>>
>>
>> --
>> Science is facts; just as houses are made of stone, so is science is made of
>> facts; but a pile of stones is not a house, and  a collection of facts is not
>> necessarily science.
>>
>> Anupam Nath Jha
>> Ph. D. Student
>> Saraswathi Vishveshwara Lab
>> Molecular Biophysics Unit
>> IISc,Bangalore-560012
>> Karnataka
>> Ph. no.-22932611
>>
>>
>>
>> --
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>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
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>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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> befor

Re: [gmx-users] protein embedded into membrane.

2010-10-04 Thread Justin A. Lemkul




#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?



Area per lipid will equilibrate with sufficient simulation.  Otherwise, use 
normal EM criteria to determine whether or not your system is in a reasonable 
configuration.


-Justin


Thanks and best regards,

lina 



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, October 04, 2010 11:27 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] protein embedded into membrane.

#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 being inflated
first, I noticed
some warnings like this:

Warning) Unusual bond between residues:  40 (protein) and 491 (none)
Warning) Unusual bond between residues:  40 (protein) and 491 (none)
Warning) Unusual bond between residues:  40 (protein) and 491 (none)

when I removed those residues such as 491 (none), not protein ones,
those warning disappeared.



VMD is detecting close contacts, not actual bonds, but since its heuristic
algorithm tells it there are bonds, then you get these warnings.  Perhaps a
simple EM will resolve them, but maybe not.


I noticed on Justine's tutorial, there were 26 iterations of scaling
down. I did those iterations step by step manually before and cost me
nearly 40 mind-not-running minutes to finish, but later I spent crazy 2
hours or more to write a short and clumsy script to save mine 40 mins
work in the future. This is not the point.  The point was that, are
there some shortcuts? I wonder whether I could avoid doing those
inflategro first, and then shrink and energy minimization also being
avoided by simply removed those lipids (I know I still need a final EM).
or,


What is presented in the tutorial is simply one way to build a membrane protein
system.  If you have an easier case, then as long as you can justify your
methods, do what you see fit.  Perhaps the iterations of InflateGRO are, in your
case, unnecessary.  There is also a new tool called g_membed that might be
useful.  It is far more automated than InflateGRO, but I have never used it 
myself.


Can we locally inflated those membrane and then locally packed them
together. Very local, or maybe just simply removed those lipids.



Not to my knowledge, unless you write this program yourself.


How could I make sure the removal ones are going to be nice, from which
sides I should check.



I don't understand what you're asking for here.

-Justin


Thanks and best regards,

lina

p.s  To avoid a very trivial description, I put some background
information below, thanks for your time.

from Tieleman's website
http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis

and Justine's webpage
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html

 I tried pack the lipids around the protein, no doubt followed perfectly
based on the tutorial before.




--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] charmm tip5p in Gmx 4.5.2

2010-10-04 Thread Yao Yao




  --- Begin Message ---

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 ---
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Re: [gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled?



- Original Message -
From: 吴鹏 
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 

> 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 set mdrun -nt to 1, i.e. 
> force GMX
> to use one thread. Otherwise, mdrun reports segmentation fault.
> 
> Questions:
> 1. I speculate that the segmentation fault is caused by thread
> conflict, i.e., I somehow break parallelization in Gromacs - is this
> right?

There are many possible causes, not least that you were using a technique that 
relied on static variables, which do not work reliably with threads.

> 2. Is it possible to perform on-fly analysis or other types of
> customization of Gromacs when multi-threading is enabled?

Yes, but you have to do it right.

> 3. If answer to 2 is yes, where can I find the documentations for
> doing so, and how difficult is it to write multi-threading code using
> Gromacs's own library?

The requirements for code that works with threading are well known, and you 
should be able to Google for them. More importantly, you would have to cope 
with the problem that under domain or particle decomposition, each process only 
has a fraction of the atomic data. Unless you need the results for the ongoing 
simulation, it is far easier to write code to do your analysis afterwards.

Mark

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[gmx-users] unconstrained_start vs. continuation in Gromacs 4.5.x manual

2010-10-04 Thread Oliver Stueker

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 :
/usr/local/gromacs-4.5.1/share/gromacs/html/online/mdp_opt.html#bond )
although that name seems to be deprecated since Gromacs 4.0.

Oliver
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[gmx-users] about COM pulling and g_dist

> 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
> 
> 
>      


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[gmx-users] about COM pulling and g_dist

> > 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
    


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[gmx-users] about COM pulling and g_dist

--- 10年10月5日，周二, zhongjin  写道：

> 发件人: zhongjin 
> 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 -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.Snap7.jpg shows distance in one
> umbrella sampling window.
> Zhongjin He
>     
> 
> 
>      


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Re: [gmx-users] unconstrained_start vs. continuation in Gromacs 4.5.x manual

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 
Date: Tuesday, October 5, 2010 10:58
Subject: [gmx-users] unconstrained_start vs. continuation in Gromacs 4.5.x 
manual
To: Discussion list for GROMACS users 

> 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 :
> /usr/local/gromacs-
> 4.5.1/share/gromacs/html/online/mdp_opt.html#bond )
> although that name seems to be deprecated since Gromacs 4.0.
> 
> Oliver
> -- 
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[gmx-users] 转发: about COM pulling and g_dist

--- 10年10月5日，周二, zhongjin  写道：

> 发件人: zhongjin 
> 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
>     
> 
> 
>      


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[gmx-users] Reg: Prodrg topology

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
error (during grompp) as atomtype CH3 not found ( as expected, i know why it
happens). hence my question is how to use oplsaa for decane molecule?

Regards
Vinoth
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Re: [gmx-users] Reg: Prodrg topology

Pre-supposing the suitability of only one tool is pretty limiting - and that's 
before you consider the weaknesses of PRODRG even for its target forcefields.

For decane, writing the topology by hand is feasible. There's at most 3 atom 
types and only 32 atoms, after all. Otherwise, consider 
http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/MKTOP

Mark
- Original Message -
From: vinothkumar mohanakrishnan 
Date: Tuesday, October 5, 2010 16:43
Subject: [gmx-users] Reg: Prodrg topology
To: Discussion list for GROMACS users 

> 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 
> error (during grompp) as atomtype CH3 not found ( as expected, i know why it 
> happens). hence my question is how to use oplsaa for decane molecule?
 > 
> Regards
> Vinoth
 > -- 
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Reg: Prodrg topology