[gmx-users] Problem using trjconv and g_potential

[Manik Mayur]

Hi,

I have a slab geometry configuration with water and some ions. I wish to
extract the charge/potential distribution due to ions in the center of my
box. For this I used trajconv to have a box of required dimensions and
center the required ions in it. And then run g_potential on it to get the
charge and potential distribution. But the g_potential fails with a
segmentation fault. I am producing the steps followed by me below so please
suggest me where could I have gone wrong.

1) My actual box dimensions are 4 X 5 X 30. I first use trjconv to center my
ions in a box of dimensions 4 X 5 X 10 (I am sure all of them will fit in
here upon centering):

trjconv -f Sim_ions.trr -o Soln.trr -s Sim_ions.tpr -n Sim_ions.ndx -b 1000
-box 4 5 10 -center

2) Select group: Ions (for both centering and output)

3) Use g_potential to plot the charge distribution and the potential
distribution-

g_potential -f Soln.trr -s Sim_ions.tpr -n Soln.ndx -o potential.xvg -oc
charge.xvg -d Z

Selected 4: 'Ions'
trn version: GMX_trn_file (single precision)
Reading frame   0 time 1000.000
Dividing the box in 10 slices
Segmentation fault

Thanks,

Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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Re: [gmx-users] Regarding Error "Atomtype OS not found"

[Mark Abraham]

On 13/04/2010 1:49 PM, Jignesh Patel wrote:

Hello,

while I am running grompp command, I am getting following error.

Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 837 of the 2346 non-bonded parameter combinations
---
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 947
Fatal error:
Atomtype OS not found

Can anyone help me to solve this problem?


Yep, they can point out that atom type OS is not found. Since at this 
stage only you know about your topology and system preparation, and more 
particularly why you're trying to #include "ff_dum.itp", only you can 
reason why. Perhaps sharing some more detail will help...


Mark
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Re: [gmx-users] Trehalose RTP file trouble

[Tsjerk Wassenaar]

Hi,

The sugars were improved in 45a3. The parameters haven't changed for
the later versions.

Cheers,

Tsjerk

On Tue, Apr 13, 2010 at 12:24 AM, Justin A. Lemkul  wrote:
>
>
> Michael McGovern wrote:
>>
>> Hi everyone.  I'm doing some simulations involving the sugar trehalose,
>> with the 53a6 force field.  There is an odd issue I am having with the rtp
>> file for trehalose.  It seems to be charged.  Here is the beginning of the
>> rtp entry:
>>
>>  [ TRH ]
>>  [ atoms ]
>>  HO4     H     0.41000     0
>>   O4    OA    -0.64200     0
>>   C4   CH1     0.23200     0
>>   C3   CH1     0.23200     1
>>   O3    OA    -0.64200     1
>>  HO3     H     0.41000     1
>>   C2   CH1     0.23200     2
>>   O2    OA    -0.64200     2
>>  HO2     H     0.41000     2
>>   C6   CH1     0.23200     3
>>   O6    OA    -0.64200     3
>>  HO6     H     0.41000     3
>>   C5   CH1     0.37800     4
>>   O5    OA    -0.45000     4
>>   C1   CH1     0.24200     4
>>   O1    OA    -0.34000     4
>>  C1'   CH1     0.24200     4
>>  O5'    OA    -0.45000     4
>>  C5'   CH1     0.37800     4
>>  C4'   CH1     0.27500     5
>>  O4'    OA    -0.6     5
>>  HO4'     H     0.47000     5
>>  C3'   CH1     0.23200     6
>>  O3'    OA    -0.64200     6
>>  HO3'     H     0.41000     6
>>  C2'   CH1     0.23200     7
>>  O2'    OA    -0.64200     7
>>  HO2'     H     0.41000     7
>>  C6'   CH1     0.23200     8
>>  O6'    OA    -0.64200     8
>>  HO6'     H     0.41000     8
>>
>> Charge group 5 has a net charge of +0.145.  Is this a typo?  Should I just
>> change it to be the same as the other C-O-H charge groups?
>>
>>
>
> The net charge certainly seems wrong.  Before making any ad hoc changes,
> though, refer to the primary literature for the force field and make sure
> everything else is right.  I think 53a6 has the same charges as 45a4,
> wherein the sugar parameters were improved from 45a3.  I don't see any
> mention of modifications to sugars in the 53a6 paper.  45a4 ref:
>
> Lins and Hunenberger (2005) J Comput Chem 26: 1400-1412.
>
> -Justin
>
> --
> 
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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[gmx-users] Regarding Error "Atomtype OS not found"

[Jignesh Patel]

Hello,

while I am running grompp command, I am getting following error.

Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 837 of the 2346 non-bonded parameter combinations
---
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 947
Fatal error:
Atomtype OS not found

Can anyone help me to solve this problem?

Any kind of help is highly appreciable.

-- 
Best Wishes,
Jignesh Patel
Pharmacoinformatics,
NIPER
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Re: [gmx-users] Trehalose RTP file trouble

[Justin A. Lemkul]

Michael McGovern wrote:
Hi everyone.  I'm doing some simulations involving the sugar trehalose, 
with the 53a6 force field.  There is an odd issue I am having with the 
rtp file for trehalose.  It seems to be charged.  Here is the beginning 
of the rtp entry:


 [ TRH ]
 [ atoms ]
  HO4 H 0.41000 0
   O4OA-0.64200 0
   C4   CH1 0.23200 0
   C3   CH1 0.23200 1
   O3OA-0.64200 1
  HO3 H 0.41000 1
   C2   CH1 0.23200 2
   O2OA-0.64200 2
  HO2 H 0.41000 2
   C6   CH1 0.23200 3
   O6OA-0.64200 3
  HO6 H 0.41000 3
   C5   CH1 0.37800 4
   O5OA-0.45000 4
   C1   CH1 0.24200 4
   O1OA-0.34000 4
  C1'   CH1 0.24200 4
  O5'OA-0.45000 4
  C5'   CH1 0.37800 4
  C4'   CH1 0.27500 5
  O4'OA-0.6 5
 HO4' H 0.47000 5
  C3'   CH1 0.23200 6
  O3'OA-0.64200 6
 HO3' H 0.41000 6
  C2'   CH1 0.23200 7
  O2'OA-0.64200 7
 HO2' H 0.41000 7
  C6'   CH1 0.23200 8
  O6'OA-0.64200 8
 HO6' H 0.41000 8

Charge group 5 has a net charge of +0.145.  Is this a typo?  Should I 
just change it to be the same as the other C-O-H charge groups?





The net charge certainly seems wrong.  Before making any ad hoc changes, though, 
refer to the primary literature for the force field and make sure everything 
else is right.  I think 53a6 has the same charges as 45a4, wherein the sugar 
parameters were improved from 45a3.  I don't see any mention of modifications to 
sugars in the 53a6 paper.  45a4 ref:


Lins and Hunenberger (2005) J Comput Chem 26: 1400-1412.

-Justin

--


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] Trehalose RTP file trouble

[Michael McGovern]

Hi everyone.  I'm doing some simulations involving the sugar trehalose, with 
the 53a6 force field.  There is an odd issue I am having with the rtp file for 
trehalose.  It seems to be charged.  Here is the beginning of the rtp entry:
 [ TRH ] [ atoms ]  HO4     H     0.41000     0   O4    OA    -0.64200     0   
C4   CH1     0.23200     0   C3   CH1     0.23200     1   O3    OA    -0.64200  
   1  HO3     H     0.41000     1   C2   CH1     0.23200     2   O2    OA    
-0.64200     2  HO2     H     0.41000     2   C6   CH1     0.23200     3   O6   
 OA    -0.64200     3  HO6     H     0.41000     3   C5   CH1     0.37800     
4   O5    OA    -0.45000     4   C1   CH1     0.24200     4   O1    OA    
-0.34000     4  C1'   CH1     0.24200     4  O5'    OA    -0.45000     4  C5'   
CH1     0.37800     4  C4'   CH1     0.27500     5  O4'    OA    -0.6     
5 HO4'     H     0.47000     5  C3'   CH1     0.23200     6  O3'    OA    
-0.64200     6 HO3'     H     0.41000     6  C2'   CH1     0.23200    
 7  O2'    OA    -0.64200     7 HO2'     H     0.41000     7  C6'   CH1     
0.23200     8  O6'    OA    -0.64200     8 HO6'     H     0.41000     8
Charge group 5 has a net charge of +0.145.  Is this a typo?  Should I just 
change it to be the same as the other C-O-H charge groups?


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Re: [gmx-users] Amino acid simulation

[Justin A. Lemkul]

Chandan Choudhury wrote:

Hello gmx-users

I am trying to simulate an amino acid (say GLN). It can be as a 
zwitterionic form or uncharged ends. Neither ffamber or ffopls force 
fields has a complete parameter for them. While in ffamber, I have the 


This is not true.  OPLS can handle isolated amino acids, you just have to 
manually choose the termini in pdb2gmx (using -ter).  Use the "zwitterion" forms 
of the termini, since in fact, you have a zwitterion.


-Justin

parameters for CGLU and NGLU, but not for a Glutamine. Do I need to 
define it there, or there is some way out. If I need to define it, how 
do I retrive the partial charges.


Any insight would be very helpful.
Thanks

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA



--


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] Amino acid simulation

[Tamas Horvath]

It's highly unusual to simulate a single amino acid. I don't exactly know
what's your purpose with it, but if you really want to do it, you need to
generate those parameters.
I know there are web services for generating gromos FF parameters for
"unusual" molecules, possibly there are such resources for amber or opls
too.

On Mon, Apr 12, 2010 at 8:36 PM, Chandan Choudhury wrote:

> Hello gmx-users
>
> I am trying to simulate an amino acid (say GLN). It can be as a
> zwitterionic form or uncharged ends. Neither ffamber or ffopls force fields
> has a complete parameter for them. While in ffamber, I have the parameters
> for CGLU and NGLU, but not for a Glutamine. Do I need to define it there, or
> there is some way out. If I need to define it, how do I retrive the partial
> charges.
>
> Any insight would be very helpful.
> Thanks
>
> Chandan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
> --
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[gmx-users] Amino acid simulation

[Chandan Choudhury]

Hello gmx-users

I am trying to simulate an amino acid (say GLN). It can be as a zwitterionic
form or uncharged ends. Neither ffamber or ffopls force fields has a
complete parameter for them. While in ffamber, I have the parameters for
CGLU and NGLU, but not for a Glutamine. Do I need to define it there, or
there is some way out. If I need to define it, how do I retrive the partial
charges.

Any insight would be very helpful.
Thanks

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] output in gromos format

[Mark Abraham]

On 13/04/2010 12:46 AM, grivet wrote:

Hi everybody,

In order to use an old set of analysis programs, I would like mdrun to
ouput my trajectory in gromos-96 format. Is this possible ?


trjconv will write .g96 format (see trjconv -h), but I don't know if 
that is a trajectory format or merely a format for single structures.



I understand that I could convert the .xtc file with trjconv. I need
rather high precision, but I am uncertain about the meaning of the
parameter xtc_precision; what does it mean?


That's why manual section 7.3 is so long :-)


Another quite unrelated question; most examples I have looked at use
rvdw = 1.0, regardless of the force field; however, the manual states
that, with GROMOS force fields, one should use rvdw>= 1.4; which is
correct ?


However the force field was parameterized - so read its literature.

Mark
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Re: [gmx-users] output in gromos format

[Justin A. Lemkul]

grivet wrote:

Hi everybody,

In order to use an old set of analysis programs, I would like mdrun to
ouput my trajectory in gromos-96 format. Is this possible ?



No, not directly.


I understand that I could convert the .xtc file with trjconv. I need
rather high precision, but I am uncertain about the meaning of the
parameter xtc_precision; what does it mean?



The xtc_precision sets how many decimal places are written.  If you want really 
high precision, just convert the .trr file (provided you have enough disk space 
for all of its frames to start with).



Another quite unrelated question; most examples I have looked at use
rvdw = 1.0, regardless of the force field; however, the manual states
that, with GROMOS force fields, one should use rvdw >= 1.4; which is
correct ?



Per the parameterization of the force field (hint: read the primary literature), 
rvdw should be set to 1.4 nm.


-Justin


Thank you in advance for your help
JP Grivet



--


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] output in gromos format

[grivet]

Hi everybody,

In order to use an old set of analysis programs, I would like mdrun to
ouput my trajectory in gromos-96 format. Is this possible ?

I understand that I could convert the .xtc file with trjconv. I need
rather high precision, but I am uncertain about the meaning of the
parameter xtc_precision; what does it mean?

Another quite unrelated question; most examples I have looked at use
rvdw = 1.0, regardless of the force field; however, the manual states
that, with GROMOS force fields, one should use rvdw >= 1.4; which is
correct ?

Thank you in advance for your help
JP Grivet

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Re: [gmx-users] install problem of ngmx

[Mark Abraham]

On 13/04/2010 12:14 AM, kecy...@sina.com wrote:

Hello, the error is like that :

*In file included from ngmx.c:50:*
 >
 > *Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory*
 >
 > *Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory*
 >
 > *Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory*
 >
 > *Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory*
 >
but in my system, it has the Xlib.h,Xutil.h,cursorfont.h,Xresource.h in
the /usr/X11R6/include /X11 file. Where I should put these documents in
can it finds?


Don't move the files anywhere. That way madness lies. Justin told you 
how to use --without-x properly. Do that, or use 
CFLAGS="-I/usr/X11R6/include/X11" properly.


Mark
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Re: [gmx-users] Lateral pressure profile in membrane simulations

[George Khelashvili]

Thank you!

I will follow your guidelines.

George

XAvier Periole wrote:


You have to rerun the trajectory ... not frame by frame!

Notes:
- that there is issue on pressure tensor calculation when constrains are
used
- simulations need to be quite long to get a reasonable convergence.

On Apr 12, 2010, at 2:41 AM, George Khelashvili wrote:


Dear users,

I am attempting to perform 3D pressure tensor calculation on 
well-converged all-atom lipid bilayer. I am using modified gromacs 
and -rerun option and analyze the output with the tools that is 
provided on Martini website. I had following question: I have a 
production trajectory from original MD calculations, and I also have 
separate snapshots saved once in 100ps. As I understand, for pressure 
calculations I need to use -rerun on separate snapshots. Is this the 
case? If so, I would get as an output bunch of local_pressure.dat 
files. How do I analyze them? One by one? I would greatly appreciate 
if somebody can describe the sequence of events that I need to go 
through in order to obtain pressure profiles.


Thank you for you assistance,

Sincerely,
George

--
George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
e-mail: gek2...@med.cornell.edu
phone:  1-212-746-6539
fax:1-212-746-6226


Martti Louhivuori wrote:

On 8 Apr 2010, at 00:45, Fernando E. Herrera wrote:
I am doing some molecular dynamics simulations of membrane systems 
and i would like to ask you if someone know or have a code for the 
calculation of the lateral pressure profile  from the data obtained 
doing  membrane simulations.


You can find everything you need from here:
http://www.cgmartini.nl/index.php/tools/114-3d-pf

It is a custom version of Gromacs that calculates a 3D pressure 
field using the -rerun option of mdrun, as explained in Ollila et 
al. (2009) PhysRevLett 102: 078101. Before you do the rerun, you 
need to redo grompp with 'userreal1' set to the desired grid size. 
The analysis tools there can then be used to calculate e.g. a 
lateral pressure profile... Note that constraints are a bit 
problematic, though, so if your lipids have constraints, the profile 
may not be accurate.


Best regards,
-martti-
--
Post-doctoral research fellow
Moleculaire Dynamica
University of Groningen
Nijenborgh 4, 9747AG Groningen, the Netherlands
tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398




--
George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
e-mail: gek2...@med.cornell.edu
phone:  1-212-746-6539
fax:1-212-746-6226

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--
George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
gek2...@med.cornell.edu
Phone: 1-212-746-6539
Fax:   1-212-746-6226


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[gmx-users] install problem of ngmx

[kecy_wu]

Hello, the error is like that :
*In file included from ngmx.c:50:*
>
> *Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory*
>
> *Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory*
>
> *Xstuff.h:51:28: error: X11/cursorfont.h: No such file or directory*
>
> *Xstuff.h:52:27: error: X11/Xresource.h: No such file or directory*
>
 but in my system, it has the Xlib.h,Xutil.h,cursorfont.h,Xresource.h in 
the /usr/X11R6/include /X11 file. Where  I should put these documents in 
can it finds?-- 
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Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl

[Justin A. Lemkul]

xi zhao wrote:


Dear Sir : In fact,  these structures were initially centered within the 
same coordinate system as your Gromacs Tutorials .




Then surely you made some sort of modification to the inflategro.pl script in 
order to make it work with a CG structure, right?  The standard script matches 
C-alpha and P positions to do scaling of coordinates, but MARTINI nomenclature 
will not match, at least in the case of the protein.  If you haven't made any 
modifications, perhaps that is the problem as well :)


-Justin

4 



--- *10年4月12日，周一, Justin A. Lemkul //* 写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] construct CG membrane protein and CG membrane
and inflategro.pl
收件人: "Gromacs Users' List" 
日期: 2010年4月12日,周一,下午9:07



xi zhao wrote:
 >
 > my procesure:
 > 1. cat cgprotein cgmembrane>system.gro (using Martini force field)

Were these structures initially centered within the same coordinate
system?  By your description, it sounds like these two components
are simply not placed properly.  There is a membrane protein
tutorial linked from the Gromacs Tutorials page that guides you
through constructing an atomistic membrane protein system using
InflateGRO.  You might find it useful.

-Justin

 > 2 perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5
area.dat
 > 3. grompp_d -f em.mdp -c system_inflated.gro  -p topol.top -o
system_inflatedem.tpr (with strong postion restraint)
 > 4. mdrun
 > 5 in the system_inflatedem.gro , the protein and membrane 
separate each other.

 > please help me !
 > 
 > 4


>
 >
 > --- *10年4月12日，周一, Justin A. Lemkul /http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/* 写道：
 >
 >
 > 发件人: Justin A. Lemkul http://cn.mc151.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>
 > 主题: Re: [gmx-users] construct CG membrane protein and CG
membrane
 > and inflategro.pl
 > 收件人: "Discussion list for GROMACS users"
http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-us...@gromacs.org>>
 > 日期: 2010年4月12日,周一,下午8:42
 >
 >
 >
 > xi zhao wrote:
 >  >
 >  >
 >  > Dear Gromacs users:
 >  > I use inflateGRO.pl to insert CG protein in to CG POPC
membrane,
 > but when carryied EM with Strong POStion REStraint, the
protien and
 > membrane were apart. Please help me!
 >
 > What does "apart" mean?  If you want free help, you have to
make it
 > easy to help you.  That means thorough descriptions of what
you're
 > doing, what you're seeing, and if necessary, posting images
online
 > (not as attachments!) for us to take a look.  The InflateGRO
method
 > should generate a configuration that has molecules separated by a
 > large amount of space, but if there is something else wrong
you'll
 > have to provide a better description.
 >
 > -Justin
 >
 >  > 4
 > 
   
 > 
   >>
 >  >
 >  >
 >  >
 > -- 
 >
 > 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
 >
 > 
 > -- gmx-users mailing listgmx-users@gromacs.org

 > 
   

 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at http://www.gromacs.org/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

Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl

[xi zhao]

Dear Sir : In fact,  these structures were initially centered within the same 
coordinate system as your Gromacs Tutorials .



--- 10年4月12日，周一, Justin A. Lemkul  写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] construct CG membrane protein and CG membrane and 
inflategro.pl
收件人: "Gromacs Users' List" 
日期: 2010年4月12日,周一,下午9:07




xi zhao wrote:
> 
> my procesure:
> 1. cat cgprotein cgmembrane>system.gro (using Martini force field)

Were these structures initially centered within the same coordinate system?  By 
your description, it sounds like these two components are simply not placed 
properly.  There is a membrane protein tutorial linked from the Gromacs 
Tutorials page that guides you through constructing an atomistic membrane 
protein system using InflateGRO.  You might find it useful.

-Justin

> 2 perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
> 3. grompp_d -f em.mdp -c system_inflated.gro  -p topol.top -o 
> system_inflatedem.tpr (with strong postion restraint)
> 4. mdrun
> 5 in the system_inflatedem.gro , the protein and membrane  separate each 
> other.
> please help me !
>  
> 4 
> 
> 
> --- *10年4月12日，周一, Justin A. Lemkul //* 写道：
> 
> 
>     发件人: Justin A. Lemkul 
>     主题: Re: [gmx-users] construct CG membrane protein and CG membrane
>     and inflategro.pl
>     收件人: "Discussion list for GROMACS users" 
>     日期: 2010年4月12日,周一,下午8:42
> 
> 
> 
>     xi zhao wrote:
>      >
>      >
>      > Dear Gromacs users:
>      > I use inflateGRO.pl to insert CG protein in to CG POPC membrane,
>     but when carryied EM with Strong POStion REStraint, the protien and
>     membrane were apart. Please help me!
> 
>     What does "apart" mean?  If you want free help, you have to make it
>     easy to help you.  That means thorough descriptions of what you're
>     doing, what you're seeing, and if necessary, posting images online
>     (not as attachments!) for us to take a look.  The InflateGRO method
>     should generate a configuration that has molecules separated by a
>     large amount of space, but if there is something else wrong you'll
>     have to provide a better description.
> 
>     -Justin
> 
>      > 4
>     
>     
>>
>      >
>      >
>      > 
>     -- 
> 
>     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
> 
>     
>     -- gmx-users mailing list    gmx-users@gromacs.org
>     
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
> 
> 
>  

-- 

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] construct CG membrane protein and CG membrane and inflategro.pl

[Justin A. Lemkul]

xi zhao wrote:


my procesure:
1. cat cgprotein cgmembrane>system.gro (using Martini force field)


Were these structures initially centered within the same coordinate system?  By 
your description, it sounds like these two components are simply not placed 
properly.  There is a membrane protein tutorial linked from the Gromacs 
Tutorials page that guides you through constructing an atomistic membrane 
protein system using InflateGRO.  You might find it useful.


-Justin


2 perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
3. grompp_d -f em.mdp -c system_inflated.gro  -p topol.top -o 
system_inflatedem.tpr (with strong postion restraint)

4. mdrun
5 in the system_inflatedem.gro , the protein and membrane  separate each 
other.

please help me !
 

4 



--- *10年4月12日，周一, Justin A. Lemkul //* 写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] construct CG membrane protein and CG membrane
and inflategro.pl
收件人: "Discussion list for GROMACS users" 
日期: 2010年4月12日,周一,下午8:42



xi zhao wrote:
 >
 >
 > Dear Gromacs users:
 > I use inflateGRO.pl to insert CG protein in to CG POPC membrane,
but when carryied EM with Strong POStion REStraint, the protien and
membrane were apart. Please help me!

What does "apart" mean?  If you want free help, you have to make it
easy to help you.  That means thorough descriptions of what you're
doing, what you're seeing, and if necessary, posting images online
(not as attachments!) for us to take a look.  The InflateGRO method
should generate a configuration that has molecules separated by a
large amount of space, but if there is something else wrong you'll
have to provide a better description.

-Justin

 > 4

>
 >
 >
 > 


-- 

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


-- gmx-users mailing listgmx-users@gromacs.org

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Please search the archive at http://www.gromacs.org/search before
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.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php


 


--


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] construct CG membrane protein and CG membrane and inflategro.pl

[xi zhao]

my procesure:
1. cat cgprotein cgmembrane>system.gro (using Martini force field)
2 perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat
3. grompp_d -f em.mdp -c system_inflated.gro  -p topol.top -o 
system_inflatedem.tpr (with strong postion restraint)
4. mdrun
5 in the system_inflatedem.gro , the protein and membrane  separate each other.
please help me !
 



--- 10年4月12日，周一, Justin A. Lemkul  写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] construct CG membrane protein and CG membrane and 
inflategro.pl
收件人: "Discussion list for GROMACS users" 
日期: 2010年4月12日,周一,下午8:42




xi zhao wrote:
> 
> 
> Dear Gromacs users:
> I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when 
> carryied EM with Strong POStion REStraint, the protien and membrane were 
> apart. Please help me!

What does "apart" mean?  If you want free help, you have to make it easy to 
help you.  That means thorough descriptions of what you're doing, what you're 
seeing, and if necessary, posting images online (not as attachments!) for us to 
take a look.  The InflateGRO method should generate a configuration that has 
molecules separated by a large amount of space, but if there is something else 
wrong you'll have to provide a better description.

-Justin

> 4 
> 
> 
> 
>  

-- 

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] construct CG membrane protein and CG membrane and inflategro.pl

[xi zhao]

protein and membranr separate ,



--- 10年4月12日，周一, Justin A. Lemkul  写道：


发件人: Justin A. Lemkul 
主题: Re: [gmx-users] construct CG membrane protein and CG membrane and 
inflategro.pl
收件人: "Discussion list for GROMACS users" 
日期: 2010年4月12日,周一,下午8:42




xi zhao wrote:
> 
> 
> Dear Gromacs users:
> I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when 
> carryied EM with Strong POStion REStraint, the protien and membrane were 
> apart. Please help me!

What does "apart" mean?  If you want free help, you have to make it easy to 
help you.  That means thorough descriptions of what you're doing, what you're 
seeing, and if necessary, posting images online (not as attachments!) for us to 
take a look.  The InflateGRO method should generate a configuration that has 
molecules separated by a large amount of space, but if there is something else 
wrong you'll have to provide a better description.

-Justin

> 4 
> 
> 
> 
>  

-- 

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] construct CG membrane protein and CG membrane and inflategro.pl

[Mark Abraham]

On 12/04/2010 10:37 PM, xi zhao wrote:



Dear Gromacs users:
I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but
when carryied EM with Strong POStion REStraint, the protien and membrane
were apart. Please help me!


Either you put them apart, or you're seeing a periodicity artefact. See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


Mark
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Re: [gmx-users] construct CG membrane protein and CG membrane and inflategro.pl

[Justin A. Lemkul]

xi zhao wrote:



Dear Gromacs users:
I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but 
when carryied EM with Strong POStion REStraint, the protien and membrane 
were apart. Please help me!


What does "apart" mean?  If you want free help, you have to make it easy to help 
you.  That means thorough descriptions of what you're doing, what you're seeing, 
and if necessary, posting images online (not as attachments!) for us to take a 
look.  The InflateGRO method should generate a configuration that has molecules 
separated by a large amount of space, but if there is something else wrong 
you'll have to provide a better description.


-Justin

4 




 



--


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] construct CG membrane protein and CG membrane and inflategro.pl

[xi zhao]

Dear Gromacs users:
I use inflateGRO.pl to insert CG protein in to CG POPC membrane, but when 
carryied EM with Strong POStion REStraint, the protien and membrane were apart. 
Please help me!



  -- 
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Re: [gmx-users] install problem of ngmx

[Justin A. Lemkul]

kecy...@sina.com wrote:



the version of the gcc is 4.1.1.


Get a better version of gcc.  Note the prominent warning on the Downloads page:

http://www.gromacs.org/index.php?title=Download_%26_Installation

-Justin



Thank you!



--


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] install problem of ngmx

[Justin A. Lemkul]

kecy...@sina.com wrote:
Hello,  my configure line is ./configure --without-X  --enable-mpi 
--enable-fortran --prefix=/mnt/soft/chemtec/gromacs4.0.5. I have been 
setted  in the ~/.bashrc like this :


 


--without-X and --without-x are different things.  Computers are literal.  Watch 
the output of ./configure to see if it complains about not finding X headers and 
libraries instead of simply saying "disabled" (which you should get if you 
./configure --without-x).


-Justin



/export PATH=/opt/mpich2wgs/bin:$PATH:/share/apps/intel/fce/10.1.022/bin/

/export CC=gcc
export CXX=g++
export CFLAGS="-03
xport CXXFLAGS="-03 "
export FFLAGS="-03 "/

/export CPPFLAGS=-I/mnt/soft/chemtec/fftw3.2.1/include
export LDFLAGS=-L/ mnt/soft/chemtec/fftw3.2.1/lib/

/export F77=ifort/

/export LD_LIBRARY_PATH=/opt/mpich2wgs/lib/:$LD_LIBRARY_PATH/

the version of the gcc is 4.1.1.

Thank you!



--


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] Lateral pressure profile in membrane simulations

[XAvier Periole]

You have to rerun the trajectory ... not frame by frame!

Notes:
- that there is issue on pressure tensor calculation when constrains are
used
- simulations need to be quite long to get a reasonable convergence.

On Apr 12, 2010, at 2:41 AM, George Khelashvili wrote:


Dear users,

I am attempting to perform 3D pressure tensor calculation on well- 
converged all-atom lipid bilayer. I am using modified gromacs and - 
rerun option and analyze the output with the tools that is provided  
on Martini website. I had following question: I have a production  
trajectory from original MD calculations, and I also have separate  
snapshots saved once in 100ps. As I understand, for pressure  
calculations I need to use -rerun on separate snapshots. Is this the  
case? If so, I would get as an output bunch of local_pressure.dat  
files. How do I analyze them? One by one? I would greatly appreciate  
if somebody can describe the sequence of events that I need to go  
through in order to obtain pressure profiles.


Thank you for you assistance,

Sincerely,
George

--
George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
e-mail: gek2...@med.cornell.edu
phone:  1-212-746-6539
fax:1-212-746-6226


Martti Louhivuori wrote:

On 8 Apr 2010, at 00:45, Fernando E. Herrera wrote:
I am doing some molecular dynamics simulations of membrane systems  
and i would like to ask you if someone know or have a code for the  
calculation of the lateral pressure profile  from the data  
obtained doing  membrane simulations.


You can find everything you need from here:
http://www.cgmartini.nl/index.php/tools/114-3d-pf

It is a custom version of Gromacs that calculates a 3D pressure  
field using the -rerun option of mdrun, as explained in Ollila et  
al. (2009) PhysRevLett 102: 078101. Before you do the rerun, you  
need to redo grompp with 'userreal1' set to the desired grid size.  
The analysis tools there can then be used to calculate e.g. a  
lateral pressure profile... Note that constraints are a bit  
problematic, though, so if your lipids have constraints, the  
profile may not be accurate.


Best regards,
-martti-
--
Post-doctoral research fellow
Moleculaire Dynamica
University of Groningen
Nijenborgh 4, 9747AG Groningen, the Netherlands
tel. +(31) 50 363 4339 | fax. +(31) 50 363 4398




--
George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
e-mail: gek2...@med.cornell.edu
phone:  1-212-746-6539
fax:1-212-746-6226

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[gmx-users] install problem of ngmx

[kecy_wu]

Hello,  my configure line is ./configure --without-X  
--enable-mpi --enable-fortran --prefix=/mnt/soft/chemtec/gromacs4.0.5. I have 
been setted  in the ~/.bashrc like this :
 
export PATH=/opt/mpich2wgs/bin:$PATH:/share/apps/intel/fce/10.1.022/bin
export CC=gcc
export CXX=g++
export CFLAGS="-03
xport CXXFLAGS="-03 "
export FFLAGS="-03 "
export CPPFLAGS=-I/mnt/soft/chemtec/fftw3.2.1/include 
export LDFLAGS=-L/ mnt/soft/chemtec/fftw3.2.1/lib
export F77=ifort
export LD_LIBRARY_PATH=/opt/mpich2wgs/lib/:$LD_LIBRARY_PATH
the version of the gcc is 4.1.1.
Thank you!-- 
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