[gmx-users] mpi run

2010-07-08 Thread nanogroup
Dear GMX Users,

I have a PC with 4 CPU, but the Gromacs only use one CPU.

the command of mpiru works on linux; however, the command of mdrun_mpi does not 
work.

Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4

Many thanks,
Mahmoud




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Re: [gmx-users] mpi run

2010-07-08 Thread Carsten Kutzner
Hi Mahmoud,

for anyone to be able to help you, you need to provide
a lot more information, at least:
- which mpi library are you using?
- how did you compile and/or install Gromacs?
- what commands do you use to run mdrun and what was
the output of it?

Best,
  Carsten


On Jul 8, 2010, at 9:41 AM, nanogroup wrote:

 Dear GMX Users,
 
 I have a PC with 4 CPU, but the Gromacs only use one CPU.
 
 the command of mpiru works on linux; however, the command of mdrun_mpi does 
 not work.
 
 Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4
 
 Many thanks,
 Mahmoud
 
 
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Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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Re: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96

2010-07-08 Thread C. Batistakis
Dear Mark

Many thanks

Chrysostomos

--- Στις Πέμ., 08/07/10, ο/η Mark Abraham mark.abra...@anu.edu.au έγραψε:

Από: Mark Abraham mark.abra...@anu.edu.au
Θέμα: Re: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96
Προς: Discussion list for GROMACS users gmx-users@gromacs.org
Ημερομηνία: Πέμπτη, 8 Ιούλιος 2010, 4:49



- Original Message -
From: C. Batistakis cbat...@yahoo.gr
Date: Wednesday, July 7, 2010 23:19
Subject: [gmx-users] Nitrile_Butadiene_Rubber simulation using Gromos96
To: gromacs gmx-users@gromacs.org

   Dear all      I am trying to simulate Nitrile-Butadiene-Rubber, using the 
Gromos96 force field. 

Let the availability of suitable parameters choose the force field :-)

   I have difficulties in finding the correct parameters from the bon.itp file 
, in order to define the polymer in the .rtp file.
A first port of call would have been the appropriate paper for the force field 
- which might have made clear whether or not nitrile parameters were likely to 
be found.
      Can someone suggest which parameters I shall choose in the following:  
In Bond-stretching parameters      For:  1)  Triple bond between Carbon and 
Nitrogen   (gb_)  2)  Double bond  CH=CH (gb_)     In 
Bond-angle bending parameters      For:  1)  CH2-CH=CH (ga_)  
2)  CH-C≡N         (ga_)     In Dihedral-angle type code     For:  
1)  CH2-CH=CH-CH2 (gd_)  2)  CH2-CH-C≡N  (gd_)     
 If these parameters do not exist in this force field, can you suggest me 
another one to use?
As a first step, try grep nitrile *.atp to see which of the atom type 
databases have nitrile in them. AMBER forcefields are probably also OK, but 
you'll have to install them seperately.

Mark

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Re: [gmx-users] problems with g_wham

2010-07-08 Thread Gavin Melaugh
Thanks Chris and Justin

I do get the output I want from grompp(below). The distance of 5.507 nm
is the distance that I want to start with and I assume it is therefore
the equilibrium distance for the harmonic potential. The COM distances
from the simulations fluctuate around this value which is what I want,
although my histogram is the wrong shape.

Pull group  natoms  pbc atom  distance at start reference at t=0
   0   8442
   1   84   126  
5.507 5.507

Cheers

Gavin

chris.ne...@utoronto.ca wrote:
 I missed that pull_start = yes, sorry. So Gavin, your run should have
 stayed around the starting position. Make the histogram directly and
 you should get a better idea.

 Chris.

 -- original message --


 To clarify, the tutorial sets pull_init1 = 0 because it is used in
 conjunction
 with pull_start = yes, in order to take the starting COM distance as
 the
 reference.  Check the grompp output to verify that you're getting what
 you think
 you should be.  Otherwise, you'd have to set pull_start = no and
 modify your
 .mdp file to reflect the proper value of pull_init1 for every window.

 -Justin





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RE: [gmx-users] mpi run

2010-07-08 Thread #ZHAO LINA#
During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi 
will work.
I suggest you to check the nodes of the cluster, probably try pbsnodes, on a 
master node no job may be run.
Note that I do not know much about your information, so the (guessing) 
suggestion maybe not fit for your problems, just cause I once confused about 
why mine 4cpus barely used before too.

Best,

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Carsten Kutzner [ckut...@gwdg.de]
Sent: Thursday, July 08, 2010 4:04 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mpi run

Hi Mahmoud,

for anyone to be able to help you, you need to provide
a lot more information, at least:
- which mpi library are you using?
- how did you compile and/or install Gromacs?
- what commands do you use to run mdrun and what was
the output of it?

Best,
  Carsten


On Jul 8, 2010, at 9:41 AM, nanogroup wrote:

Dear GMX Users,

I have a PC with 4 CPU, but the Gromacs only use one CPU.

the command of mpiru works on linux; however, the command of mdrun_mpi does not 
work.

Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4

Many thanks,
Mahmoud



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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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Re: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory

2010-07-08 Thread Carsten Kutzner
Hi,

you can check with

ldd mdrun_mpi

whether really all needed libraries were found. Is libimf.so in 
/opt/intel/fc/10.1.008/lib ? The intel compilers also come with
files called iccvars.sh or ictvars.sh. If you do

source /path/to/iccvars.sh

everything should be set as needed. Check the Intel Compiler
documentation.

Carsten


On Jul 8, 2010, at 10:52 AM, zhongjin wrote:

 Dear users,
   When I am using GROMACS 4.0.7 on the Compute node ,executing command:
 mpiexec -n 4  mdrun_mpi -deffnm SWNT66nvt /dev/null 
 and then met a problem :mdrun_mpi: error while loading shared libraries: 
 libimf.so: cannot open shared object file: No such file or directory
 but I have added export LD_LIBRARY_PATH=/opt/intel/fc/10.1.008/lib
 in the .bash_profile, the libimf.so is in this directory.
 However,when  executing command:mdrun -deffnm SWNT66nvt ,it's OK ! Anybody 
 could help me? Thanks a lot!
 Zhongjin He
 
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Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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Re: [gmx-users] mdrun_mpi: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory

2010-07-08 Thread Mark Abraham


- Original Message -
From: zhongjin zhongjin1...@yahoo.com.cn
Date: Thursday, July 8, 2010 18:53
Subject: [gmx-users] mdrun_mpi: error while loading shared libraries: 
libimf.so: cannot open shared object file: No such file or directory
To: gmx-users@gromacs.org

---
|  Dear users,
   When I am using GROMACS 4.0.7 on the Compute node ,executing command:  
 mpiexec -n 4  mdrun_mpi -deffnm SWNT66nvt /dev/null 
 and then met a problem :mdrun_mpi: error while loading shared libraries: 
 libimf.so: cannot open shared object file: No such file or directory
 but I have added export LD_LIBRARY_PATH=/opt/intel/fc/10.1.008/lib
 in the .bash_profile, the libimf.so is in this directory.  However,when  
 executing command:mdrun -deffnm SWNT66nvt ,it's OK ! Anybody could help me? 
 Thanks a lot!

Looks like the either MPI compiler is doing things differently from the normal 
compiler, or your execution environment does not have access to that /opt path, 
or even the environment variable. Consider also the use of LD_RUN_PATH - see 
compiler docs. It also might help to use gcc as the underlying compiler for 
mpicc - it's about the same as Intel - but that depends on what the underlying 
problem is.

Mark
 |
---

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Re: RE: [gmx-users] mpi run

2010-07-08 Thread Mark Abraham


- Original Message -
From: #ZHAO LINA# zhao0...@e.ntu.edu.sg
Date: Thursday, July 8, 2010 18:53
Subject: RE: [gmx-users] mpi run
To: Discussion list for GROMACS users gmx-users@gromacs.org


   P {margin-top:0;margin-bottom:0;} 
---
| 

 
  During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi 
  will work.

--program-suffix merely appends that suffix. --enable-mpi is necessary to 
actually create MPI-enable mdrun. It is normal to use both of them together.

Mark

  I suggest you to check the nodes of the cluster, probably try pbsnodes, on a 
 master node no job may be run. 
  Note that I do not know much about your information, so the (guessing) 
 suggestion maybe not fit for your problems, just cause I once confused about 
 why mine 4cpus barely used before too.
  
  Best,
  
  lina
   ---
  From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on 
  behalf of Carsten Kutzner [ckut...@gwdg.de]
  Sent: Thursday, July 08, 2010 4:04 PM
  To: Discussion list for GROMACS users
  Subject: Re: [gmx-users] mpi run
  
Hi Mahmoud, 
   for anyone to be able to help you, you need to provide  a lot more 
information, at least:  - which mpi library are you using?  - how did you 
compile and/or install Gromacs?  - what commands do you use to run mdrun and 
what was  the output of it?  
   Best,Carsten  
   
   On Jul 8, 2010, at 9:41 AM, nanogroup wrote:
---
   |   Dear GMX Users,
  
  I have a PC with 4 CPU, but the Gromacs only use one CPU.
  
  the command of mpiru works on linux; however, the command of mdrun_mpi does 
 not work.
  
  Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4
  
  Many thanks,
  Mahmoud
  
  | 
  ---
  
  -- 
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  http://lists.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at http://www.gromacs.org/search before posting!
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  --  Dr. Carsten Kutzner  Max Planck Institute for Biophysical 
Chemistry  Theoretical and Computational Biophysics  Am Fassberg 11, 37077 
Goettingen, Germany  Tel. +49-551-2012313, Fax: +49-551-2012302  
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne  
 
  |
---
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Re: [gmx-users] Compiling problems on MacOS X 10.6.4

2010-07-08 Thread J. Rui Rodrigues
Hi,

Please post the output of the following commands: 
nm -arch i386 /opt/local/lib/libxml2.a | head 
nm -arch x86_64 /opt/local/lib/libxml2.a | head 

and in the directory where you typed make: 
file src/*/*.o | head 



Rui Rodrigues 

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Re: [gmx-users] problems with g_wham

2010-07-08 Thread Justin A. Lemkul


Have you watched the trajectory?  That will show you what your pull group is 
doing.  Is this a periodicity effect?  It should be fairly obvious iff the sign 
of dX, etc flip-flops in the pullx.xvg file.


-Justin

Gavin Melaugh wrote:

Thanks Chris and Justin

I do get the output I want from grompp(below). The distance of 5.507 nm
is the distance that I want to start with and I assume it is therefore
the equilibrium distance for the harmonic potential. The COM distances
from the simulations fluctuate around this value which is what I want,
although my histogram is the wrong shape.

Pull group  natoms  pbc atom  distance at start reference at t=0
   0   8442
   1   84   126  
5.507 5.507


Cheers

Gavin

chris.ne...@utoronto.ca wrote:

I missed that pull_start = yes, sorry. So Gavin, your run should have
stayed around the starting position. Make the histogram directly and
you should get a better idea.

Chris.

-- original message --


To clarify, the tutorial sets pull_init1 = 0 because it is used in
conjunction
with pull_start = yes, in order to take the starting COM distance as
the
reference.  Check the grompp output to verify that you're getting what
you think
you should be.  Otherwise, you'd have to set pull_start = no and
modify your
.mdp file to reflect the proper value of pull_init1 for every window.

-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] question about non-bonded parameters for CHARMM in GROMACS

2010-07-08 Thread Michael Francis Hagan
Dear All,

 

I am confused about the proper choice of non-bonded parameters for
simulating the CHARMM force field  in GROMACS. With other packages I use
VDW-switch and PME with both VDW and the direct space coulomb cut-off at
1.2 and a neighbor-list cut-off of 1.4.  The requirement in GROMACS that
rlist=rcoulomb seems to make that parameter set impossible (unless one
uses PME-switch, which is recommended against in the manual and not
consistent with the original force field parameterization). I have seen a
suggestion to use rvdw=rcoulomb=rlist=1.2, but grompp complains unless
rlistrvdw under VDW-switch. That seems like a reasonable complaint, but I
am  new to GROMACS and wonder if I'm missing something.  What is the
recommended set of non-bonded parameters?

 

Thanks in advance,

Mike Hagan

 

-

Physics Department

Brandeis University 

http://www.brandeis.edu/departments/physics/hagan/index.html

-

 

 

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Re: [gmx-users] problems with g_wham

2010-07-08 Thread Gavin Melaugh
Hi Justin

I am not using periodic boundary conditions for the simulations. I may
have sorted it out now. I was generating velocities in the umbrella.mdp
file, I have since set gen_vel = no, and the histogram has the correct
shape (should this make a difference?)

Cheers

Gavin

Justin A. Lemkul wrote:

 Have you watched the trajectory?  That will show you what your pull
 group is doing.  Is this a periodicity effect?  It should be fairly
 obvious iff the sign of dX, etc flip-flops in the pullx.xvg file.

 -Justin

 Gavin Melaugh wrote:
 Thanks Chris and Justin

 I do get the output I want from grompp(below). The distance of 5.507 nm
 is the distance that I want to start with and I assume it is therefore
 the equilibrium distance for the harmonic potential. The COM distances
 from the simulations fluctuate around this value which is what I want,
 although my histogram is the wrong shape.

 Pull group  natoms  pbc atom  distance at start reference at t=0
0   8442
1   84   126 
 5.507 5.507

 Cheers

 Gavin

 chris.ne...@utoronto.ca wrote:
 I missed that pull_start = yes, sorry. So Gavin, your run should have
 stayed around the starting position. Make the histogram directly and
 you should get a better idea.

 Chris.

 -- original message --


 To clarify, the tutorial sets pull_init1 = 0 because it is used in
 conjunction
 with pull_start = yes, in order to take the starting COM distance as
 the
 reference.  Check the grompp output to verify that you're getting what
 you think
 you should be.  Otherwise, you'd have to set pull_start = no and
 modify your
 .mdp file to reflect the proper value of pull_init1 for every window.

 -Justin







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Re: [gmx-users] problems with g_wham

2010-07-08 Thread Justin A. Lemkul



Gavin Melaugh wrote:

Hi Justin

I am not using periodic boundary conditions for the simulations. I may
have sorted it out now. I was generating velocities in the umbrella.mdp
file, I have since set gen_vel = no, and the histogram has the correct
shape (should this make a difference?)



If you generate velocities without doing equilibration, then your system may not 
be at equilibrium and thus you are doing inaccurate sampling.  Thus, if your 
system gets kicked in the wrong direction, the umbrella potential may have to 
fight to pull the desired group back to where it thinks it should be, might be 
overcompensating, etc.


-Justin


Cheers

Gavin

Justin A. Lemkul wrote:

Have you watched the trajectory?  That will show you what your pull
group is doing.  Is this a periodicity effect?  It should be fairly
obvious iff the sign of dX, etc flip-flops in the pullx.xvg file.

-Justin

Gavin Melaugh wrote:

Thanks Chris and Justin

I do get the output I want from grompp(below). The distance of 5.507 nm
is the distance that I want to start with and I assume it is therefore
the equilibrium distance for the harmonic potential. The COM distances
from the simulations fluctuate around this value which is what I want,
although my histogram is the wrong shape.

Pull group  natoms  pbc atom  distance at start reference at t=0
   0   8442
   1   84   126 
5.507 5.507


Cheers

Gavin

chris.ne...@utoronto.ca wrote:

I missed that pull_start = yes, sorry. So Gavin, your run should have
stayed around the starting position. Make the histogram directly and
you should get a better idea.

Chris.

-- original message --


To clarify, the tutorial sets pull_init1 = 0 because it is used in
conjunction
with pull_start = yes, in order to take the starting COM distance as
the
reference.  Check the grompp output to verify that you're getting what
you think
you should be.  Otherwise, you'd have to set pull_start = no and
modify your
.mdp file to reflect the proper value of pull_init1 for every window.

-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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Re: [gmx-users] problems with g_wham

2010-07-08 Thread Gavin Melaugh
Many thanks

Justin A. Lemkul wrote:


 Gavin Melaugh wrote:
 Hi Justin

 I am not using periodic boundary conditions for the simulations. I may
 have sorted it out now. I was generating velocities in the umbrella.mdp
 file, I have since set gen_vel = no, and the histogram has the correct
 shape (should this make a difference?)


 If you generate velocities without doing equilibration, then your
 system may not be at equilibrium and thus you are doing inaccurate
 sampling.  Thus, if your system gets kicked in the wrong direction,
 the umbrella potential may have to fight to pull the desired group
 back to where it thinks it should be, might be overcompensating, etc.

 -Justin

 Cheers

 Gavin

 Justin A. Lemkul wrote:
 Have you watched the trajectory?  That will show you what your pull
 group is doing.  Is this a periodicity effect?  It should be fairly
 obvious iff the sign of dX, etc flip-flops in the pullx.xvg file.

 -Justin

 Gavin Melaugh wrote:
 Thanks Chris and Justin

 I do get the output I want from grompp(below). The distance of
 5.507 nm
 is the distance that I want to start with and I assume it is therefore
 the equilibrium distance for the harmonic potential. The COM distances
 from the simulations fluctuate around this value which is what I want,
 although my histogram is the wrong shape.

 Pull group  natoms  pbc atom  distance at start reference at t=0
0   8442
1   84   126
 5.507 5.507

 Cheers

 Gavin

 chris.ne...@utoronto.ca wrote:
 I missed that pull_start = yes, sorry. So Gavin, your run should have
 stayed around the starting position. Make the histogram directly and
 you should get a better idea.

 Chris.

 -- original message --


 To clarify, the tutorial sets pull_init1 = 0 because it is used in
 conjunction
 with pull_start = yes, in order to take the starting COM
 distance as
 the
 reference.  Check the grompp output to verify that you're getting
 what
 you think
 you should be.  Otherwise, you'd have to set pull_start = no and
 modify your
 .mdp file to reflect the proper value of pull_init1 for every window.

 -Justin








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RE: [gmx-users] Compiling problems on MacOS X 10.6.4

2010-07-08 Thread Patargias, George
Thanks for your reply. The output from nm -arch i386 /opt/local/lib/libxml2.a | 
head is

nm: file: /opt/local/lib/libxml2.a does not contain architecture: i386

and from nm -arch x86_64 /opt/local/lib/libxml2.a | head

/opt/local/lib/libxml2.a(SAX.o):
3050 s EH_frame1
02a0 T _initdocbDefaultSAXHandler
30c8 S _initdocbDefaultSAXHandler.eh
0160 T _inithtmlDefaultSAXHandler
3098 S _inithtmlDefaultSAXHandler.eh
 T _initxmlDefaultSAXHandler
3068 S _initxmlDefaultSAXHandler.eh
 U _xmlParserError

Best wishes
George



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt]
Sent: Thursday, July 08, 2010 5:57 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Compiling problems on MacOS X 10.6.4

Hi,

Please post the output of the following commands:
nm -arch i386 /opt/local/lib/libxml2.a | head
nm -arch x86_64 /opt/local/lib/libxml2.a | head

and in the directory where you typed make:
file src/*/*.o | head



Rui Rodrigues

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[gmx-users] problems with g_wham

2010-07-08 Thread chris . neale
Depending on your system and chosen thermostat, gen-vel=no can be a  
dangerous idea (very small original velocities simply get scaled up);  
besides, you should be able to equilibrate from a gen-vel=yes pretty  
quickly. I don't disagree with Justin's comment, but just because it  
works doesn't mean its what you should do. I'd stick to an established  
procedure.


Chris.

-- original mesage --

Hi Justin

I am not using periodic boundary conditions for the simulations. I may
have sorted it out now. I was generating velocities in the umbrella.mdp
file, I have since set gen_vel = no, and the histogram has the correct
shape (should this make a difference?)

Cheers

Gavin


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Re: [gmx-users] problems with g_wham

2010-07-08 Thread Gavin Melaugh
O.K cheers Chris. I do intend to equilibrate the system at the desired
temperature before constructing the histogram.
chris.ne...@utoronto.ca wrote:
 Depending on your system and chosen thermostat, gen-vel=no can be a
 dangerous idea (very small original velocities simply get scaled up);
 besides, you should be able to equilibrate from a gen-vel=yes pretty
 quickly. I don't disagree with Justin's comment, but just because it
 works doesn't mean its what you should do. I'd stick to an established
 procedure.

 Chris.

 -- original mesage --

 Hi Justin

 I am not using periodic boundary conditions for the simulations. I may
 have sorted it out now. I was generating velocities in the umbrella.mdp
 file, I have since set gen_vel = no, and the histogram has the correct
 shape (should this make a difference?)

 Cheers

 Gavin



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RE: [gmx-users] Compiling problems on MacOS X 10.6.4

2010-07-08 Thread Patargias, George
Sorry, I forgot to post the output of file src/*/*.o | head 

src/gmxlib/3dview.o:  Mach-O object i386
src/gmxlib/atomprop.o:Mach-O object i386
src/gmxlib/bondfree.o:Mach-O object i386
src/gmxlib/calcgrid.o:Mach-O object i386
src/gmxlib/calch.o:   Mach-O object i386
src/gmxlib/chargegroup.o: Mach-O object i386
src/gmxlib/checkpoint.o:  Mach-O object i386
src/gmxlib/cinvsqrtdata.o:Mach-O object i386
src/gmxlib/confio.o:  Mach-O object i386
src/gmxlib/copyrite.o:Mach-O object i386



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt]
Sent: Thursday, July 08, 2010 5:57 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Compiling problems on MacOS X 10.6.4

Hi,

Please post the output of the following commands:
nm -arch i386 /opt/local/lib/libxml2.a | head
nm -arch x86_64 /opt/local/lib/libxml2.a | head

and in the directory where you typed make:
file src/*/*.o | head



Rui Rodrigues

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[gmx-users] Location of a molecule in a dodecahedron

2010-07-08 Thread Birgit Hischenhuber
Hi,

 

I simulate a molecule in a dodecahedron.

I used at the step with the editconf:

 

editconf -f name.gro -o name.dod.pdb -bt dodecahedron -d 2.0

 

After my simulation I looked at the first frame and saw, that at two
direction the molecule is actually 2 nm away of my edge, but the at the
third edge the molecule is not in the middle, but near the edge.

I looked also at the other pdb-files with the water before the simulation,
and there the location of the molecule is the same, in my opinion not in the
middle of the body.

 

Is this a bug? Or have I done anything wrong?

 

Thanks a lot for your helps!

 

Greets, Birgit

 

---

 

DI Birgit Hischenhuber

Unit for Medical Statistics and Informatics 

Section for Biomedical Computersimulation and Bioinformatics

Medical University of Vienna

General Hospital

Spitalgasse 23, BT88

A-1090 Vienna

 

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Re: [gmx-users] Location of a molecule in a dodecahedron

2010-07-08 Thread Justin A. Lemkul



Birgit Hischenhuber wrote:

Hi,

 


I simulate a molecule in a dodecahedron.

I used at the step with the editconf:

 


editconf -f name.gro -o name.dod.pdb -bt dodecahedron -d 2.0

 

After my simulation I looked at the first frame and saw, that at two 
direction the molecule is actually 2 nm away of my edge, but the at the 
third edge the molecule is not in the middle, but near the edge.


I looked also at the other pdb-files with the water before the 
simulation, and there the location of the molecule is the same, in my 
opinion not in the middle of the body.


 


Is this a bug? Or have I done anything wrong?

 


There is no bug.  The representation is simply a triclinic cell, and probably 
periodicity effects.  For visualization purposes only, you can correct the 
representation with trjconv -pbc mol -ur compact.


-Justin



Thanks a lot for your helps!

 


Greets, Birgit

 


---

 


DI Birgit Hischenhuber

Unit for Medical Statistics and Informatics

Section for Biomedical Computersimulation and Bioinformatics

Medical University of Vienna

General Hospital

Spitalgasse 23, BT88

A-1090 Vienna

 



--


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] Compiling problems on MacOS X 10.6.4

2010-07-08 Thread J. Rui Rodrigues
Hi,

Looks like auto-detection for 64bit support on macs is not working with your 
machine.
I had a similar problem some time ago on a Mac 10.5.8:
http://lists.gromacs.org/pipermail/gmx-users/2010-April/050501.html

As a workaround, you could pass the following flags to configure to see if it 
cures your problem:
CFLAGS=-m64 -std=gnu99 -O3

Hope this helps,
Rui Rodrigues




On Thu, 8 Jul 2010 10:14:16 -0400, Patargias, George wrote
 Sorry, I forgot to post the output of file src/*/*.o | head
 
 src/gmxlib/3dview.o:  Mach-O object i386
 src/gmxlib/atomprop.o:Mach-O object i386
 src/gmxlib/bondfree.o:Mach-O object i386
 src/gmxlib/calcgrid.o:Mach-O object i386
 src/gmxlib/calch.o:   Mach-O object i386
 src/gmxlib/chargegroup.o: Mach-O object i386
 src/gmxlib/checkpoint.o:  Mach-O object i386
 src/gmxlib/cinvsqrtdata.o:Mach-O object i386
 src/gmxlib/confio.o:  Mach-O object i386
 src/gmxlib/copyrite.o:Mach-O object i386
 
 
 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
 Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt] Sent: Thursday, July 
 08, 2010 5:57 AM To: Discussion list for GROMACS users Subject: Re: [gmx-
 users] Compiling problems on MacOS X 10.6.4
 
 Hi,
 
 Please post the output of the following commands:
 nm -arch i386 /opt/local/lib/libxml2.a | head
 nm -arch x86_64 /opt/local/lib/libxml2.a | head
 
 and in the directory where you typed make:
 file src/*/*.o | head
 
 Rui Rodrigues
 
 --
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 Please search the archive at http://www.gromacs.org/search before posting!
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 www interface or send it to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] P4_error for extending coarse grained MD simulations

2010-07-08 Thread 张春雷
Dear all,

I have post this question about a two weeks ago. During these days, I
followed suggestions from Mark and weixin, but did not fix it. Here, I
repeat it again to seek more help.

I attempt to extend MD simulation for a coarse-grained system. CG models are
in MARTINI form. Simulation was carried out on Gromacs 4.02, 4.03 or 4.07.

I tried to use check point file state.cpt to extend my simulation. The mdrun
program can read to the check file. But it reported error like this:

Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010

Loaded with Money

starting mdrun 'Protein in POPE bilayer'
2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps).
step 1200, remaining runtime: 0 s
p0_6991:  p4_error: interrupt SIGSEGV: 11

I check the *state.cpt* file using *gmxdump* and compare it with other
checkpoint files that can be used for extending All-atom simulations. I
found that in the CG check point file, some sections are missing: *box-v
(3x3)* and *thermostat-integral*.
I am not sure whether this missing sections cause my run crash. If it is,
could any one tell me possible reasons that result in the loss of box-v and
thermostat-integral and how to fix the problem?

Your suggestions are greatly helpful and appreciated.

Justin Zhang



在 2010年6月25日 下午4:45,张春雷 chunleizhang@gmail.com写道:

 Information shown by gmxcheck:

 *Checking file state.cpt*

 # Atoms  9817
 Last frame -1 time 36.000


 Item#frames Timestep (ps)
 Step 1
 Time 1
 Lambda   1
 Coords   1
 Velocities   1
 Forces   0
 Box  1

 *Checking file state_prev.cpt*

 # Atoms  9817
 Last frame -1 time 359010.000


 Item#frames Timestep (ps)
 Step 1
 Time 1
 Lambda   1
 Coords   1
 Velocities   1
 Forces   0
 Box  1

 *Checking file md_360ns.trr*
 trn version: GMX_trn_file (double precision)
 Reading frame   0 time0.000
 # Atoms  9817
 Reading frame2000 time 30.000


 Item#frames Timestep (ps)
 Step  2401150
 Time  2401150
 Lambda2401150
 Coords2401150
 Velocities2401150
 Forces   0
 Box   2401150

 Is anything wrong?


 2010/6/25 Mark Abraham mark.abra...@anu.edu.au



 - Original Message -
 From: 张春雷 chunleizhang@gmail.com
 Date: Friday, June 25, 2010 16:46
 Subject: Re: [gmx-users] P4_error for extending coarse grained MD
 simulations
 To: Discussion list for GROMACS users gmx-users@gromacs.org

  The last .gro file only provides coordinates of the system. No velocity
 is recorded. Actually, what I attempt to achieve is a binary identical
 trajectory. So I think the velocity from the last step is critical.
 
  I have tried another approach in which the checkpoint file is
 neglected.
 
  $mdrun_mpi_d -s md_720ns.tpr  -e md_720ns.edr -o md_720ns.trr -g
 md_720ns.log
 
  It works. So the checkpoint file appears to contain some error. But it
 is generated by a normally finished production simulation.

 What does gmxcheck say about all the files involved?

 Mark


  Have  you encountered similar things?
 
  Thank you for your suggestions!
 
 
 
  在 2010年6月25日 上午9:16,weixin xwx...@gmail.com写道:

 
  How about using the last .gro file to continue your simulation?
 
 
 
  2010/6/24 张春雷 chunleizhang@gmail.com

  Dear GMX-users,
 
  This is Justin.
  I am performing coarse-grained simulation on a protein-lipid bilayer
 system. This is a MARTINI CG model.
  I have successfully completed a 360ns simulation, during which the
 time step is 30 fs.
 
  I would like to extend the simulation to 1micro-second. The commands
 I used are:
 
  $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr
 
  $mdrun_mpi_d -s md_720ns.tpr  -append -e md_360ns.edr -o md_360ns.trr
 -g md_360ns.log -cpi state.cpt
 
  However, I received the following message:
 
  Checkpoint file is from part 1, new output files will be suffixed
 part0002.
  Getting Loaded...
  Reading file md_720ns.tpr, VERSION 4.0.3 (double precision)
 
  Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010
 
  Loaded with Money
 
  starting mdrun 'Protein in POPE bilayer'
  2400 steps, 72.0 ps (continuing from step 1200, 36.0
 ps).
  step 1200, remaining runtime: 0 s
  p0_6991:  p4_error: interrupt SIGSEGV: 11
 
  I have searched the mail-list, but found no similar report. I also
 search through google, but no answer seems satisfactory.
 
  I once performed extending simulation for all atom simulation, and
 the method mentioned above worked.
 
  Is anyone familiar with MARTINI CG simulation?
  Could you give me some suggestions?
 
  Many thanks!
 
  Justin
 
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RE: [gmx-users] Compiling problems on MacOS X 10.6.4

2010-07-08 Thread Patargias, George
Yes, it did work. 
Thanks a lot!

George

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf 
Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt]
Sent: Thursday, July 08, 2010 12:32 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Compiling problems on MacOS X 10.6.4

Hi,

Looks like auto-detection for 64bit support on macs is not working with your 
machine.
I had a similar problem some time ago on a Mac 10.5.8:
http://lists.gromacs.org/pipermail/gmx-users/2010-April/050501.html

As a workaround, you could pass the following flags to configure to see if it 
cures your problem:
CFLAGS=-m64 -std=gnu99 -O3

Hope this helps,
Rui Rodrigues




On Thu, 8 Jul 2010 10:14:16 -0400, Patargias, George wrote
 Sorry, I forgot to post the output of file src/*/*.o | head

 src/gmxlib/3dview.o:  Mach-O object i386
 src/gmxlib/atomprop.o:Mach-O object i386
 src/gmxlib/bondfree.o:Mach-O object i386
 src/gmxlib/calcgrid.o:Mach-O object i386
 src/gmxlib/calch.o:   Mach-O object i386
 src/gmxlib/chargegroup.o: Mach-O object i386
 src/gmxlib/checkpoint.o:  Mach-O object i386
 src/gmxlib/cinvsqrtdata.o:Mach-O object i386
 src/gmxlib/confio.o:  Mach-O object i386
 src/gmxlib/copyrite.o:Mach-O object i386

 
 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
 Of J. Rui Rodrigues [joaquim.rodrig...@estg.ipleiria.pt] Sent: Thursday, July
 08, 2010 5:57 AM To: Discussion list for GROMACS users Subject: Re: [gmx-
 users] Compiling problems on MacOS X 10.6.4

 Hi,

 Please post the output of the following commands:
 nm -arch i386 /opt/local/lib/libxml2.a | head
 nm -arch x86_64 /opt/local/lib/libxml2.a | head

 and in the directory where you typed make:
 file src/*/*.o | head

 Rui Rodrigues

 --
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[gmx-users] genbox and water model

2010-07-08 Thread Sai Pooja
Hi,

I am using CHARMM forcefield with the tip3p. What input file(-cs) should i
use to solvate the protein using the genbox command? The default is
spc216.gro. What would be compatible with my system?

I looked up the directory which has spc216.gro file. It has tip4p.gro file
but for some reason doesnt have a tip3p.gro file.

Pooja

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Re: [gmx-users] genbox and water model

2010-07-08 Thread Justin A. Lemkul



Sai Pooja wrote:

Hi,

I am using CHARMM forcefield with the tip3p. What input file(-cs) should 
i use to solvate the protein using the genbox command? The default is 
spc216.gro. What would be compatible with my system? 

I looked up the directory which has spc216.gro file. It has tip4p.gro 
file but for some reason doesnt have a tip3p.gro file.


http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file

-Justin



Pooja

--
Quaerendo Invenietis-Seek and you shall discover.



--


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] how to determine the box size

2010-07-08 Thread jojo J
Hello Mark,

Thank you for your reply. AS for the steps you mentioned to solvate a
molecule: I have a simple molecule replicated by genconf -nbox in one
direction. When I try to energy minimize this single molecule grompp em
gives error: rlist is longer than half box size or longer than shortest
diagnal boz size... I increase the size and everything is fine but can you
please tell me what is the criterion to specify the size. Does boxsize
affect results in MD? ( I am asking this because if I want to use genconf to
replicate this molecule which is in a large boxzise the final size of the
system can become very large so I have to use  editconf to reduce the size
again)

Also sometimes some parts of the molcule in the box are outside the box when
I see the trajectory (ngmx) at the beginning.. and I think because of the
pbc it jups inthebox from the otherside. Should the particle be entirely in
box at the beginning?

Thanks,

On 8 July 2010 01:47, Mark Abraham mark.abra...@anu.edu.au wrote:

 Please start new emails for new discussion topics. That way you increase
 the chance that people with the interest and expertise can use their time
 efficiently, and that you get an answer. Also, archives work better if you
 separate topics.

  Please Let me ask two more simple questions about solvating a molecule.
 I am using genbox to solvate a solute. I have solute.gro and solvent.gro.
 What should be the dimension of box in solvent.gro if i want to put -nmol
 numbers in the solute box. Does it matter what size the box of solvent is
 (last line in gro)?

 I don't think you are using the right tool for your problem, but your
 description is so opaque it's hard to tell. genbox -nmol will try to fill
 interstices, which need to exist for it to do any good. That means you need
 to have prepared your solvent.gro with your solute in mind.

  I have solvated the solute with 50 moleecules of solvent. I have the
 structure file obtained from genbox. To run em or MD I need to have top
 file. so I am using pdb2gmx and I get a top file for the solute and 50
 solvents but I have one moleculetype (named protein by default). I am
 confused If I need to have 2 molecuels types for solute and solvent, also if
 I need to enter the number of solvent molecules at the end of the top file
 [mols] option, or what I have now is fine and I can proceed to em and md
 usuing mdp files? :)

 1. use pdb2gmx on an unsolvated .gro to get your protein .top
 2. use editconf to set the simulation box how you want it
 3. use genbox -p to add solvent and take care of modifying your .top
 (unless your solvent is not water, in which case you'll probably have to do
 some manual editing of your .top)
 4. grompp and mdrun

 Perhaps doing some tutorial material will make this and other workflows
 more readily understood?

 Mark
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[gmx-users] top file

2010-07-08 Thread jojo J
Helllo,

I got top file using pdb2gmx but I did not comment unnecessary lines at the
end of the file ( no water in my system
). With this top file I energy minimized my system. I wanted to know if I am
fine ...?

Thank you,
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Re: [gmx-users] how to determine the box size

2010-07-08 Thread Justin A. Lemkul



jojo J wrote:

Hello Mark,

Thank you for your reply. AS for the steps you mentioned to solvate a 
molecule: I have a simple molecule replicated by genconf -nbox in one 
direction. When I try to energy minimize this single molecule grompp em 
gives error: rlist is longer than half box size or longer than shortest 
diagnal boz size... I increase the size and everything is fine but can 
you please tell me what is the criterion to specify the size. Does 
boxsize affect results in MD? ( I am asking this because if I want to 
use genconf to replicate this molecule which is in a large boxzise the 
final size of the system can become very large so I have to use  
editconf to reduce the size again)




http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

...and perhaps some textbook reading.  If you make a system too small, you'll 
waste a whole lot of time generating meaningless trajectories.


Also sometimes some parts of the molcule in the box are outside the box 
when I see the trajectory (ngmx) at the beginning.. and I think because 
of the pbc it jups inthebox from the otherside. Should the particle be 
entirely in box at the beginning? 



Depends on how you set it up.  In the absence of the actual commands you used, 
there's no way to know whether you've positioned your molecule properly.


-Justin


Thanks,

On 8 July 2010 01:47, Mark Abraham mark.abra...@anu.edu.au 
mailto:mark.abra...@anu.edu.au wrote:


Please start new emails for new discussion topics. That way you
increase the chance that people with the interest and expertise can
use their time efficiently, and that you get an answer. Also,
archives work better if you separate topics.

  Please Let me ask two more simple questions about solvating a
molecule. I am using genbox to solvate a solute. I have solute.gro
and solvent.gro. What should be the dimension of box in solvent.gro
if i want to put -nmol numbers in the solute box. Does it matter
what size the box of solvent is (last line in gro)?

I don't think you are using the right tool for your problem, but
your description is so opaque it's hard to tell. genbox -nmol will
try to fill interstices, which need to exist for it to do any good.
That means you need to have prepared your solvent.gro with your
solute in mind.

  I have solvated the solute with 50 moleecules of solvent. I have
the structure file obtained from genbox. To run em or MD I need to
have top file. so I am using pdb2gmx and I get a top file for the
solute and 50 solvents but I have one moleculetype (named protein by
default). I am confused If I need to have 2 molecuels types for
solute and solvent, also if I need to enter the number of solvent
molecules at the end of the top file [mols] option, or what I have
now is fine and I can proceed to em and md usuing mdp files? :)

1. use pdb2gmx on an unsolvated .gro to get your protein .top
2. use editconf to set the simulation box how you want it
3. use genbox -p to add solvent and take care of modifying your .top
(unless your solvent is not water, in which case you'll probably
have to do some manual editing of your .top)
4. grompp and mdrun

Perhaps doing some tutorial material will make this and other
workflows more readily understood?

Mark
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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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Re: [gmx-users] top file

2010-07-08 Thread Justin A. Lemkul



jojo J wrote:

Helllo,

I got top file using pdb2gmx but I did not comment unnecessary lines at 
the end of the file ( no water in my system
). With this top file I energy minimized my system. I wanted to know if 
I am fine ...?




Depends on your definition of fine.  Do you mean to ask if you've done the 
procedure right, or if the results should be trusted, or something else?


-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] top file

2010-07-08 Thread jojo J
Hello,

Thank you for your answer. I mean if I need to go back and comment those
lines. (if the results are trusted ..actually I forgot to comment the
lines..)



On 8 July 2010 23:10, Justin A. Lemkul jalem...@vt.edu wrote:



 jojo J wrote:

 Helllo,

 I got top file using pdb2gmx but I did not comment unnecessary lines at
 the end of the file ( no water in my system
 ). With this top file I energy minimized my system. I wanted to know if I
 am fine ...?


 Depends on your definition of fine.  Do you mean to ask if you've done
 the procedure right, or if the results should be trusted, or something else?

 -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

 
 --
 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
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Re: [gmx-users] top file

2010-07-08 Thread Justin A. Lemkul



jojo J wrote:

Hello,

Thank you for your answer. I mean if I need to go back and comment those 
lines. (if the results are trusted ..actually I forgot to comment the 
lines..)





There's no need to comment out lines referring to solvent, ions, etc if they are 
not present.  These statements just include extra (unnecessary) information. 
For more, see Chapter 5 of the Gromacs manual, and the short version of the 
topic here to understand what's going on:


http://www.gromacs.org/Documentation/Include_File_Mechanism

-Justin



On 8 July 2010 23:10, Justin A. Lemkul jalem...@vt.edu 
mailto:jalem...@vt.edu wrote:




jojo J wrote:

Helllo,

I got top file using pdb2gmx but I did not comment unnecessary
lines at the end of the file ( no water in my system
). With this top file I energy minimized my system. I wanted to
know if I am fine ...?


Depends on your definition of fine.  Do you mean to ask if you've
done the procedure right, or if the results should be trusted, or
something else?

-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 http://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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Re: [gmx-users] how to determine the box size

2010-07-08 Thread Mark Abraham

On 9/07/2010 12:59 PM, jojo J wrote:

Hello Mark,

Thank you for your reply. AS for the steps you mentioned to solvate a 
molecule: I have a simple molecule replicated by genconf -nbox in one 
direction. When I try to energy minimize this single molecule grompp 
em gives error: rlist is longer than half box size or longer than 
shortest diagnal boz size... I increase the size and everything is 
fine but can you please tell me what is the criterion to specify the 
size. Does boxsize affect results in MD? ( I am asking this because if 
I want to use genconf to replicate this molecule which is in a large 
boxzise the final size of the system can become very large so I have 
to use  editconf to reduce the size again)


Your conception of the workflow seems a bit confused. If you want to 
minimize your initial configuration before replication, then it is best 
to do that with an .mdp file that turns off PBC. Some reading in section 
7.3 of the manual will (eventually) let you see how to do that - and 
what you don't need to know right now will be useful later. 
Alternatively, make the box size large enough now, do EM.


Then, with the post-minimization structure, pick a box size suitable for 
replication, then use genconf. Then, do whatever you want to do with the 
replicated structure.


Mark



Also sometimes some parts of the molcule in the box are outside the 
box when I see the trajectory (ngmx) at the beginning.. and I think 
because of the pbc it jups inthebox from the otherside. Should the 
particle be entirely in box at the beginning?


Thanks,

On 8 July 2010 01:47, Mark Abraham mark.abra...@anu.edu.au 
mailto:mark.abra...@anu.edu.au wrote:


Please start new emails for new discussion topics. That way you
increase the chance that people with the interest and expertise
can use their time efficiently, and that you get an answer. Also,
archives work better if you separate topics.

 Please Let me ask two more simple questions about solvating a
molecule. I am using genbox to solvate a solute. I have solute.gro
and solvent.gro. What should be the dimension of box in
solvent.gro if i want to put -nmol numbers in the solute box. Does
it matter what size the box of solvent is (last line in gro)?

I don't think you are using the right tool for your problem, but
your description is so opaque it's hard to tell. genbox -nmol will
try to fill interstices, which need to exist for it to do any
good. That means you need to have prepared your solvent.gro with
your solute in mind.

 I have solvated the solute with 50 moleecules of solvent. I have
the structure file obtained from genbox. To run em or MD I need to
have top file. so I am using pdb2gmx and I get a top file for the
solute and 50 solvents but I have one moleculetype (named protein
by default). I am confused If I need to have 2 molecuels types for
solute and solvent, also if I need to enter the number of solvent
molecules at the end of the top file [mols] option, or what I have
now is fine and I can proceed to em and md usuing mdp files? :)

1. use pdb2gmx on an unsolvated .gro to get your protein .top
2. use editconf to set the simulation box how you want it
3. use genbox -p to add solvent and take care of modifying your
.top (unless your solvent is not water, in which case you'll
probably have to do some manual editing of your .top)
4. grompp and mdrun

Perhaps doing some tutorial material will make this and other
workflows more readily understood?

Mark
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[gmx-users] energygrp_excl and PME

2010-07-08 Thread jasmine
Hi everyone;

I am simulating a functionalized nanotube with (CH3) group .the nanotube
atoms are uncharged and rigid but  the atoms of  (CH3) group are charged  and
flexible  ,and  are defined in the residue name of [atom]  section of  topology
file with (CNT)and (FUNC) , Respectively. I have decided to freeze my  CNT  in
all 3 directions. In fact , I have flexible group anchored to a  frozen
surface of CNT . thus , I used  (energygrp_exl = CNT  CNT   ,   freezegrps  =
CNT  ,   coulombtype  = PME  ) ,but I get the following warning upon running
grompp.

Can not exclude the lattice coulomb energy between energy groups

Please correct my   .mdp file and add any requisite option  in this p case.


coulombtype= PME

energygrps= CNT  FUNC

constraints = none

energygrp_excl   = CNT  CNT

freezegrps   = CNT

freezedim= Y Y Y
Thank you
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[gmx-users] Adding ions

2010-07-08 Thread Sai Pooja
Hi,

When I start from a energy minimized protein in vacuum and solvate it using
genbox, the output message says that the protein has zero charge. So I skip
the genion step. I follow this with energy minimization of the solvated
protein followed by restraining the protein and then doing a short mdrun (as
is the usual procedure outlined in most tutorials). However, when I run the
grompp command as the first step for the position restrained md, it runs but
prints a note saying that the system has non-zero charge ~ -  0..

NOTE 2 [file finalnoss.top, line 8070]:
  System has non-zero total charge: -9.94e-01

I dont understand. Do I need to run the genion step anyway or is it okay to
continue with this system?

Pooja

-- 
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