RE: [gmx-users] find the relevant structure out

2010-11-24 Thread #ZHAO LINA#
I do not know how to extract some special frames out (professionally),
so I just simply use vim to take the relevant models out and put into a new pdb 
file.
Are there some good ways to extract one or two frames at the end of those whole 
frames?

Base on your answering, now I start to suspect I might make something wrong 
cause I did it really clumsily.

Thanks for your answering,

lina


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Wednesday, November 24, 2010 3:19 PM
To: Discussion list for GROMACS users
Subject: Re: RE: [gmx-users] find the relevant structure out



- Original Message -
From: #ZHAO LINA# zhao0...@e.ntu.edu.sg
Date: Wednesday, November 24, 2010 17:52
Subject: RE: [gmx-users] find the relevant structure out
To: Discussion list for GROMACS users gmx-users@gromacs.org

 Hi,

 Thanks for your answering.

 Due to the difference in assignment, so I wonder which one I
 should build a bit much more faith on?

 I read (by eyes) the ss.xpm produced by do_dssp, and find the
 relevant resi out which showed as beta-sheet, but in pymol, it's
 really so standard alpha-helix, when I tried alter in pymol to
 show the beat-sheet as the way Justine mentioned in early email,
 it's really look weird.


It's rather more likely that you're comparing two different (parts of) 
structures, than one secondary structure algorithm assigns sheet and one 
assigns helix to the same part of the same structure. Is the residue/atom 
numbering consistent. What does do_dssp say about the frame you cut out to give 
to pymol?


Mark


 I noticed lots of paper they use DSSP to say something.

 Thanks,

 lina
 
 From: gmx-users-boun...@gromacs.org [gmx-users-
 boun...@gromacs.org] on behalf of Tsjerk Wassenaar [tsje...@gmail.com]
 Sent: Wednesday, November 24, 2010 1:27 PM
 To: Discussion list for GROMACS users
 Subject: Re: [gmx-users] find the relevant structure out

 Hi,

  Visualization software can sometimes assign the secondary
 structure incorrectly.

 There has been an interesting discussion on this on the Pymol user
 list years ago (http://www.mail-archive.com/pymol-
 us...@lists.sourceforge.net/msg01574.html).Secondary structure
 assignment is foremost human defined. You can use
 different metrics to obtain assignments, and should be careful
 to take
 any one of them as 'correct'. For instance, it makes a difference
 whether you assign three types (helical, sheet, loop), as Pymol does,
 or like seven types, as DSSP does.

 In pymol you can set the secondary structure type manually, but
 I find
 that the internal command 'dss' usually does a good job. Note
 that it
 only works on one frame and then uses the assignment for that
 frame on
 all of them, although there may be a workaround (I'll check; something
 with discrete_states). The frame to use for the assignment can be
 given to the 'dss' command through the argument state=N, where N is
 the frame number. If dss doesn't give the assignment you want,
 you can
 also try 'util.ss' that uses a different metric.

 Hope it helps,

 Tsjerk

  On 21/11/2010 11:43 PM, #ZHAO LINA# wrote:
  Hi,
 
  I had done 10ns simulation,
 
  by dssp, can see the beta-sheet appeared very apparently,
 before it's
  alpha-helix.
 
  there were 5000 frames, I based on the time of the picture
 got from dssp, I
  can guess around which frames is supposed to have those beta
 sheets.
  After I took few frames which I thought might be
 representive, but under
  pymol, show cartoon, there is none beta sheet at all. There
 were 5000 frames,
  I really do not know which one is most representive.
 
  Or maybe some parts I understand wrong.
 
  Thanks for any advice and if I am wrong please let me know,
 
  We've really no idea of the detail of what you've done, so
 can't guess. Just
  about anything could be the problem - all the way from you
 are looking at
  the wrong files, to pymol's definition of a beta sheet
 doesn't agree with
  dssp.
 
  If you can't report the command lines you used easily, then
 your method was
  not reproducible enough, or not recorded well enough :-)
 
  Mark
 
 
 
  
 
  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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 http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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 --
 Tsjerk A. 

[gmx-users] perl script for g_hbond / summary_HBmap.dat

2010-11-24 Thread leila karami
Dear Justin

Thank you so much for help.

I  used # symbol in where you said and problem was solved. a output was
obtained with name summary_HBmap.dat.
this file is as follows:

#DonorAcceptor% Exist.
 5.478
  NGL1 N  NGL1H2 0.040
  LYP2   HB2  LYP2   HG1 0.040
  LYP2 O  GLY3 H 6.158
  GLN5 N  GLN5CA 0.040
  GLN5 C  VAL6 N 0.040
  VAL6  3HG2  VAL6 O 0.320
  ARG7   HD2  ARG7HE 0.040
  PHE8HA  PHE8   HB1 8.517
  PHE8 C  SER9 N 1.439
 ASN10CA ASN10CB 0.600
 ASP11HA ASP11   HB1 0.040
 GLN12   HB2 GLN12   HG1 0.440
 THR13CB THR13   CG2 3.199
 ILE14HB ILE14  1HG2 0.800
 GLU15 H GLU15HA 3.798
 LEU16 H LEU16HA 0.040
 LEU16  3HD2 LEU16 O 0.040
 GLU17   OE2 GLU17 O 2.279
 LYP18   HD2 LYP18   HE130.508
 LYP19   HB1 LYP19CG23.231
 LYP19 C PHE20 N 0.840
 PHE20HZ PHE20   HE2 0.040
 GLU21   HG1 GLU21CD 0.480
 THR22  2HG2 THR22   OG1 4.518
 GLN23   HG2 GLN23   OE1 0.360
 LYP24CG LYP24   HG2 0.120
 TYR25 N TYR25CA 0.080
 TYR25   CE2 TYR25   CD2 1.519
 LEU26   CD1 LEU26  2HD110.716
 SER27   HB1 SER27OG 3.958
 PRO28   HB2 PRO28HA 0.120
 PRO29CA PRO29 C 0.440
 GLU30   OE1 GLU30 C11.955
17.193
  NGL1 N 5.718
  GLU30 N 7.837
 SER27OG 1.279
 SER27 N 6.078
 LEU26 N 0.040
 TYR25OH 0.080
 TYR25 N49.100
 LYP24NZ89.204
 LYP24 N 7.917
 GLN23   NE225.590
 GLN23 N73.051
 THR22   OG1 1.719
 THR22 N93.882
 GLU21 N 1.839
 PHE20 N 0.200
 LYP19NZ 0.040

I have some question:

1) when I used g_hbond for obtaining hbond.ndx and hbmap.xpm and hbond.log
file, I selected two groups(1- protein nad 2- dna).In hbond.log and
hbond.ndx file there are acceptors and donors belonging to both of protein
and dna, while in my summary_HBmap.dat file both of donors and acceptors
only belongs to protein. is there problem?

2) at the end of this file, there are only donors. what is means of %exist
for these donors. This file should give me existence of each hbond during my
trajectory and not donors.

3) I think that %exist should be determined for each of
donor-hydrogen-acceptor being in hbond.ndx file.Isn't it?


-- 

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Re: [gmx-users] Problem with large number of frames only one frame can be read from trajectory bug ?

2010-11-24 Thread maria goranovic
Resolved:

I have found the error. Apparently I was using -dt 20, and the condition
that t mod dt = first time (ps) was not being met because the first time was
a funny number. Have rectified it. Apologies for the inconvenience.



-- 
Maria G.
Technical University of Denmark
Copenhagen
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Re: [gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU

2010-11-24 Thread Rossen Apostolov

Hi,

On 11/24/10 2:59 AM, lin hen wrote:

hi,

I am testing the dhfr benchmarks with gromacs 4.5.2

1. for the benchmarks: dhfr-solv-RF-1nm.bench and 
dhfr-solv-RF-2nm.bench, set the steps = 1,

The GPU version running results shows as following:
   ./mdrun-gpu

 Pre-simulation ~15s memtest in progress...done, no errors detected
starting mdrun 'Protein in water'
1 steps, 20.0 ps.
Writing final coordinates.
Back Off! I just backed up confout.gro to ./#confout.gro.2#
Post-simulation ~15s memtest in progress...done, no errors detected
OpenMM run - timing based on wallclock.
*  NODE (s)   Real (s)  (%)
   Time: 90.796 90.796100.0
   1:30
   (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:  0.000  0.060 19.034  1.261*
gcq#100: Jesus Can't Save You, Though It's Nice to Think He Tried 
(Black Crowes)


 The CPU version running results shows as following:
./mdrun

Writing final coordinates.
Back Off! I just backed up confout.gro to ./#confout.gro.3#
 Average load imbalance: 4.7 %
 Part of the total run time spent waiting due to load imbalance: 2.7 %
 Steps where the load balancing was limited by -rdd, -rcon and/or 
-dds: X 0 % Y 0 % Z 0 %


Parallel run - timing based on wallclock.
*  NODE (s)   Real (s)  (%)
   Time: 86.176 86.176100.0
   1:26
   (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:741.634 35.849 20.054  1.197*
gcq#0: Thanx for Using GROMACS - Have a Nice Day


The gpu version looks *slower *than cpu version, does it make sense? 
Is there anyway I could optimize?




In the default build, the CPU version will use all available cores on 
the machine and it's faster.




2.  For the CPU benchmark dhfr-impl-1nm.bench, when I run :
 ./mdrun
 Back Off! I just backed up md.log to ./#md.log.9#
Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single 
precision)

Starting 16 threads
---
Program mdrun, VERSION 4.5.2
Source code file: domdec.c, line: 6428
Fatal error:
There is no domain decomposition for 16 nodes that is compatible with 
the given box and a minimum cell size of 1.02425 nm
Change the number of nodes or mdrun option -rcon or -dds or your LINCS 
settings

Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---
Thanx for Using GROMACS - Have a Nice Day


Where could I modify this nodes#?


Give the option -nt to mdrun to specify the number of threads you want 
to launch, e.g.


$ mdrun -nt 8



3.  for CPU benchmark dhfr-impl-inf.bench
I modified cpu-imp-RF-inf.mdp:  nsteps  1
grompp -f cpu-imp-RF-inf.mdp -o topol.tpr
it will show:
NOTE 1 [file cpu-imp-RF-inf.mdp]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.
Generated 2278 of the 2278 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2278 of the 2278 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
turning all bonds into constraints...
NOTE 2 [file topol.top, line 23568]:
  System has non-zero total charge: -1.10e+01

GB parameter(s) missing or negative for atom type 'H0'
---
Program grompp, VERSION 4.5.1
Source code file: grompp.c, line: 870
Fatal error:
Can't do GB electrostatics; the forcefield is missing 1 values for
atomtype radii, or they might be negative
.
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---
Everybody's Good Enough For Some Change (LIVE)

and when I run ./mdrun
the steps still -1, infinite time
How could I genete the right topol.tpr?


Did you search the mailing lists?

Copy and paste the error message in 
http://www.gromacs.org/Support/Mailing_Lists/Search

and you will get a top hit
http://lists.gromacs.org/pipermail/gmx-users/2010-September/053764.html

You are using grompp 4.5.1 and mdrun 4.5.2 !? Remove all gromacs 
installs that you have, make a clean 4.5.3 install and try again.


Rossen



Thanks a lot.


YY


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Re: [gmx-users] perl script for g_hbond / summary_HBmap.dat

2010-11-24 Thread Justin A. Lemkul
Quoting leila karami karami.lei...@gmail.com:

 Dear Justin

 Thank you so much for help.

 I  used # symbol in where you said and problem was solved. a output was
 obtained with name summary_HBmap.dat.
 this file is as follows:

 #DonorAcceptor% Exist.
  5.478
   NGL1 N  NGL1H2 0.040
   LYP2   HB2  LYP2   HG1 0.040
   LYP2 O  GLY3 H 6.158
   GLN5 N  GLN5CA 0.040
   GLN5 C  VAL6 N 0.040
   VAL6  3HG2  VAL6 O 0.320
   ARG7   HD2  ARG7HE 0.040
   PHE8HA  PHE8   HB1 8.517
   PHE8 C  SER9 N 1.439
  ASN10CA ASN10CB 0.600
  ASP11HA ASP11   HB1 0.040
  GLN12   HB2 GLN12   HG1 0.440
  THR13CB THR13   CG2 3.199
  ILE14HB ILE14  1HG2 0.800
  GLU15 H GLU15HA 3.798
  LEU16 H LEU16HA 0.040
  LEU16  3HD2 LEU16 O 0.040
  GLU17   OE2 GLU17 O 2.279
  LYP18   HD2 LYP18   HE130.508
  LYP19   HB1 LYP19CG23.231
  LYP19 C PHE20 N 0.840
  PHE20HZ PHE20   HE2 0.040
  GLU21   HG1 GLU21CD 0.480
  THR22  2HG2 THR22   OG1 4.518
  GLN23   HG2 GLN23   OE1 0.360
  LYP24CG LYP24   HG2 0.120
  TYR25 N TYR25CA 0.080
  TYR25   CE2 TYR25   CD2 1.519
  LEU26   CD1 LEU26  2HD110.716
  SER27   HB1 SER27OG 3.958
  PRO28   HB2 PRO28HA 0.120
  PRO29CA PRO29 C 0.440
  GLU30   OE1 GLU30 C11.955
 17.193
   NGL1 N 5.718
   GLU30 N 7.837
  SER27OG 1.279
  SER27 N 6.078
  LEU26 N 0.040
  TYR25OH 0.080
  TYR25 N49.100
  LYP24NZ89.204
  LYP24 N 7.917
  GLN23   NE225.590
  GLN23 N73.051
  THR22   OG1 1.719
  THR22 N93.882
  GLU21 N 1.839
  PHE20 N 0.200
  LYP19NZ 0.040

 I have some question:

 1) when I used g_hbond for obtaining hbond.ndx and hbmap.xpm and hbond.log
 file, I selected two groups(1- protein nad 2- dna).In hbond.log and
 hbond.ndx file there are acceptors and donors belonging to both of protein
 and dna, while in my summary_HBmap.dat file both of donors and acceptors
 only belongs to protein. is there problem?

 2) at the end of this file, there are only donors. what is means of %exist
 for these donors. This file should give me existence of each hbond during my
 trajectory and not donors.


Your output is total nonsense.  Please refer to the header of the script for
proper input.  I suspect the problem is with the index file.  You should NOT
pass the entire hbond.ndx file to the script.

 3) I think that %exist should be determined for each of
 donor-hydrogen-acceptor being in hbond.ndx file.Isn't it?



It is, provided you pass proper input to the script.

-Justin

 --

 Leila Karami
 Ph.D. student of Physical Chemistry
 K.N. Toosi University of Technology
 Theoretical Physical Chemistry Group





Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech

Re: [gmx-users] A periodic boundary trajectory with lots of objects: how to get rid of artefacts?

2010-11-24 Thread ms

On 24/11/10 02:47, Mark Abraham wrote:

On 24/11/2010 5:04 AM, ms wrote:

On 23/11/10 17:00, Mark Abraham wrote:

There is no general solution for bonds visualized on a
single set of coordinates, however - over a trajectory, either molecules
appear to diffuse out of the box, or appear to break.


Yep, but if they appear broken because they are at the pbc boundaries
is no big deal. The problem (and with this I answer also Florian
Dommert) is that using -pbc tends to break stuff *inside* the box.


That can't be true in general. Use of one of the five different -pbc
options, possibly with -center and -ur, possibly over several
invocations has always worked for anything I've wanted. However it's
hard to answer an assertion that something is broken if you don't know
what the person has tried :-)


You are absolutely right, but well, it was not needed for the aestethic 
purposes so far required :)


Of course if and when needed for analysis, I'll try harder with trjconv 
-pbc arcanes.


thanks!
m.

--
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http://devicerandom.org
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[gmx-users] perl script for g_hbond / summary_HBmap.dat

2010-11-24 Thread leila karami
Dear Justin

thanks for your attention

with chang of hbond.ndx file my problem was solved.

I have another question about g_hbond: if I want to obtain same information
(percentage of existence of each hbond during my trajectory) about water
mediated hydrogen bonds between protein and dna, for obtaining of hbond.ndx
and hbmap.xpm files from g_hbond tool, what groups should be select?

in previous state (protein-dna direct hydrogen bond), I selected 1) protein
and 2) dna.



-- 

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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[gmx-users] Electric field: phosphate moves in the wrong direction

2010-11-24 Thread Susana Tomasio
Dear users,

I am applying an Electric Field along the z-axis to a system comprising a
protein nanopore and a PO4- in order to see if gets into the pore.
In some of the simulations the phosphate doesn't move on the opposite
direction of the applied field but in the same direction!
I wonder if anyone has experienced this behaviour and if you have any
suggestions.
What I can think of, is that the box might not be big enough, but I am not
sure if that's the only reason.
Thank you in advance,
Susana
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Re: [gmx-users] perl script for g_hbond / summary_HBmap.dat

2010-11-24 Thread Erik Marklund

Hi,

If you mean interactions bridged by a watermolecule, Protein-H2O-DNA, 
then I don't know of any gromacs related tools for this. You need to 
write your own tool for this. One way would be to multiply the existence 
functions for hbonds between protein and water and the hbonds between 
water and DNA, then use Justin's script to get the percentage.


Erik

leila karami skrev 2010-11-24 15.42:

Dear Justin

thanks for your attention

with chang of hbond.ndx file my problem was solved.

I have another question about g_hbond: if I want to obtain same 
information (percentage of existence of each hbond during my 
trajectory) about water mediated hydrogen bonds between protein and 
dna, for obtaining of hbond.ndx and hbmap.xpm files from g_hbond tool, 
what groups should be select?


in previous state (protein-dna direct hydrogen bond), I selected 1) 
protein and 2) dna.




--
Leila Karami
Ph.D. student of Physical Chemistry

K.N. Toosi University of Technology
Theoretical Physical Chemistry Group




--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] installation

2010-11-24 Thread Rossella Noschese
Hi all, I'm trying to install gromacs.4.5.3 on fedora 13.
I followed the instruction on the website, I completed my make install and
this was the output:
  GROMACS is installed under /usr/local/gromacs.
Make sure to update your PATH and MANPATH to find the
programs and unix manual pages, and possibly LD_LIBRARY_PATH
or /etc/ld.so.conf if you are using dynamic libraries.

Please run make tests now to verify your installation.

If you want links to the executables in /usr/local/bin,
you can issue make links now.

Since I understood I could set my environment later, I directly complete my
make links.
Then I added in my .bashrc the line:
source /usr/local/gromacs/bin/GMXRC.bash

and it was added to mi $PATH and also my $MANPATH seems to be right
(/usr/local/gromacs/share/man:)

When I type GMXRC in the shell it comes:
[rosse...@topolone ~]$ GMXRC
/usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a
function or sourced script
/usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found
/usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token
`setenv'
/usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv
LD_LIBRARY_PATH '

Is there anyone that could help me?
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Re: [gmx-users] installation

2010-11-24 Thread Justin A. Lemkul
Quoting Rossella Noschese noschese.rosse...@gmail.com:

 Hi all, I'm trying to install gromacs.4.5.3 on fedora 13.
 I followed the instruction on the website, I completed my make install and
 this was the output:
   GROMACS is installed under /usr/local/gromacs.
 Make sure to update your PATH and MANPATH to find the
 programs and unix manual pages, and possibly LD_LIBRARY_PATH
 or /etc/ld.so.conf if you are using dynamic libraries.

 Please run make tests now to verify your installation.

 If you want links to the executables in /usr/local/bin,
 you can issue make links now.

 Since I understood I could set my environment later, I directly complete my
 make links.
 Then I added in my .bashrc the line:
 source /usr/local/gromacs/bin/GMXRC.bash

 and it was added to mi $PATH and also my $MANPATH seems to be right
 (/usr/local/gromacs/share/man:)

 When I type GMXRC in the shell it comes:
 [rosse...@topolone ~]$ GMXRC
 /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a
 function or sourced script
 /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found
 /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token
 `setenv'
 /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv
 LD_LIBRARY_PATH '

 Is there anyone that could help me?


You don't run GMXRC directly, you have to source GMXRC, but since you've
already done that in your .bashrc, there's no need to do it again.

-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] g_hbond -ac -life

2010-11-24 Thread shahab shariati
Dear gromacs users

I used g_hbond -f .trr -s .tpr -n .ndx -ac -life.

Can anyone clarify last 2 columns in hblife.xvg and last 4 columns hbac.xvg
files by details. Also, I want to know what is difference between p(t) in
hblife.xvg and c(t) in
hbac.xvg file? which of them is more suitable for HB lifetime?

any help will highly appreciated
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Re: [gmx-users] installation

2010-11-24 Thread Rossella Noschese
ok, but when I type luck it says command not found, where's my mistake?

2010/11/24 Justin A. Lemkul jalem...@vt.edu

 Quoting Rossella Noschese noschese.rosse...@gmail.com:

  Hi all, I'm trying to install gromacs.4.5.3 on fedora 13.
  I followed the instruction on the website, I completed my make install
 and
  this was the output:
GROMACS is installed under /usr/local/gromacs.
  Make sure to update your PATH and MANPATH to find the
  programs and unix manual pages, and possibly LD_LIBRARY_PATH
  or /etc/ld.so.conf if you are using dynamic libraries.
 
  Please run make tests now to verify your installation.
 
  If you want links to the executables in /usr/local/bin,
  you can issue make links now.
 
  Since I understood I could set my environment later, I directly complete
 my
  make links.
  Then I added in my .bashrc the line:
  source /usr/local/gromacs/bin/GMXRC.bash
 
  and it was added to mi $PATH and also my $MANPATH seems to be right
  (/usr/local/gromacs/share/man:)
 
  When I type GMXRC in the shell it comes:
  [rosse...@topolone ~]$ GMXRC
  /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a
  function or sourced script
  /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found
  /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected
 token
  `setenv'
  /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH)
 setenv
  LD_LIBRARY_PATH '
 
  Is there anyone that could help me?
 

 You don't run GMXRC directly, you have to source GMXRC, but since you've
 already done that in your .bashrc, there's no need to do it again.

 -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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 Please don't post (un)subscribe requests to the list. Use the
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Re: [gmx-users] g_hbond -ac -life

2010-11-24 Thread Erik Marklund

shahab shariati skrev 2010-11-24 16.24:

Dear gromacs users

I used g_hbond -f .trr -s .tpr -n .ndx -ac -life.

Can anyone clarify last 2 columns in hblife.xvg and last 4 columns 
hbac.xvg
files by details. Also, I want to know what is difference between p(t) 
in hblife.xvg and c(t) in

hbac.xvg file? which of them is more suitable for HB lifetime?

any help will highly appreciated

For hblife, I don't know. in hbac.xvg the first column is the 
autocorrelation function (acf) with a (somewhat dubious) correction to 
compensate for a finite system (the acf sohuld approac zero for large 
distances, but for a periodic finite system the tail is proprotional to 
1/N, N being the number of particles). The second one is the 'raw' acf. 
Third column is the cross correlation between the hb-existence functions 
and corresponding contact-existence function (contacts fulfil the 
distace criterium but not the angular criterium). The fourth column is 
the derivative of the first column.


The problem with -life, as far as I know, is that it models the hbond 
breaking/formation as a simple one step process, which may not be a good 
description. See the Luzar and Chandler papers for the theory behind the 
constants reported by g_hbond -ac. Therefore I'd use -ac to determine 
the rate for hb breaking.


Cheers,

--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] installation

2010-11-24 Thread Rossella Noschese
it was g_luck!!!it changed...ok, now it seems it wors!
Thanks

2010/11/24 Rossella Noschese noschese.rosse...@gmail.com

 ok, but when I type luck it says command not found, where's my mistake?

 2010/11/24 Justin A. Lemkul jalem...@vt.edu

 Quoting Rossella Noschese noschese.rosse...@gmail.com:

  Hi all, I'm trying to install gromacs.4.5.3 on fedora 13.
  I followed the instruction on the website, I completed my make install
 and
  this was the output:
GROMACS is installed under /usr/local/gromacs.
  Make sure to update your PATH and MANPATH to find the
  programs and unix manual pages, and possibly LD_LIBRARY_PATH
  or /etc/ld.so.conf if you are using dynamic libraries.
 
  Please run make tests now to verify your installation.
 
  If you want links to the executables in /usr/local/bin,
  you can issue make links now.
 
  Since I understood I could set my environment later, I directly complete
 my
  make links.
  Then I added in my .bashrc the line:
  source /usr/local/gromacs/bin/GMXRC.bash
 
  and it was added to mi $PATH and also my $MANPATH seems to be right
  (/usr/local/gromacs/share/man:)
 
  When I type GMXRC in the shell it comes:
  [rosse...@topolone ~]$ GMXRC
  /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a
  function or sourced script
  /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found
  /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected
 token
  `setenv'
  /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH)
 setenv
  LD_LIBRARY_PATH '
 
  Is there anyone that could help me?
 

 You don't run GMXRC directly, you have to source GMXRC, but since you've
 already done that in your .bashrc, there's no need to do it again.

 -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] g_hbond -ac -life

2010-11-24 Thread shahab shariati
Dear Erik

thanks.

thus -ac is only for determine the rate for hb breaking. is it true? or
there is other usable case for -ac option?
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[gmx-users] perl script for g_hbond / summary_HBmap.dat

2010-11-24 Thread leila karami
Dear Erik

I'm confused. is there h(t) in hbmap.xpm file?

where is h(t)? which output file of g_hbond tool?

-- 

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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[gmx-users] Re: perl script for g_hbond / summary_HBmap.dat

2010-11-24 Thread Causgrove, Tim
Hi,

There is a bridging waters TCL script available for VMD which may be useful.
It can be found at 
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bridging_waters/

-- 
Tim Causgrove
Associate Professor
Texas AM University - Corpus Christi
6300 Ocean Drive, Unit 5802
Corpus Christi, TX 78412
361-825-2399



 Date: Wed, 24 Nov 2010 18:37:45 +0330
 From: leila karami karami.lei...@gmail.com
 Subject: [gmx-users] perl script for g_hbond / summary_HBmap.dat
 To: gmx-users gmx-users@gromacs.org
 Message-ID:
 aanlktikmoxojwnbffpcsbzywmbezjznjjwvsegjho...@mail.gmail.com
 Content-Type: text/plain; charset=iso-8859-1
 
 Dear Erik and Justin
 
 Thank you so much for ypur help.
 
 yes I mean water mediated hydrogen bonds (protein-H2O-dna).
 
 since I'm beginner in perl script, please clarify your answer and explain
 more. what is your mean of
 existence functions exactly?
 
 do using of -ins option in g_hbond tool help me?
 
 
 --
 
 Leila Karami
 Ph.D. student of Physical Chemistry
 K.N. Toosi University of Technology
 Theoretical Physical Chemistry Group
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Re: [gmx-users] installation

2010-11-24 Thread Carsten Kutzner
On Nov 24, 2010, at 4:04 PM, Rossella Noschese wrote:

 Hi all, I'm trying to install gromacs.4.5.3 on fedora 13.
 I followed the instruction on the website, I completed my make install and 
 this was the output:
   GROMACS is installed under /usr/local/gromacs.
 Make sure to update your PATH and MANPATH to find the
 programs and unix manual pages, and possibly LD_LIBRARY_PATH
 or /etc/ld.so.conf if you are using dynamic libraries.
 
 Please run make tests now to verify your installation.
 
 If you want links to the executables in /usr/local/bin,
 you can issue make links now.
 
 Since I understood I could set my environment later, I directly complete my 
 make links.
 Then I added in my .bashrc the line: 
 source /usr/local/gromacs/bin/GMXRC.bash
 
 and it was added to mi $PATH and also my $MANPATH seems to be right 
 (/usr/local/gromacs/share/man:)
 
 When I type GMXRC in the shell it comes:
GMXRC is for setting the paths to your Gromacs executables. You
can do that by typing source GMXRC, but this you have already done
in your bashrc, so everything is already set up and fine! You will find
all the Gromacs programs at your fingertips, e.g. mdrun -h prints
out help for the main MD program.

Carsten


 [rosse...@topolone ~]$ GMXRC
 /usr/local/gromacs/bin/GMXRC: line 35: return: can only `return' from a 
 function or sourced script
 /usr/local/gromacs/bin/GMXRC: line 44: CSH:: command not found
 /usr/local/gromacs/bin/GMXRC.csh: line 8: syntax error near unexpected token 
 `setenv'
 /usr/local/gromacs/bin/GMXRC.csh: line 8: `if (! $?LD_LIBRARY_PATH) setenv 
 LD_LIBRARY_PATH '
 
 Is there anyone that could help me?
 
 
 -- 
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 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


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[gmx-users] (no subject)

2010-11-24 Thread Olga Ivchenko
Dear gromacs users,

I want to heat system from 0K till 300K. Than do equilibration dynamics in
water. I can not find any .mdp files where the system is gradually heated
from initial temperature (0K) till needed temperature. I can only find NVP
and NVT equilibration dynamics. Please can you advice me on this?

best,
Olga
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Re: [gmx-users] (no subject)

2010-11-24 Thread Justin A. Lemkul
Quoting Olga Ivchenko olga.ivche...@gmail.com:

 Dear gromacs users,

 I want to heat system from 0K till 300K. Than do equilibration dynamics in
 water. I can not find any .mdp files where the system is gradually heated
 from initial temperature (0K) till needed temperature. I can only find NVP
 and NVT equilibration dynamics. Please can you advice me on this?


Please read in the manual about simulated annealing.  There is even an example
in the online manual (manual.gromacs.org).

-Justin

 best,
 Olga





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] heme

2010-11-24 Thread shahid nayeem
Dear all
I am trying MD of cyt C containing heme. I am able to generate bonds with
specbond.dat by pdb2gmx. After using editconf and genbox, when I tried
grompp I got error about unrecognized bonds/angles. I made bond with MET SD
and FE of Heme. As earlier suggested on this list I wrote to get parameter
for these bonds but I couldnt get it. If someone on this mailing list can
help me I will be grateful. Cyt C is very widely modelled protein with
Gomacs in literature hence I expect to get some help from the forum.
shahid nayeem
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Re: [gmx-users] g_hbond -ac -life

2010-11-24 Thread Erik Marklund

shahab shariati skrev 2010-11-24 16.45:

Dear Erik
thanks.
thus -ac is only for determine the rate for hb breaking. is it true? 
or there is other usable case for -ac option?





And formation. And equillibrium constant.

--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] perl script for g_hbond / summary_HBmap.dat

2010-11-24 Thread Erik Marklund
Well, yes. The 'h' notation is never used in the xpm file. I just 
borrowed it from Luzar and chandler. Every line in the xpm data is the 
h(t) for a particular hydrogen bond.


Erik

leila karami skrev 2010-11-24 16.50:

Dear Erik

I'm confused. is there h(t) in hbmap.xpm file?

where is h(t)? which output file of g_hbond tool?

--
Leila Karami
Ph.D. student of Physical Chemistry

K.N. Toosi University of Technology
Theoretical Physical Chemistry Group




--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] heme

2010-11-24 Thread Erik Marklund

shahid nayeem skrev 2010-11-24 18.02:

Dear all
I am trying MD of cyt C containing heme. I am able to generate bonds 
with specbond.dat by pdb2gmx. After using editconf and genbox, when I 
tried grompp I got error about unrecognized bonds/angles. I made bond 
with MET SD and FE of Heme. As earlier suggested on this list I wrote 
to get parameter for these bonds but I couldnt get it. If someone on 
this mailing list can help me I will be grateful. Cyt C is very widely 
modelled protein with Gomacs in literature hence I expect to get some 
help from the forum.

shahid nayeem
A long time ago I simulated CytC with one of the gromos force fields. It 
worked right out of the box. What forcefield are you using?


--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] Nose-Hoover Thermostat for Non Equilibrium Simulations

2010-11-24 Thread Apoorv Kalyankar
Hello GROMACS users,

I have a questions regarding how a Nose-Hoover thermostat works in non
equilibrium simulations
in GROMACS . If I apply some constant acceleration in the x direction, is
the thermostat applied
to all degrees of freedom or is it applied only in the y and z direction.
Thanks.

Apoorv
Graduate Student
University of Illinois
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[gmx-users] Martini parameters for formyl group

2010-11-24 Thread George Khelashvili

Dear users,

I was wondering if there is Martini topology available for simple formyl 
(or aldehyde) group H - C = O. I would appreciate if somebody can direct 
me to the place where such force field parameters are discussed.


Thanks,
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
gek2...@med.cornell.edu
Phone: 1-212-746-6539
Fax:   1-212-746-6226


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Re: [gmx-users] heme

2010-11-24 Thread Justin A. Lemkul



Erik Marklund wrote:

shahid nayeem skrev 2010-11-24 18.02:

Dear all
I am trying MD of cyt C containing heme. I am able to generate bonds 
with specbond.dat by pdb2gmx. After using editconf and genbox, when I 
tried grompp I got error about unrecognized bonds/angles. I made bond 
with MET SD and FE of Heme. As earlier suggested on this list I wrote 
to get parameter for these bonds but I couldnt get it. If someone on 
this mailing list can help me I will be grateful. Cyt C is very widely 
modelled protein with Gomacs in literature hence I expect to get some 
help from the forum.

shahid nayeem
A long time ago I simulated CytC with one of the gromos force fields. It 
worked right out of the box. What forcefield are you using?




The same problem is frequently reported.  The inter-residue bonds and angles are 
not assigned in pdb2gmx, nor are they present in the force field, IIRC.  Hence 
the fatal errors.  Perhaps something has changed since a long time ago, but I 
am sure problems exist in recent versions.


-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] Reg: Interfacial tension

2010-11-24 Thread vinothkumar mohanakrishnan
Hi all

How to find the interfacial tension between two immiscible liquids in
gromacs?. how one should start abou it. any help is highly is appreciated.

Regards
Vinoth
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Re: [gmx-users] heme

2010-11-24 Thread shahid nayeem
I am using ffG43a1 forcefield. its .rtp file contains topology of Heme but
Met SD and FE bond is not there.
Shahid Nayeem

On Thu, Nov 25, 2010 at 5:11 AM, Justin A. Lemkul jalem...@vt.edu wrote:



 Erik Marklund wrote:

 shahid nayeem skrev 2010-11-24 18.02:

 Dear all
 I am trying MD of cyt C containing heme. I am able to generate bonds with
 specbond.dat by pdb2gmx. After using editconf and genbox, when I tried
 grompp I got error about unrecognized bonds/angles. I made bond with MET SD
 and FE of Heme. As earlier suggested on this list I wrote to get parameter
 for these bonds but I couldnt get it. If someone on this mailing list can
 help me I will be grateful. Cyt C is very widely modelled protein with
 Gomacs in literature hence I expect to get some help from the forum.
 shahid nayeem

 A long time ago I simulated CytC with one of the gromos force fields. It
 worked right out of the box. What forcefield are you using?


 The same problem is frequently reported.  The inter-residue bonds and
 angles are not assigned in pdb2gmx, nor are they present in the force field,
 IIRC.  Hence the fatal errors.  Perhaps something has changed since a long
 time ago, but I am sure problems exist in recent versions.

 -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] Reg: Interfacial tension

2010-11-24 Thread vinothkumar mohanakrishnan
Hi all

I want to calculate the interfacial tension of two immiscible liquids using
the surface tension option in gromacs. when i do that i am getting the error
message as

One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off..I dont know
what is it due to?. Below is my mdp file used for the mdrun. any help is
highly appreciated.


integrator  = md
nsteps= 50
dt   = 0.002
nstxout= 1000
nstvout= 1000
nstenergy= 1000
nstlog= 1000
nstxtcout= 1000
xtc_precision= 1000
xtc_grps= system
constraint_algorithm = shake
constraints= none
unconstrained_start= yes
shake_tol= 0.0001
morse= no
ns_type= grid
nstlist= 5
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
vdwtype= Cut-off
rvdw= 1.0
pme_order= 4
fourierspacing= 0.16
pbc= xyz
tcoupl= V-rescale
tc-grps= system
tau_t= 0.1
ref_t= 300
pcoupl= Berendsen
pcoupltype= surface-tension
tau_p= 1.0 1.0
ref_p= 5101.0
compressibility = 4.50e-50
DispCorr= EnerPres
gen_vel= no

Regards
Vinoth
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[gmx-users] RMSD and Resolution

2010-11-24 Thread ahmet yıldırım
Hi,

Is there a relationship between RMSD value obtained from the calculation and
Resolution value in PDB file?

Thanks in advance

-- 
Ahmet YILDIRIM
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