[gmx-users] installation

2009-06-02 Thread Samik Bhattacharya
hi,I
 
i am facing a lot of troubles in installing Gromacs in my Redhat machine..I've 
followed all the instructions given in the manual as well as in the website. 
ialso have installed fftw,its compiling with no problem. . but whenever i run 
pdb2gmx or command lke that its giving an error command not found. a little 
help regarding this matter will be very encouraging. 
thankx
 Shamik



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Re: [gmx-users] installation

2009-06-02 Thread Manik Mayur
On Tue, Jun 2, 2009 at 12:21 PM, Samik Bhattacharya
samikb...@yahoo.co.inwrote:

  hi,I

 i am facing a lot of troubles in installing Gromacs in my Redhat
 machine..I've followed all the instructions given in the manual as well as
 in the website. ialso have installed fftw,its compiling with no problem. .
 but whenever i run pdb2gmx or command lke that its giving an error command
 not found. a little help regarding this matter will be very encouraging.


Have you executed make links ?


 thankx
  Shamik

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Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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Re: [gmx-users] installation

2009-06-02 Thread Mark Abraham

Samik Bhattacharya wrote:

hi,I
 
i am facing a lot of troubles in installing Gromacs in my Redhat 
machine..I've followed all the instructions given in the manual as well 
as in the website. ialso have installed fftw,its compiling with no 
problem. . but whenever i run pdb2gmx or command lke that its giving an 
error command not found. a little help regarding this matter will be 
very encouraging.


The instructions here will probably help

http://wiki.gromacs.org/index.php/Installation

Mark
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[gmx-users] Fwd: Segmentation fault while running gromacs 4.0.4

2009-06-02 Thread Ms. Aswathy S


Dept. Biotechnology
Ext. 3108

- Forwarded Message -
From: Ms. Aswathy S aswat...@amritapuri.amrita.edu
To: gmx-users@gromacs.org
Sent: Tuesday, June 2, 2009 11:54:56 AM GMT +05:30 Chennai, Kolkata, Mumbai, 
New Delhi
Subject: Segmentation fault while running gromacs 4.0.4

Hi,

I am working in GROMACS 4.0.4 and trying to do a receptor -ligand simulation.

But when I run the grommp for equilibration of about 30 ps, it shows 
Segmentaion Fault. I din't get any idea that what type of error it causing from 
the log file. When i run the free command it has a free space of 33 MB. Is that 
could be the reason?. But I already read that gromacs doesnot consume that much 
memory(10-20Mb). If so tell me what could be the possibilities. attaching the 
mdp file and log file
I will explain all the steps i have did,

1. The protein and ligand i minimized in vaccum.
2. Then added water and again minimized the whole system (During both 1  2 
minimization, Steepest Descents converged to machine precision in early steps 
)
3. I used the otput file from the above result for equilibration steps(is that 
the reason??!!!)

then i faced the segmentatuion fault. Please help me

thanks in advance

Dept. Biotechnology
Ext. 3108
Log file opened on Mon Jun  1 11:53:59 2009
Host: localhost.localdomain  pid: 8316  nodeid: 0  nnodes:  1
The Gromacs distribution was built Wed May 13 12:15:31 IST 2009 by
r...@localhost.localdomain (Linux 2.6.18-92.el5xen i686)


 :-)  G  R  O  M  A  C  S  (-:

   Groningen Machine for Chemical Simulation

:-)  VERSION 4.0.4  (-:


  Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

:-)  mdrun  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  

Input Parameters:
   integrator   = md
   nsteps   = 5000
   init_step= 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 1
   comm_mode= Linear
   nstlog   = 100
   nstxout  = 250
   nstvout  = 1000
   nstfout  = 0
   nstenergy= 10
   nstxtcout= 100
   init_t   = 0
   delta_t  = 0.002
   xtcprec  = 1000
   nkx  = 60
   nky  = 60
   nkz  = 60
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = Berendsen
   epc  = Berendsen
   epctype  = Isotropic
   tau_p= 0.5
   ref_p (3x3):
  ref_p[0]={ 1.0e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  1.0e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  1.0e+00}
   compress (3x3):
  compress[0]={ 4.5e-05,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  4.5e-05,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  4.5e-05}
   refcoord_scaling = No
   posres_com (3):
  posres_com[0]= 0.0e+00
  posres_com[1]= 0.0e+00
  posres_com[2]= 0.0e+00
   posres_comB (3):
  

Re: [gmx-users] Fwd: Segmentation fault while running gromacs 4.0.4

2009-06-02 Thread Mark Abraham

Ms. Aswathy S wrote:


Dept. Biotechnology
Ext. 3108

- Forwarded Message -
From: Ms. Aswathy S aswat...@amritapuri.amrita.edu
To: gmx-users@gromacs.org
Sent: Tuesday, June 2, 2009 11:54:56 AM GMT +05:30 Chennai, Kolkata, Mumbai, 
New Delhi
Subject: Segmentation fault while running gromacs 4.0.4

Hi,

I am working in GROMACS 4.0.4 and trying to do a receptor -ligand simulation.

But when I run the grommp for equilibration of about 30 ps, it shows 
Segmentaion Fault. I din't get any idea that what type of error it causing from 
the log file. When i run the free command it has a free space of 33 MB. Is that 
could be the reason?. But I already read that gromacs doesnot consume that much 
memory(10-20Mb). If so tell me what could be the possibilities. attaching the 
mdp file and log file
I will explain all the steps i have did,

1. The protein and ligand i minimized in vaccum.
2. Then added water and again minimized the whole system (During both 1  2 minimization, 
Steepest Descents converged to machine precision in early steps )
3. I used the otput file from the above result for equilibration steps(is that 
the reason??!!!)

then i faced the segmentatuion fault. Please help me


Your simulation is blowing up 
http://wiki.gromacs.org/index.php/blowing_up, probably because your 
starting structure is badly broken (huge energy components, infinite 
temperature).


Mark
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[gmx-users] plain cutoff coulomb

2009-06-02 Thread Cheong Wee Loong, Daniel
Hi all,

This seems like a really simple and silly question, but I have read through the 
manual and the archives and can't seem to find anything about it.

If I were to set coulombtype = cutoff, g_energy will still calculate Coul-LR 
term which suggests that Gromacs calculates some long range correction term for 
the coulomb interactions beyond the cut-off rcoulomb.  But I can't seem to find 
any explanation on how the interactions beyond rcoulomb is calculated when not 
using Ewald or PME.  Can anyone enlighten me?

Thank you!


This email is confidential and may be privileged. If you are not the intended 
recipient, please delete it and notify us immediately. Please do not copy or 
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Re: [gmx-users] plain cutoff coulomb

2009-06-02 Thread Mark Abraham

Cheong Wee Loong, Daniel wrote:

Hi all,

 

This seems like a really simple and silly question, but I have read 
through the manual and the archives and can’t seem to find anything 
about it.


 

If I were to set coulombtype = cutoff, g_energy will still calculate 
Coul-LR term which suggests that Gromacs calculates some long range 
correction term for the coulomb interactions beyond the cut-off 
rcoulomb.  But I can’t seem to find any explanation on how the 
interactions beyond rcoulomb is calculated when not using Ewald or PME.  
Can anyone enlighten me? 


GROMACS uses twin-range cutoffs, so the LR term exists when coulombtype 
= cutoff, rlist  rcoulomb, and is updated on nstlist steps, or 
something similar. Search for twin-range in the manual.


Mark
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[gmx-users] Gromacs 4.0.4 problem in extending MARTINI run by 600 ns, but no problem extending run by 60 ns using tpbconv

2009-06-02 Thread himanshu khandelia
Dear All,

I have run into this problem while using tpbconv. I typically write a new
set of output files every ~ 600 ns. However, after about 108 repeats,
tpbconv fails to write a new .tpr file:

###
tpbconv -s poptocg25-108.tpr -extend 60 -o poptocg25-109.tpr

...
...
Reading toplogy and shit from poptocg25-108.tpr
Reading file poptocg25-108.tpr, VERSION 4.0.4 (single precision)
Extending remaining runtime of by 60 ps (now -2134967296 steps)
You've simulated long enough. Not writing tpr file
###

However, there is no problem if I try to extend the run by only 60 ns?

###
tpbconv -s poptocg25-108.tpr -extend 60 -o poptocg25-109.tpr

...
...

Reading toplogy and shit from poptocg25-108.tpr
Reading file poptocg25-108.tpr, VERSION 4.0.4 (single precision)
Extending remaining runtime of by 6 ps (now 214200 steps)
Writing statusfile with starting step  0 and length 214200
steps...
time  0.000 and length 6426.000 ps
###

Thank you for the help,

-himanshu
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Re: [gmx-users] Gromacs 4.0.4 problem in extending MARTINI run by 600 ns, but no problem extending run by 60 ns using tpbconv

2009-06-02 Thread Mark Abraham

himanshu khandelia wrote:

Dear All,

I have run into this problem while using tpbconv. I typically write a 
new set of output files every ~ 600 ns. However, after about 108 
repeats, tpbconv fails to write a new .tpr file:


###
tpbconv -s poptocg25-108.tpr -extend 60 -o poptocg25-109.tpr

...
...
Reading toplogy and shit from poptocg25-108.tpr
Reading file poptocg25-108.tpr, VERSION 4.0.4 (single precision)
Extending remaining runtime of by 60 ps (now -2134967296 steps)


There's the problem. The variable that counts the number of steps is 
signed, and has overflowed. It seems even a long variable is not 
enough for CG simulations :-) Please post a bugzilla and it will get 
fixed for the next version.


Meantime, you can work around the situation by building a new .tpr that 
continues from your last endpoint.


Mark


You've simulated long enough. Not writing tpr file
###

However, there is no problem if I try to extend the run by only 60 ns?

###
tpbconv -s poptocg25-108.tpr -extend 60 -o poptocg25-109.tpr

...
...

Reading toplogy and shit from poptocg25-108.tpr
Reading file poptocg25-108.tpr, VERSION 4.0.4 (single precision)
Extending remaining runtime of by 6 ps (now 214200 steps)
Writing statusfile with starting step  0 and length 214200 
steps...

time  0.000 and length 6426.000 ps
###

Thank you for the help,

-himanshu




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Re: [gmx-users] installation

2009-06-02 Thread Nuno Azoia
Hello!

Just like Manik Mayur suggested, the problem should be the links:
Gromacs gives you the possibility to create links to /usr/bin directory
(ot something similar). If you didn't do that, one of the option is
trying to run the programs using the full path. Instead of using
pdb2gmx, try to use /usr/local/gromacs/bin/pdb2gmx. Replace
/usr/local/gromacs with the directory where you install gromacs. If
you didn't choose anything it probably is /usr/local/gromacs.

I hope this can help

Nuno Azoia

On Tue, 2009-06-02 at 12:21 +0530, Samik Bhattacharya wrote:
 hi,I
  
 i am facing a lot of troubles in installing Gromacs in my Redhat
 machine..I've followed all the instructions given in the manual as
 well as in the website. ialso have installed fftw,its compiling with
 no problem. . but whenever i run pdb2gmx or command lke that its
 giving an error command not found. a little help regarding this
 matter will be very encouraging. 
 thankx
  Shamik
 
 
 
 __
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 Travel Click here!
 ___
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Finishing Research Laboratory
Textile Engineering Department
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
Portugal
 
Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293
 
Mobile: +351 965 382 487
E-mail: naz...@det.uminho.pt

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[gmx-users] mdrun seems stuck

2009-06-02 Thread Stefano Meliga
Hello,

I'd like to run a position restrained MD of a protein in water with
3000 (protein) + 4 (SOL) atoms.

I preprocess the input with the command line:

$grxdir/grompp -f 4AKEprePRMD.mdp -po 4AKE_PRMD.mdp -c 4AKE_EMcg.gro
-p 4AKEallHion.top -pp 4AKEprePRMD.top -o 4AKE_PRMD.tpr

4AKEprePRMD.mdp is:

title   =  4AKE_PRMD
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt  =  0.002; ps !
nsteps  =  5000 ; total 10.0 ps.
nstcomm =  1; [steps] frequency for center of mass
motion removal
nstxout =  100  ; [steps] frequency to write
coordinates to output trajectory file
nstvout =  100  ; [steps] frequency to write
velocities to output trajectory
nstfout =  0; [steps] frequency to write forces to
output trajectory
nstlog  =  10   ; [steps] frequency to write energies
to log file
nstenergy   =  10   ; [steps] frequency to write energies
to energy file
nstlist =  5; neighbour searching
ns_type =  grid
rlist   =  1.0
coulombtype =  EWALD
rcoulomb=  1.0
vdwtype =  Cut-off
rvdw=  1.0

; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tau_t   =  0.1  0.1
tc-grps =  Protein  Non-Protein
ref_t   =  300  300
; Energy monitoring
energygrps  =  Protein  SOL
; Pressure coupling is on
Pcoupl  =  berendsen
Pcoupltype  =  isotropic
tau_p   =  0.5
compressibility =  4.5e-5   ; [1/bar] compressibility of water
ref_p   =  1.0  ; [bar] reference pressure for coupling
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529


Then I run the PR MD:
$grxdir/mdrun -s 4AKE_PRMD.tpr -o 4AKE_PRMD.trr -c 4AKE_PRMD.gro -e
4AKE_PRMD.edr -g 4AKE_PRMD.log -v

These lines appear on the terminal:
starting mdrun 'Protein in water'
5000 steps, 10.0 ps.

...but from this point on nothing more is displayed. I see neither
steps nor time left.
Are the parameter in the mdp file defining a too expensive simulation?

I've tryied removing pressure and temperature coupling but the problem remains.
How can I solve this issue?

-DPOSRES refers to posre.itp, I guess. posre.itp was created from the
original pdb before the energy minimization. Should I run pdb2gmx once
again after the EM to create a new posre.itp?

Thanks,

Stefano
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Re: [gmx-users] mdrun seems stuck

2009-06-02 Thread Nuno Azoia
Take a look to your .log file. Gromacs writes everything there.

Nuno Azoia

On Tue, 2009-06-02 at 10:45 +0100, Stefano Meliga wrote:
 Hello,
 
 I'd like to run a position restrained MD of a protein in water with
 3000 (protein) + 4 (SOL) atoms.
 
 I preprocess the input with the command line:
 
 $grxdir/grompp -f 4AKEprePRMD.mdp -po 4AKE_PRMD.mdp -c 4AKE_EMcg.gro
 -p 4AKEallHion.top -pp 4AKEprePRMD.top -o 4AKE_PRMD.tpr
 
 4AKEprePRMD.mdp is:
 
 title   =  4AKE_PRMD
 cpp =  /usr/bin/cpp
 define  =  -DPOSRES
 constraints =  all-bonds
 integrator  =  md
 dt  =  0.002; ps !
 nsteps  =  5000 ; total 10.0 ps.
 nstcomm =  1; [steps] frequency for center of mass
 motion removal
 nstxout =  100  ; [steps] frequency to write
 coordinates to output trajectory file
 nstvout =  100  ; [steps] frequency to write
 velocities to output trajectory
 nstfout =  0; [steps] frequency to write forces to
 output trajectory
 nstlog  =  10   ; [steps] frequency to write energies
 to log file
 nstenergy   =  10   ; [steps] frequency to write energies
 to energy file
 nstlist =  5; neighbour searching
 ns_type =  grid
 rlist   =  1.0
 coulombtype =  EWALD
 rcoulomb=  1.0
 vdwtype =  Cut-off
 rvdw=  1.0
 
 ; Berendsen temperature coupling is on in two groups
 Tcoupl  =  berendsen
 tau_t   =  0.1  0.1
 tc-grps =  Protein  Non-Protein
 ref_t   =  300  300
 ; Energy monitoring
 energygrps  =  Protein  SOL
 ; Pressure coupling is on
 Pcoupl  =  berendsen
 Pcoupltype  =  isotropic
 tau_p   =  0.5
 compressibility =  4.5e-5   ; [1/bar] compressibility of water
 ref_p   =  1.0  ; [bar] reference pressure for coupling
 ; Generate velocites is on at 300 K.
 gen_vel =  yes
 gen_temp=  300.0
 gen_seed=  173529
 
 
 Then I run the PR MD:
 $grxdir/mdrun -s 4AKE_PRMD.tpr -o 4AKE_PRMD.trr -c 4AKE_PRMD.gro -e
 4AKE_PRMD.edr -g 4AKE_PRMD.log -v
 
 These lines appear on the terminal:
 starting mdrun 'Protein in water'
 5000 steps, 10.0 ps.
 
 ...but from this point on nothing more is displayed. I see neither
 steps nor time left.
 Are the parameter in the mdp file defining a too expensive simulation?
 
 I've tryied removing pressure and temperature coupling but the problem 
 remains.
 How can I solve this issue?
 
 -DPOSRES refers to posre.itp, I guess. posre.itp was created from the
 original pdb before the energy minimization. Should I run pdb2gmx once
 again after the EM to create a new posre.itp?
 
 Thanks,
 
 Stefano
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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.
 Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 
Nuno Gonçalo Azoia Lopes
 
Finishing Research Laboratory
Textile Engineering Department
Universidade do Minho
Campus de Azurém
4800-058 Guimarães
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Re: [gmx-users] mdrun seems stuck

2009-06-02 Thread Stefano Meliga

The simulation seems just very slow.
step 0 has appeared on the screen after several minutes and in the log 
file there's only step zero as well.


Stefano

Nuno Azoia ha scritto:

Take a look to your .log file. Gromacs writes everything there.

Nuno Azoia

On Tue, 2009-06-02 at 10:45 +0100, Stefano Meliga wrote:
  

Hello,

I'd like to run a position restrained MD of a protein in water with
3000 (protein) + 4 (SOL) atoms.

I preprocess the input with the command line:

$grxdir/grompp -f 4AKEprePRMD.mdp -po 4AKE_PRMD.mdp -c 4AKE_EMcg.gro
-p 4AKEallHion.top -pp 4AKEprePRMD.top -o 4AKE_PRMD.tpr

4AKEprePRMD.mdp is:

title   =  4AKE_PRMD
cpp =  /usr/bin/cpp
define  =  -DPOSRES
constraints =  all-bonds
integrator  =  md
dt  =  0.002; ps !
nsteps  =  5000 ; total 10.0 ps.
nstcomm =  1; [steps] frequency for center of mass
motion removal
nstxout =  100  ; [steps] frequency to write
coordinates to output trajectory file
nstvout =  100  ; [steps] frequency to write
velocities to output trajectory
nstfout =  0; [steps] frequency to write forces to
output trajectory
nstlog  =  10   ; [steps] frequency to write energies
to log file
nstenergy   =  10   ; [steps] frequency to write energies
to energy file
nstlist =  5; neighbour searching
ns_type =  grid
rlist   =  1.0
coulombtype =  EWALD
rcoulomb=  1.0
vdwtype =  Cut-off
rvdw=  1.0

; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tau_t   =  0.1  0.1
tc-grps =  Protein  Non-Protein
ref_t   =  300  300
; Energy monitoring
energygrps  =  Protein  SOL
; Pressure coupling is on
Pcoupl  =  berendsen
Pcoupltype  =  isotropic
tau_p   =  0.5
compressibility =  4.5e-5   ; [1/bar] compressibility of water
ref_p   =  1.0  ; [bar] reference pressure for coupling
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529


Then I run the PR MD:
$grxdir/mdrun -s 4AKE_PRMD.tpr -o 4AKE_PRMD.trr -c 4AKE_PRMD.gro -e
4AKE_PRMD.edr -g 4AKE_PRMD.log -v

These lines appear on the terminal:
starting mdrun 'Protein in water'
5000 steps, 10.0 ps.

...but from this point on nothing more is displayed. I see neither
steps nor time left.
Are the parameter in the mdp file defining a too expensive simulation?

I've tryied removing pressure and temperature coupling but the problem remains.
How can I solve this issue?

-DPOSRES refers to posre.itp, I guess. posre.itp was created from the
original pdb before the energy minimization. Should I run pdb2gmx once
again after the EM to create a new posre.itp?

Thanks,

Stefano
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Re: [gmx-users] mdrun seems stuck

2009-06-02 Thread Jussi Lehtola
On Tue, 2009-06-02 at 11:13 +0100, Stefano Meliga wrote:
 The simulation seems just very slow.
 step 0 has appeared on the screen after several minutes and in the log 
 file there's only step zero as well.

You have 43 000 atoms and are using Ewald summation which is O(N^2), so
the simulation really is that slow.

Switch to using coulombtype = PME, that should speed things up.
-- 
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
--


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[gmx-users] segfault(11) -- simulation blows up on first step

2009-06-02 Thread Inon Sharony


Hi everyone! 

I'm trying to run a simulation of a single diatomic Sulfur molecule. When I run 
an equilibration scheme (generating velocities from a 300K Maxwell-Boltzmann 
distribution) it runs fine, but when I take the equilibrated molecule and 
couple one atom to a 0K heat bath (using Stochastic Dynamics) the simulation 
segfaults at the first step. 

I've enclosed as much information as I could. Notice (at the very bottom) that 
the md.log file shows an initial temperature of 17884.7K, but already in the 
report for step 0 the temperature, as well as many other thermodynamic 
quantities, are NaN. 

I've encountered one reference to the same error I'm getting, but itjust said 
that there was some problem with the input files, but didn'tsay what was the 
problem... 

I hope you will find some stupid mistake in the *.mdp file, or something easily 
remedied... 

P.S. 

I know GROMACS is not optimized for simulating tiny molecules, but I don't see 
why it should be such a critical problem... 

A wholotta supplemental data: 

MDRUN_MPI STD-I/O:
==

step 0
[hydrogen:15285] *** Process received signal ***
[hydrogen:15285] Signal: Segmentation fault (11)
[hydrogen:15285] Signal code: Address not mapped (1)
[hydrogen:15285] Failing at address: 0xfffe16c50a90
[hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]
[hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]
[hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]
[hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]
[hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]
[hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]
[hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]
[hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x355b41d8b4]
[hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]
[hydrogen:15285] *** End of error message ***
./test-2-6-09.sh: line 16: 15285 Segmentation fault  mdrun_mpi -c md -v



MD.MDP
==

integrator=sd;stochastic dynamics (velocity Langevin) using a 
leap-frog algorithm
dt=0.0001
nsteps=1; [steps] == total (nsteps*dt) 
ps.
nstxout=1
nstvout=1
nstfout=1
; nstxtcout=1
nstenergy=1; write energies to energy file every 1000 steps 
(default 100)
nstlog=1
energygrps=SLSR
ns_type=simple
periodic_molecules=no
coulombtype=PME
tc-grps=SLSR
tau_t=01; mass/gamma
ref_t=0   0; refference (bath) temperature
Pcoupl=no
gen_vel=no
gen_seed=-1; random seed based on computer clock
constraints=none



1S2.itp
===

[ atomtypes ]
;atomtype m (u) q (e)part.type V(cr)W(cr)
SX32.06000.000A1E-031E-05

[ moleculetype ]
; Name nrexcl
1S2  2

[ atoms ]
;   nrtype  resnr resid  atom  cgnr   charge mass
1  SX 1  1S2 SL 10.000  32.0600
2  SX 1  1S2 SR 20.000  32.0600

[ bonds ]
; ai  aj  fuc0, c1, ...
   1   2   20.2040  5.3E+60.2040  5.3E+6 ;   SL SR



TRAJ.TRR


traj.trr frame 0:
   natoms= 2  step= 0  time=0.000e+00  lambda= 0
   box (3x3):
  box[0]={ 6.37511e+00,  0.0e+00,  0.0e+00}
  box[1]={ 0.0e+00,  6.37511e+00,  0.0e+00}
  box[2]={ 0.0e+00,  0.0e+00,  6.37511e+00}
   x (2x3):
  x[0]={ 3.19756e+00,  3.20532e+00,  3.18725e+00}
  x[1]={ 3.03044e+00,  3.21568e+00,  3.08875e+00}
   v (2x3):
  v[0]={ 2.22763e+00, -2.56083e-01,  1.38905e+00}
  v[1]={-2.22763e+00,  2.56083e-01, -1.38905e+00}
   f (2x3):
  f[0]={ 3.43615e+03, -2.13216e+02,  2.02509e+03}
  f[1]={-3.43615e+03,  2.13216e+02, -2.02509e+03}



MD.LOG
==

Input Parameters:
   integrator   = sd
   nsteps   = 1
   init_step= 0
   ns_type  = Simple
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 1
   comm_mode= Linear
   nstlog   = 1
   nstxout  = 1
   nstvout  = 1
   nstfout  = 1
   nstenergy= 1
   nstxtcout= 0
   init_t   = 0
   delta_t  = 0.0001
   xtcprec  = 1000
   nkx  = 54
   nky  = 54
   nkz  = 54
   pme_order= 4
   ewald_rtol   = 1e-05
   

Re: [gmx-users] segfault(11) -- simulation blows up on first step

2009-06-02 Thread Itamar Kass
Hi,
I don't see any immediate problem in your file, except the fact that you
have to couple all molecule to a heat bath. Second, has much as I know, you
can't reach 0K, so what the meaning?

Best,
Itamar

On Tue, Jun 2, 2009 at 9:11 PM, Inon Sharony inons...@tau.ac.il wrote:

  Hi everyone!

 I'm trying to run a simulation of a single diatomic Sulfur molecule. When I
 run an equilibration scheme (generating velocities from a 300K
 Maxwell-Boltzmann distribution) it runs fine, but when I take the
 equilibrated molecule and couple one atom to a 0K heat bath (using
 Stochastic Dynamics) the simulation segfaults at the first step.

 I've enclosed as much information as I could. Notice (at the very bottom)
 that the md.log file shows an initial temperature of 17884.7K, but already
 in the report for step 0 the temperature, as well as many other
 thermodynamic quantities, are NaN.

 I've encountered one reference to the same error I'm getting, but itjust
 said that there was some problem with the input files, but didn'tsay what
 was the problem...

 I hope you will find some stupid mistake in the *.mdp file, or something
 easily remedied...

 P.S.

 I know GROMACS is not optimized for simulating tiny molecules, but I don't
 see why it should be such a critical problem...


  A wholotta supplemental data:


 MDRUN_MPI STD-I/O:
 ==

 step 0
 [hydrogen:15285] *** Process received signal ***
 [hydrogen:15285] Signal: Segmentation fault (11)
 [hydrogen:15285] Signal code: Address not mapped (1)
 [hydrogen:15285] Failing at address: 0xfffe16c50a90
 [hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]
 [hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]
 [hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]
 [hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]
 [hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]
 [hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]
 [hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]
 [hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4)
 [0x355b41d8b4]
 [hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]
 [hydrogen:15285] *** End of error message ***
 ./test-2-6-09.sh: line 16: 15285 Segmentation fault  mdrun_mpi -c md -v



 

 MD.MDP
 ==

 integrator=sd;stochastic dynamics (velocity Langevin) using a
 leap-frog algorithm
 dt=0.0001
 nsteps=1; [steps] == total
 (nsteps*dt) ps.
 nstxout=1
 nstvout=1
 nstfout=1
 ; nstxtcout=1
 nstenergy=1; write energies to energy file every 1000 steps
 (default 100)
 nstlog=1
 energygrps=SLSR
 ns_type=simple
 periodic_molecules=no
 coulombtype=PME
 tc-grps=SLSR
 tau_t=01; mass/gamma
 ref_t=0   0; refference (bath) temperature
 Pcoupl=no
 gen_vel=no
 gen_seed=-1; random seed based on computer clock
 constraints=none


 

 1S2.itp
 ===

 [ atomtypes ]
 ;atomtype m (u) q (e)part.type V(cr)W(cr)
 SX32.06000.000A1E-031E-05

 [ moleculetype ]
 ; Name nrexcl
 1S2  2

 [ atoms ]
 ;   nrtype  resnr resid  atom  cgnr   charge mass
 1  SX 1  1S2 SL 10.000  32.0600
 2  SX 1  1S2 SR 20.000  32.0600

 [ bonds ]
 ; ai  aj  fuc0, c1, ...
1   2   20.2040  5.3E+60.2040  5.3E+6 ;   SL SR


 

 TRAJ.TRR
 

 traj.trr frame 0:
natoms= 2  step= 0  time=0.000e+00  lambda=
 0
box (3x3):
   box[0]={ 6.37511e+00,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  6.37511e+00,  0.0e+00}
   box[2]={ 0.0e+00,  0.0e+00,  6.37511e+00}
x (2x3):
   x[0]={ 3.19756e+00,  3.20532e+00,  3.18725e+00}
   x[1]={ 3.03044e+00,  3.21568e+00,  3.08875e+00}
v (2x3):
   v[0]={ 2.22763e+00, -2.56083e-01,  1.38905e+00}
   v[1]={-2.22763e+00,  2.56083e-01, -1.38905e+00}
f (2x3):
   f[0]={ 3.43615e+03, -2.13216e+02,  2.02509e+03}
   f[1]={-3.43615e+03,  2.13216e+02, -2.02509e+03}



 

 MD.LOG
 ==



 Input Parameters:
integrator   = sd
nsteps   = 1
init_step= 0
ns_type  = Simple
nstlist  = 10
ndelta   = 2
nstcomm  = 1
comm_mode= Linear
nstlog   = 1
nstxout

[gmx-users] segfault(11) -- simulation blows up on first step

2009-06-02 Thread Inon Sharony


 Sorry for the previous mail, I guess the appended content was too long. 
Anyway, here it is as an attached file 

Sorry, and thanks again

-- 
Inon   Sharony
ינון שרוני
+972(3)6407634
atto.TAU.ac.IL/~inonshar
Please consider your environmental responsibility before printing this e-mail.
MDRUN_MPI STD-I/O:
==

step 0
[hydrogen:15285] *** Process received signal ***
[hydrogen:15285] Signal: Segmentation fault (11)
[hydrogen:15285] Signal code: Address not mapped (1)
[hydrogen:15285] Failing at address: 0xfffe16c50a90
[hydrogen:15285] [ 0] /lib64/libpthread.so.0 [0x355c00de80]
[hydrogen:15285] [ 1] mdrun_mpi(gmx_pme_do+0x28b2) [0x4b56f2]
[hydrogen:15285] [ 2] mdrun_mpi(do_force_lowlevel+0x1023) [0x47f6f3]
[hydrogen:15285] [ 3] mdrun_mpi(do_force+0xe6e) [0x4c99ce]
[hydrogen:15285] [ 4] mdrun_mpi(do_md+0x48f0) [0x42c4a0]
[hydrogen:15285] [ 5] mdrun_mpi(mdrunner+0x831) [0x42d771]
[hydrogen:15285] [ 6] mdrun_mpi(main+0x3c0) [0x42e6a0]
[hydrogen:15285] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x355b41d8b4]
[hydrogen:15285] [ 8] mdrun_mpi [0x4131a9]
[hydrogen:15285] *** End of error message ***
./test-2-6-09.sh: line 16: 15285 Segmentation fault  mdrun_mpi -c md -v




MD.MDP
==

integrator  =   sd  ;stochastic dynamics (velocity Langevin) using 
a leap-frog algorithm
dt  =   0.0001
nsteps  =   1   ; 
[steps] == total (nsteps*dt) ps.
nstxout =   1
nstvout =   1
nstfout =   1
; nstxtcout =   1
nstenergy   =   1   ; write energies to energy file every 1000 
steps (default 100)
nstlog  =   1
energygrps  =   SL  SR
ns_type =   simple
periodic_molecules  =   no
coulombtype =   PME
tc-grps =   SL  SR
tau_t   =   0   1   ; mass/gamma
ref_t   =   0   0   ; refference (bath) temperature
Pcoupl  =   no
gen_vel =   no
gen_seed=   -1  ; random seed based on computer clock
constraints =   none



1S2.itp
===

[ atomtypes ]
;atomtype   m (u)   q (e)   part.type   V(cr)   W(cr)
SX  32.0600 0.000   A   1E-03   1E-05

[ moleculetype ]
; Name nrexcl
1S2  2

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
1  SX 1  1S2 SL 10.000  32.0600
2  SX 1  1S2 SR 20.000  32.0600

[ bonds ]
; ai  aj  fuc0, c1, ...
   1   2   20.2040  5.3E+60.2040  5.3E+6 ;   SL SR



TRAJ.TRR


traj.trr frame 0:
   natoms= 2  step= 0  time=0.000e+00  lambda= 0
   box (3x3):
  box[0]={ 6.37511e+00,  0.0e+00,  0.0e+00}
  box[1]={ 0.0e+00,  6.37511e+00,  0.0e+00}
  box[2]={ 0.0e+00,  0.0e+00,  6.37511e+00}
   x (2x3):
  x[0]={ 3.19756e+00,  3.20532e+00,  3.18725e+00}
  x[1]={ 3.03044e+00,  3.21568e+00,  3.08875e+00}
   v (2x3):
  v[0]={ 2.22763e+00, -2.56083e-01,  1.38905e+00}
  v[1]={-2.22763e+00,  2.56083e-01, -1.38905e+00}
   f (2x3):
  f[0]={ 3.43615e+03, -2.13216e+02,  2.02509e+03}
  f[1]={-3.43615e+03,  2.13216e+02, -2.02509e+03}




MD.LOG
==



Input Parameters:
   integrator   = sd
   nsteps   = 1
   init_step= 0
   ns_type  = Simple
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 1
   comm_mode= Linear
   nstlog   = 1
   nstxout  = 1
   nstvout  = 1
   nstfout  = 1
   nstenergy= 1
   nstxtcout= 0
   init_t   = 0
   delta_t  = 0.0001
   xtcprec  = 1000
   nkx  = 54
   nky  = 54
   nkz  = 54
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = No
   epc  = No
   epctype  = Isotropic
   tau_p= 1
   ref_p (3x3):
  ref_p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress (3x3):
  compress[0]={ 0.0e+00,  

Re: [gmx-users] segfault(11) -- simulation blows up on first step

2009-06-02 Thread Justin A. Lemkul



Inon Sharony wrote:



Hi everyone!

I'm trying to run a simulation of a single diatomic Sulfur molecule. 
When I run an equilibration scheme (generating velocities from a 300K 
Maxwell-Boltzmann distribution) it runs fine, but when I take the 
equilibrated molecule and couple one atom to a 0K heat bath (using 
Stochastic Dynamics) the simulation segfaults at the first step.


I've enclosed as much information as I could. Notice (at the very 
bottom) that the md.log file shows an initial temperature of 17884.7K, 
but already in the report for step 0 the temperature, as well as many 
other thermodynamic quantities, are NaN.


I've encountered one reference to the same error I'm getting, but itjust 
said that there was some problem with the input files, but didn'tsay 
what was the problem...


I hope you will find some stupid mistake in the *.mdp file, or something 
easily remedied...


P.S.

I know GROMACS is not optimized for simulating tiny molecules, but I 
don't see why it should be such a critical problem...



A wholotta supplemental data:


snip


tau_t=01; mass/gamma


tau_t for the sd integrator is given in ps^-1; therefore a value of zero could 
be causing the sd integrator to use some sort of infinite friction coefficient.


If you are trying to use tau_t = 0 to turn off temperature coupling, it may not 
work with sd (not sure), or it could be causing some physically unrealistic 
condition.  Why would two bonded atoms experience different temperatures or 
coupling/lack thereof?


-Justin


ref_t=0   0; refference (bath) temperature
Pcoupl=no
gen_vel=no
gen_seed=-1; random seed based on computer clock
constraints=none



1S2.itp
===

[ atomtypes ]
;atomtype m (u) q (e)part.type V(cr)W(cr)
SX32.06000.000A1E-031E-05

[ moleculetype ]
; Name nrexcl
1S2  2

[ atoms ]
;   nrtype  resnr resid  atom  cgnr   charge mass
1  SX 1  1S2 SL 10.000  32.0600
2  SX 1  1S2 SR 20.000  32.0600

[ bonds ]
; ai  aj  fuc0, c1, ...
   1   2   20.2040  5.3E+60.2040  5.3E+6 ;   SL SR



TRAJ.TRR


traj.trr frame 0:
   natoms= 2  step= 0  time=0.000e+00  lambda= 0
   box (3x3):
  box[0]={ 6.37511e+00,  0.0e+00,  0.0e+00}
  box[1]={ 0.0e+00,  6.37511e+00,  0.0e+00}
  box[2]={ 0.0e+00,  0.0e+00,  6.37511e+00}
   x (2x3):
  x[0]={ 3.19756e+00,  3.20532e+00,  3.18725e+00}
  x[1]={ 3.03044e+00,  3.21568e+00,  3.08875e+00}
   v (2x3):
  v[0]={ 2.22763e+00, -2.56083e-01,  1.38905e+00}
  v[1]={-2.22763e+00,  2.56083e-01, -1.38905e+00}
   f (2x3):
  f[0]={ 3.43615e+03, -2.13216e+02,  2.02509e+03}
  f[1]={-3.43615e+03,  2.13216e+02, -2.02509e+03}




MD.LOG
==



Input Parameters:
   integrator   = sd
   nsteps   = 1
   init_step= 0
   ns_type  = Simple
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 1
   comm_mode= Linear
   nstlog   = 1
   nstxout  = 1
   nstvout  = 1
   nstfout  = 1
   nstenergy= 1
   nstxtcout= 0
   init_t   = 0
   delta_t  = 0.0001
   xtcprec  = 1000
   nkx  = 54
   nky  = 54
   nkz  = 54
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = No
   epc  = No
   epctype  = Isotropic
   tau_p= 1
   ref_p (3x3):
  ref_p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress (3x3):
  compress[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord_scaling = No
   posres_com (3):
  posres_com[0]= 0.0e+00
  posres_com[1]= 0.0e+00
  posres_com[2]= 0.0e+00
   posres_comB (3):
  posres_comB[0]= 0.0e+00
  posres_comB[1]= 0.0e+00
  posres_comB[2]= 0.0e+00
   andersen_seed= 815131
   rlist= 1
   rtpi = 0.05
   coulombtype 

[gmx-users] problem with generation of .gro file

2009-06-02 Thread subarna thakur
Hello,
I am running the pdb2gmx command for a homodimer protein with SF4 (a 
ferro-sulphur cluster) ligand but it fails to generate the .gro file. A error 
is coming SF4 not found in residue topology database. I have trired all 
the different force fields. Can anybody please tell me how to correct the 
error? How to modify the rtp file to consider the ligand? 

Subarna thakur
University of north bengal


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Re: [gmx-users] problem with generation of .gro file

2009-06-02 Thread Justin A. Lemkul



subarna thakur wrote:

Hello,
I am running the pdb2gmx command for a homodimer protein with SF4 (a 
ferro-sulphur cluster) ligand but it fails to generate the .gro file. A 
error is coming SF4 not found in residue topology database. I have 
trired all the different force fields. Can anybody please tell me how to 
correct the error? How to modify the rtp file to consider the ligand? 
 


Dealing with the error:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

The unfortunate news that you have your work cut out for you:

http://wiki.gromacs.org/index.php/Parameterization
http://wiki.gromacs.org/index.php/Exotic_Species

Parameterization is an advanced topic, especially when dealing with strange 
species like an iron-sulfur cluster.  Read the exotic species article closely.


-Justin


Subarna thakur
University of north bengal


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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Normal of the benzene and z axis.

2009-06-02 Thread Eudes Fileti
Dear gmx users;How can I calculate the angle distribution forthe angle
between the normal of the benzene and z axis?
Bests
eef
___
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Universidade Federal do ABC — CCNH
Av. dos Estados, 5001
Santo André - SP - Brasil
CEP 09210-971
+55.11.4437-0196
http://fileti.ufabc.edu.br
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Re: [gmx-users] crystals of KCl during simulation

2009-06-02 Thread moura
Hi Rebeca,

the paper David suggests is certainly more complete, I just compared OPLS
and Aqvist's parameters for sodium for the specific case of anionic
micelles. anyway, if want to try the Aqvist's parameters take a look
inside ffoplsaa.atp file (opls_408 for K+).

best regards,

André

 Rebeca García Fandiño wrote:

  Thank you very much, André. Could you please indicate me how could
 I use these parameters in Gromacs? I have not seen them included in
 ions.itp and I could not find anything in the manual.
 Best wishes,
 Rebeca.


 I would recommend reading the following paper, even though it only is
 about NaCl it compares the properties of four different parameter sets,
 and IIRC Åqvist's parameters were not so great.

 @Article{ Hess2006c,
author =   B. Hess and C. Holm and N. {van der Vegt},
title =Osmotic coefficients of atomistic NaCl (aq) force
fields,
journal =  J. Chem. Phys.,
year = 2006,
volume =   124,
pages =164509,
abstract = Solvated ions are becoming increasingly important
for (bio)molecular simulations. But there are not
much suitable data to validate the
intermediate-range solution structure that ion-water
force fields produce. We compare six selected
combinations of four biomolecular Na-Cl force fields
and four popular water models by means of effective
ion-ion potentials. First we derive an effective
potential at high dilution from simulations of two
ions in explicit water. At higher ionic
concentration multibody effects will become
important. We propose to capture those by employing
a concentration dependent dielectric
permittivity. With the so obtained effective
potentials we then perform implicit solvent
simulations. We demonstrate that our effective
potentials accurately reproduce ion-ion coordination
numbers and the local structure. They allow us
furthermore to calculate osmotic coefficients that
can be directly compared with experimental data. We
show that the osmotic coefficient is a sensitive and
accurate measure for the effective ion-ion
interactions and the intermediate-range structure of
the solution. It is therefore a suitable and useful
quantity for validating and parametrizing atomistic
ion-water force fields. (c) 2006 American Institute
of Physics. 0021-9606
 }





   Date: Mon, 1 Jun 2009 14:52:35 -0300
   Subject: RE: [gmx-users] crystals of KCl during simulation
   From: mo...@ufscar.br
   To: gmx-users@gromacs.org
  
   Hi Rebeca,
  
   I found out a few years ago that OPLS parameters for Na+ were
 inadequate
   for my simulations on surfactants aggregation due to the formation of
   stable (and unrealistic) ionic bridges. I got better structures using
   Aqvist's parameters (available in GROMACS), maybe you could try these
   parameters for K+ as well.
  
   please let me know if that works.
  
   best regards,
  
   André
  
  
   
Yes, I use PME.
   
Date: Mon, 1 Jun 2009 19:34:27 +0200
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] crystals of KCl during simulation
   
Rebeca García Fandiño wrote:
 Thank you very much for your answer. I have read some recent
literature,
 and you are right, it is a problem about the parameters for ions
 in
Amber.

 I have found this paper:
 Parameters of Monovalent Ions in the Amber-99 Forcefield:
 Assesment of
 Inaccuracies and Proposed Improvements
 http://pubs.acs.org/doi/abs/10.1021/jp0765392

 There, they simulate nucleic acids using a combination of Amber
 and
 OPLS sigma and epsilon for the ions. I have tried that in the
 case of
my
 protein, just changing the ion sigma and epsilon in the topology
 by
 those corresponding to OPLS, but I still observe aggregation for
 the
ions.

 Would this combination of Amber and OPLS have any kind of
 potential
 problem during the simulation? Has anybody any idea to avoid
 this type
 of artefact?
   
Just checking, do you use PME? (You should...)

 Thank you very much in advance,

 Rebeca.

  To: gmx-users@gromacs.org
  Subject: Re: [gmx-users] crystals of KCl during simulation
  Date: Mon, 1 Jun 2009 14:34:55 +0200
  From: baa...@smplinux.de
 
 
  Hi,
 
  rega...@hotmail.com said:
   [..] but after equilibration I have observed that KCl is
 aggregating, like
   if it was making 

Re: [gmx-users] installation

2009-06-02 Thread Mark Abraham

Nuno Azoia wrote:

Hello!

Just like Manik Mayur suggested, the problem should be the links:


Making links may fix the problem of finding executables if that link 
location is already in your path, but it won't fix your other 
environment variables, or perhaps if you used configure --prefix.



Gromacs gives you the possibility to create links to /usr/bin directory
(ot something similar). If you didn't do that, one of the option is
trying to run the programs using the full path. Instead of using
pdb2gmx, try to use /usr/local/gromacs/bin/pdb2gmx. Replace
/usr/local/gromacs with the directory where you install gromacs. If
you didn't choose anything it probably is /usr/local/gromacs.


Call source /path/to/GMXRC, then go do science.

Mark


I hope this can help

Nuno Azoia

On Tue, 2009-06-02 at 12:21 +0530, Samik Bhattacharya wrote:

hi,I
 
i am facing a lot of troubles in installing Gromacs in my Redhat

machine..I've followed all the instructions given in the manual as
well as in the website. ialso have installed fftw,its compiling with
no problem. . but whenever i run pdb2gmx or command lke that its
giving an error command not found. a little help regarding this
matter will be very encouraging. 
thankx

 Shamik



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Re: [gmx-users] Normal of the benzene and z axis.

2009-06-02 Thread Mark Abraham

Eudes Fileti wrote:

Dear gmx users;
How can I calculate the angle distribution for
the angle between the normal of the benzene and z axis?


The function of various tools are discussed in section 8 of the manual. 
The clue you seek is there.


Mark
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[gmx-users] gromacs invsqrt() overlaps with icc invsqrt()

2009-06-02 Thread chris . neale

Hello,

I have just compiled gromacs 4.0.4 using the intel compiler. While I  
believe that gromacs itself doesn't get a huge benefit from icc, fftw  
certainly does and it's on the order of a 10% speedup, which is  
significant enough for me to dedicate some time to getting this working.


Problem is, invsqrt is defined both in gromacs and in the icc  
libraries, as is already known:

http://www.gromacs.org/pipermail/gmx-users/2006-June/022009.html

../../../include/vec.h(152): warning #147: declaration is incompatible  
with double invsqrt(double) (declared at line 635 of  
/opt/sharcnet/intel/11.0.083/icc/include/math.h)

  static inline real invsqrt(real x)

I have solved this problem by the following procedure:

#
#!/bin/bash
for i in `find ./gromacs-4.0.4`; do
  sed 's/invsqrt/invSAFEsqrt/g' $i  tmp;
  mv tmp $i;
done
chmod +x ./gromacs-4.0.4/configure
mv ./gromacs-4.0.4/src/gmxlib/cinvsqrtdata.c  
./gromacs-4.0.4/src/gmxlib/cinvSAFEsqrtdata.c

#

And it now compiles without warning.

I was unable to link an icc-compiled fftw to a PGI or gcc compilation  
of gromacs, due to linking problems, although I imagine that that is  
possible.


First, does anybody see any immediate problems with this?

Second, is there still a motivation to get rid of this problem?

Third, does anybody know how I can link an icc-compiled fftw to a PGI  
or gcc compilation of gromacs, and if there is any reason that this is  
a bad idea?


Thanks,
Chris.

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[gmx-users] g_dist

2009-06-02 Thread gmx-users-bounces

Dear Gromacs Users,

I need to extract all possible distances between any two atom pairs of  
a small hexa- to dodecamer from a trajectory.
The same is necessary for all dihedral angles of this protein. Now I  
wonder if this is possible without defining all of them manually in  
the ndx file and call g_dist for each of them ?
Is there a short answer on that ? Maybe I missed the answer to that  
question in the forum ?!


greetings,
joern


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Re: [gmx-users] gromacs invsqrt() overlaps with icc invsqrt()

2009-06-02 Thread Mark Abraham

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

Hello,

I have just compiled gromacs 4.0.4 using the intel compiler. While I 
believe that gromacs itself doesn't get a huge benefit from icc, fftw 
certainly does and it's on the order of a 10% speedup, which is 
significant enough for me to dedicate some time to getting this working.


Problem is, invsqrt is defined both in gromacs and in the icc libraries, 
as is already known:

http://www.gromacs.org/pipermail/gmx-users/2006-June/022009.html

../../../include/vec.h(152): warning #147: declaration is incompatible 
with double invsqrt(double) (declared at line 635 of 
/opt/sharcnet/intel/11.0.083/icc/include/math.h)

  static inline real invsqrt(real x)

I have solved this problem by the following procedure:

#
#!/bin/bash
for i in `find ./gromacs-4.0.4`; do
  sed 's/invsqrt/invSAFEsqrt/g' $i  tmp;
  mv tmp $i;
done
chmod +x ./gromacs-4.0.4/configure


Using sed -i is a bit more elegant and keeps the permissions, IIRC.

mv ./gromacs-4.0.4/src/gmxlib/cinvsqrtdata.c 
./gromacs-4.0.4/src/gmxlib/cinvSAFEsqrtdata.c

#

And it now compiles without warning.

I was unable to link an icc-compiled fftw to a PGI or gcc compilation of 
gromacs, due to linking problems, although I imagine that that is possible.


First, does anybody see any immediate problems with this?


Looks OK.


Second, is there still a motivation to get rid of this problem?


It seems reasonable to get the GROMACS function out of the standard 
namespace, or to test for and use a library function with configure.


Third, does anybody know how I can link an icc-compiled fftw to a PGI or 
gcc compilation of gromacs, and if there is any reason that this is a 
bad idea?


I would have expected it to just work, however I have had multiple 
inexplicable problems with various icc versions on IA64 hardware.


Mark
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Re: [gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories

2009-06-02 Thread Oliver Stueker
On 6/1/09 11:48 PM, Mark Abraham wrote:
 Jinyao Wang wrote:
 Hi,gmx-users
 I am running a editconf commond like this,
 editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
 but I am getting the following the fatal error:
 Fatal error:
 Library file aminoacids.dat not found in current dir nor in default 
 directories.
 (You can set the directories to search with the GMXLIB path variable)
 How can I solve it?
 
 See
 http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation
 
 Mark

The procedure on that Wiki-Page actually works in (from my personal experience)
only ~90% of the cases:

After I installed Gromacs 4.0.5 on a Cluster in my home-directory, tools like
pdb2gmx kept complaining they couldn't find the topology files, as GMXLIB was
actually not set by GMXRC.

Fortunately adding the line:
export GMXLIB=${GMXDATA}/gromacs/top

just after sourcing GMXRC in my .bashrc, worked for me.

Oliver
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Re: [gmx-users] installation

2009-06-02 Thread Nuno Azoia
On Wed, 2009-06-03 at 00:42 +1000, Mark Abraham wrote:
 Nuno Azoia wrote:
  Hello!
  
  Just like Manik Mayur suggested, the problem should be the links:
 
 Making links may fix the problem of finding executables if that link 
 location is already in your path, but it won't fix your other 
 environment variables, or perhaps if you used configure --prefix.
 
  Gromacs gives you the possibility to create links to /usr/bin directory
  (ot something similar). If you didn't do that, one of the option is
  trying to run the programs using the full path. Instead of using
  pdb2gmx, try to use /usr/local/gromacs/bin/pdb2gmx. Replace
  /usr/local/gromacs with the directory where you install gromacs. If
  you didn't choose anything it probably is /usr/local/gromacs.
 
 Call source /path/to/GMXRC, then go do science.

That's what I love the most in this list, always learning something
interesting.
Thanks.

Nuno Azoia
 
 Mark
 
  I hope this can help
  
  Nuno Azoia
  
  On Tue, 2009-06-02 at 12:21 +0530, Samik Bhattacharya wrote:
  hi,I
   
  i am facing a lot of troubles in installing Gromacs in my Redhat
  machine..I've followed all the instructions given in the manual as
  well as in the website. ialso have installed fftw,its compiling with
  no problem. . but whenever i run pdb2gmx or command lke that its
  giving an error command not found. a little help regarding this
  matter will be very encouraging. 
  thankx
   Shamik
 
 
 
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  Travel Click here!
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[gmx-users] Computer simulation details

2009-06-02 Thread Pramod Akula
Hi everyone,

I would like to run GPCR protein dynamics in lipid bilayer along with
water molecules and ions. As you all know it becomes huge system and
may take very long time to obtain results on ordinary PCs.I would like
to run the above mentioned simulation on my personnel laptop.

Please let me know your best suggestions from experience ,which one
would be the most efficient to do the same, I mean the constitution of
the laptop like GB in RAM, number of cores required, processor clock,
3D graphics compatability, hard disc size and finally the brand.

Your suggestions would be of great help to many.

Regards,

Akula
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RE: [gmx-users] Computer simulation details

2009-06-02 Thread Kukol, Andreas
As you already pointed out, it may take a very long time on ordinary PCs. On a 
laptop it would take even longer ...

Use a Linux workstation with 4 processor cores minimum.

Andreas

 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
 On Behalf Of Pramod Akula
 Sent: 02 June 2009 17:07
 To: gmx-users@gromacs.org
 Subject: [gmx-users] Computer simulation details

 Hi everyone,

 I would like to run GPCR protein dynamics in lipid bilayer along with
 water molecules and ions. As you all know it becomes huge system and
 may take very long time to obtain results on ordinary PCs.I would like
 to run the above mentioned simulation on my personnel laptop.

 Please let me know your best suggestions from experience ,which one
 would be the most efficient to do the same, I mean the constitution of
 the laptop like GB in RAM, number of cores required, processor clock,
 3D graphics compatability, hard disc size and finally the brand.

 Your suggestions would be of great help to many.

 Regards,

 Akula
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RE: [gmx-users] crystals of KCl during simulation

2009-06-02 Thread Rebeca García Fandiño

Thank you very much for your answers. Anyway, if I want to simulate my protein 
with Amber, would it be a big problem to combine parameter from Amber with 
parameters from OPLS for water and/or ions?

 

Best wishes,

 

Rebeca.
 
 Date: Tue, 2 Jun 2009 09:51:12 -0300
 Subject: Re: [gmx-users] crystals of KCl during simulation
 From: mo...@ufscar.br
 To: gmx-users@gromacs.org
 
 Hi Rebeca,
 
 the paper David suggests is certainly more complete, I just compared OPLS
 and Aqvist's parameters for sodium for the specific case of anionic
 micelles. anyway, if want to try the Aqvist's parameters take a look
 inside ffoplsaa.atp file (opls_408 for K+).
 
 best regards,
 
 André
 
  Rebeca García Fandiño wrote:
 
  Thank you very much, André. Could you please indicate me how could
  I use these parameters in Gromacs? I have not seen them included in
  ions.itp and I could not find anything in the manual.
  Best wishes,
  Rebeca.
 
 
  I would recommend reading the following paper, even though it only is
  about NaCl it compares the properties of four different parameter sets,
  and IIRC Åqvist's parameters were not so great.
 
  @Article{ Hess2006c,
  author = B. Hess and C. Holm and N. {van der Vegt},
  title = Osmotic coefficients of atomistic NaCl (aq) force
  fields,
  journal = J. Chem. Phys.,
  year = 2006,
  volume = 124,
  pages = 164509,
  abstract = Solvated ions are becoming increasingly important
  for (bio)molecular simulations. But there are not
  much suitable data to validate the
  intermediate-range solution structure that ion-water
  force fields produce. We compare six selected
  combinations of four biomolecular Na-Cl force fields
  and four popular water models by means of effective
  ion-ion potentials. First we derive an effective
  potential at high dilution from simulations of two
  ions in explicit water. At higher ionic
  concentration multibody effects will become
  important. We propose to capture those by employing
  a concentration dependent dielectric
  permittivity. With the so obtained effective
  potentials we then perform implicit solvent
  simulations. We demonstrate that our effective
  potentials accurately reproduce ion-ion coordination
  numbers and the local structure. They allow us
  furthermore to calculate osmotic coefficients that
  can be directly compared with experimental data. We
  show that the osmotic coefficient is a sensitive and
  accurate measure for the effective ion-ion
  interactions and the intermediate-range structure of
  the solution. It is therefore a suitable and useful
  quantity for validating and parametrizing atomistic
  ion-water force fields. (c) 2006 American Institute
  of Physics. 0021-9606
  }
 
 
 
 
 
   Date: Mon, 1 Jun 2009 14:52:35 -0300
   Subject: RE: [gmx-users] crystals of KCl during simulation
   From: mo...@ufscar.br
   To: gmx-users@gromacs.org
  
   Hi Rebeca,
  
   I found out a few years ago that OPLS parameters for Na+ were
  inadequate
   for my simulations on surfactants aggregation due to the formation of
   stable (and unrealistic) ionic bridges. I got better structures using
   Aqvist's parameters (available in GROMACS), maybe you could try these
   parameters for K+ as well.
  
   please let me know if that works.
  
   best regards,
  
   André
  
  
   
Yes, I use PME.
   
Date: Mon, 1 Jun 2009 19:34:27 +0200
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] crystals of KCl during simulation
   
Rebeca García Fandiño wrote:
 Thank you very much for your answer. I have read some recent
literature,
 and you are right, it is a problem about the parameters for ions
  in
Amber.

 I have found this paper:
 Parameters of Monovalent Ions in the Amber-99 Forcefield:
  Assesment of
 Inaccuracies and Proposed Improvements
 http://pubs.acs.org/doi/abs/10.1021/jp0765392

 There, they simulate nucleic acids using a combination of Amber
  and
 OPLS sigma and epsilon for the ions. I have tried that in the
  case of
my
 protein, just changing the ion sigma and epsilon in the topology
  by
 those corresponding to OPLS, but I still observe aggregation for
  the
ions.

 Would this combination of Amber and OPLS have any kind of
  potential
 problem during the simulation? Has anybody any idea to avoid
  this type
 of artefact?
   
Just checking, do you use PME? (You should...)

 Thank you very much in advance,

 Rebeca.

  To: gmx-users@gromacs.org
  Subject: Re: [gmx-users] crystals of KCl during simulation
  Date: Mon, 1 Jun 2009 14:34:55 +0200
  From: baa...@smplinux.de
 
 
  Hi,
 
  rega...@hotmail.com said:
   [..] but after equilibration I have observed that KCl is
 aggregating, like
   if it was making crystals. When I used NaCl instead KCl,
  this not
   happened.
 
   Does anybody has any idea about the reason of 

[gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

2009-06-02 Thread Shay Amram
Dear GROMACS users,

 

I have been trying to expand a membrane by a non-integer multiplier (for
example X1.5). This can be done using

 

genbox -cs Membrane.gro -o Expanded_membrane.gro -box 1.5X 1.5Y Z

 

This has worked very good with homogenous membranes, and only very short
equilibrium times were required to re-equilibrate the membrane (~10-20ns).

Now I am trying to deal the same way with heterogeneous membrane (POPG/POPE
mixture, Mikko Karttunen et. al). 

 

When trying to invoke the above command to the POPG/POPE membrane I get a
membrane with different compositions of lipids in the upper and lower
leaflets.

This happens (so I suspect) because the arrangement of lipids in each
leaflet is somewhat different so that the molecules that get' to be
multiplied do not conserve the 

same ratio of different lipids as in the original structure (which has ratio
of 1:3 POPG/POPE).

 

Is there a way to multiply the membrane by a non-integer number AND somehow
conserve the ratio of different lipid species too?

Or at the very least, to have both upper and lower leaflets identical after
multiplication? (This, too, would help immensely).

 

Thanks,

-Shay

 

 

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Re: [gmx-users] Resizing heterogeneous membrane (POPG/POPE mixture)

2009-06-02 Thread Justin A. Lemkul



Shay Amram wrote:

Dear GROMACS users,

 

I have been trying to expand a membrane by a non-integer multiplier (for 
example X1.5). This can be done using


 


*genbox -cs Membrane.gro -o Expanded_membrane.gro –box 1.5X 1.5Y Z***

 

This has worked very good with _homogenous_ membranes, and only very 
short equilibrium times were required to re-equilibrate the membrane 
(~10-20ns).


Now I am trying to deal the same way with _heterogeneous_ membrane 
(POPG/POPE mixture, Mikko Karttunen et. al).


 

When trying to invoke the above command to the POPG/POPE membrane I get 
a membrane with different compositions of lipids in the upper and lower 
leaflets.


This happens (so I suspect) because the arrangement of lipids in each 
leaflet is somewhat different so that the molecules that get' to be 
multiplied do not conserve the


same ratio of different lipids as in the original structure (which has 
ratio of 1:3 POPG/POPE).


 


If you have an excess of POPE, you can (either manually, or by using a script) 
randomly choose some POPE to be converted to (or replaced with) POPG by some 
clever means.  This is not a trivial task.




Is there a way to multiply the membrane by a _non-integer_ number AND 
somehow conserve the ratio of different lipid species too?




The output is dependent upon the configuration of the input and the box size, so 
no, there is no straightforward, automatic, way of doing so given the 
constraints of your box dimensions.


Or at the very least, to have both upper and lower leaflets identical 
after multiplication? (This, too, would help immensely).


 


If you can construct a satisfactory monolayer, you can manipulate its 
coordinates (i.e. horizontal flip and translation) to create a bilayer.  You 
would have to do plenty of equilibration after doing so, of course.


-Justin



Thanks,

-Shay

 

 





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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Re: [gmx-developers] Fwd: Simulating Gases with GROMACS 4.0

2009-06-02 Thread Justin A. Lemkul


This message is better discussed on the gmx-users list, since it is not 
pertinent to development.  I have CC'ed gmx-users@gromacs.org, and further 
discussion belongs there.


PRADEEP VENKATARAMAN wrote:



-- Forwarded message --
From: *PRADEEP VENKATARAMAN* pvtul...@gmail.com 
mailto:pvtul...@gmail.com

Date: Tue, Jun 2, 2009 at 5:37 PM
Subject: Simulating Gases with GROMACS 4.0
To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org


Hi

I am trying to simulate all atom methane gas (no solvent) at 1 bar and 
300 K.


I minimized 300 methane molecules in 25X25X25 ang^3 box.



Then I doubt you are in the gas phase.  Just because you don't have solvent 
(i.e., water) does not mean you have a gas.  This box is probably too small to 
properly describe a gaseous system, which is mostly empty space.


When I try running at NPT simulation using the following pressure 
coupling parameters,


Pcoupl =   parrinello-rahman
Pcoupltype   =   isotropic
tau_p   =   2.0
compressibility =   9.9e-1
ref_p   =   1.0



Posting the rest of your .mdp file is more useful.  Snippets like this hide the 
possibility that you've done something else wrong.



I encounter the following error. Please help

==
Step 16271, time 32.542 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001545, max 0.019029 (between atoms 556 and 557)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
556560   55.30.1113   0.1072  0.1092
556557   50.90.1114   0.1071  0.1092

---
Program mdrun_mpi, VERSION 4.0.5
Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (1001)
If you know what you are doing you can adjust the lincs warning 
threshold in your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem




This issue is reported frequently in the case of an unstable system, i.e.:

http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings
http://wiki.gromacs.org/index.php/blowing_up

If you want any more useful advice, you'll have to describe:

1. Your parameters (force field)
2. The full .mdp file
3. Your preparation steps (minimization, equilibration)

-Justin


Thanks,

Pradeep




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] crystals of KCl during simulation

2009-06-02 Thread Mark Abraham

Rebeca García Fandiño wrote:
Thank you very much for your answers. Anyway, if I want to simulate 
my protein with Amber, would it be a big problem to combine parameter 
from Amber with parameters from OPLS for water and/or ions?


Parameters for water might well be the same. Generally speaking, mixing 
forcefields is a bad idea. See 
http://wiki.gromacs.org/index.php/Parameterization. You might survive 
borrowing an ion, but check the literature thoroughly for any reports of 
suitable ions, and/or reconsider your force field choice.


Mark


  Date: Tue, 2 Jun 2009 09:51:12 -0300
  Subject: Re: [gmx-users] crystals of KCl during simulation
  From: mo...@ufscar.br
  To: gmx-users@gromacs.org
 
  Hi Rebeca,
 
  the paper David suggests is certainly more complete, I just compared OPLS
  and Aqvist's parameters for sodium for the specific case of anionic
  micelles. anyway, if want to try the Aqvist's parameters take a look
  inside ffoplsaa.atp file (opls_408 for K+).
 
  best regards,
 
  André
 
   Rebeca García Fandiño wrote:
  
   Thank you very much, André. Could you please indicate me how could
   I use these parameters in Gromacs? I have not seen them included in
   ions.itp and I could not find anything in the manual.
   Best wishes,
   Rebeca.
  
  
   I would recommend reading the following paper, even though it only is
   about NaCl it compares the properties of four different parameter sets,
   and IIRC Åqvist's parameters were not so great.
  
   @Article{ Hess2006c,
   author = B. Hess and C. Holm and N. {van der Vegt},
   title = Osmotic coefficients of atomistic NaCl (aq) force
   fields,
   journal = J. Chem. Phys.,
   year = 2006,
   volume = 124,
   pages = 164509,
   abstract = Solvated ions are becoming increasingly important
   for (bio)molecular simulations. But there are not
   much suitable data to validate the
   intermediate-range solution structure that ion-water
   force fields produce. We compare six selected
   combinations of four biomolecular Na-Cl force fields
   and four popular water models by means of effective
   ion-ion potentials. First we derive an effective
   potential at high dilution from simulations of two
   ions in explicit water. At higher ionic
   concentration multibody effects will become
   important. We propose to capture those by employing
   a concentration dependent dielectric
   permittivity. With the so obtained effective
   potentials we then perform implicit solvent
   simulations. We demonstrate that our effective
   potentials accurately reproduce ion-ion coordination
   numbers and the local structure. They allow us
   furthermore to calculate osmotic coefficients that
   can be directly compared with experimental data. We
   show that the osmotic coefficient is a sensitive and
   accurate measure for the effective ion-ion
   interactions and the intermediate-range structure of
   the solution. It is therefore a suitable and useful
   quantity for validating and parametrizing atomistic
   ion-water force fields. (c) 2006 American Institute
   of Physics. 0021-9606
   }
  
  
  
  
  
Date: Mon, 1 Jun 2009 14:52:35 -0300
Subject: RE: [gmx-users] crystals of KCl during simulation
From: mo...@ufscar.br
To: gmx-users@gromacs.org
   
Hi Rebeca,
   
I found out a few years ago that OPLS parameters for Na+ were
   inadequate
for my simulations on surfactants aggregation due to the 
formation of
stable (and unrealistic) ionic bridges. I got better structures 
using
Aqvist's parameters (available in GROMACS), maybe you could try 
these

parameters for K+ as well.
   
please let me know if that works.
   
best regards,
   
André
   
   

 Yes, I use PME.

 Date: Mon, 1 Jun 2009 19:34:27 +0200
 From: sp...@xray.bmc.uu.se
 To: gmx-users@gromacs.org
 Subject: Re: [gmx-users] crystals of KCl during simulation

 Rebeca García Fandiño wrote:
  Thank you very much for your answer. I have read some recent
 literature,
  and you are right, it is a problem about the parameters for 
ions

   in
 Amber.
 
  I have found this paper:
  Parameters of Monovalent Ions in the Amber-99 Forcefield:
   Assesment of
  Inaccuracies and Proposed Improvements
  http://pubs.acs.org/doi/abs/10.1021/jp0765392
 
  There, they simulate nucleic acids using a combination of Amber
   and
  OPLS sigma and epsilon for the ions. I have tried that in the
   case of
 my
  protein, just changing the ion sigma and epsilon in the 
topology

   by
  those corresponding to OPLS, but I still observe 
aggregation for

   the
 ions.
 
  Would this combination of Amber and OPLS have any kind of
   potential
  problem during the simulation? Has anybody any idea to avoid
   this type
  of artefact?

 Just checking, do you use PME? (You should...)
 
  Thank you very much in advance,
 
  Rebeca.
 
   To: 

Re: [gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories

2009-06-02 Thread Mark Abraham
Oliver Stueker wrote:
 On 6/1/09 11:48 PM, Mark Abraham wrote:
 Jinyao Wang wrote:
 Hi,gmx-users
 I am running a editconf commond like this,
 editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
 but I am getting the following the fatal error:
 Fatal error:
 Library file aminoacids.dat not found in current dir nor in default 
 directories.
 (You can set the directories to search with the GMXLIB path variable)
 How can I solve it?
 See
 http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation

 Mark
 
 The procedure on that Wiki-Page actually works in (from my personal 
 experience)
 only ~90% of the cases:
 
 After I installed Gromacs 4.0.5 on a Cluster in my home-directory, tools like
 pdb2gmx kept complaining they couldn't find the topology files, as GMXLIB was
 actually not set by GMXRC.
 
 Fortunately adding the line:
 export GMXLIB=${GMXDATA}/gromacs/top
 
 just after sourcing GMXRC in my .bashrc, worked for me.

Sigh, indeed, you're right. I've always overridden GMXLIB by hand to
accommodate some of my foibles. GMXRC not setting GMXLIB seems to defeat
the point.

Mark
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[gmx-users] PME on BlueGene

2009-06-02 Thread Jakob Wohlert
Hi,

I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the
configuration options from the wiki I have succeeded insofar that I have a
working program as long as I don't use PME.

I have tried many different variants of fftw - 2.1.5, 3.2.1, single
precision, double precision, different compiler optimizations and so on,
but it all ends the same: mdrun getting stuck somewhere in the
initialization process.

However, by using the built in fft library FFTPACK instead of FFTW, PME
will work, but that is not really an alternative.

In at least a few cases I have been able to pinpoint the location where it
hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls
MPI_Sendrecv, but then nothing else happens as far as I can tell.

I'm confused and I have sort of ran out of ideas right now. Has anyone
else encountered a problem like this, or has anyone any suggestions how to
proceed from here?

Thanks,
Jakob Wohlert



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Re: [gmx-users] PME on BlueGene

2009-06-02 Thread Mark Abraham

Jakob Wohlert wrote:

Hi,

I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the
configuration options from the wiki I have succeeded insofar that I have a
working program as long as I don't use PME.

I have tried many different variants of fftw - 2.1.5, 3.2.1, single
precision, double precision, different compiler optimizations and so on,
but it all ends the same: mdrun getting stuck somewhere in the
initialization process.

However, by using the built in fft library FFTPACK instead of FFTW, PME
will work, but that is not really an alternative.

In at least a few cases I have been able to pinpoint the location where it
hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls
MPI_Sendrecv, but then nothing else happens as far as I can tell.

I'm confused and I have sort of ran out of ideas right now. Has anyone
else encountered a problem like this, or has anyone any suggestions how to
proceed from here?


That looks to me like the separate PME nodes are dying through some 
linking problem and the problem is only manifest on node 0 when its 
sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when 
all the nodes die at the first point they refer to a symbol in the FFT 
library.


Otherwise, looking at warnings/errors from the linker will be required. 
Are you compiling an FFT library version for the back end, or the front end?


Mark
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RE: [gmx-users] PME on BlueGene

2009-06-02 Thread He, Yang


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Tuesday, June 02, 2009 7:55 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] PME on BlueGene

Jakob Wohlert wrote:
 Hi,

 I'm trying to compile Gromacs 4.0.4 for BlueGene/P, and using the
 configuration options from the wiki I have succeeded insofar that I have a
 working program as long as I don't use PME.

 I have tried many different variants of fftw - 2.1.5, 3.2.1, single
 precision, double precision, different compiler optimizations and so on,
 but it all ends the same: mdrun getting stuck somewhere in the
 initialization process.

 However, by using the built in fft library FFTPACK instead of FFTW, PME
 will work, but that is not really an alternative.

 In at least a few cases I have been able to pinpoint the location where it
 hangs - it's in pme.c, subroutine pme_dd_sendrecv. The program calls
 MPI_Sendrecv, but then nothing else happens as far as I can tell.

 I'm confused and I have sort of ran out of ideas right now. Has anyone
 else encountered a problem like this, or has anyone any suggestions how to
 proceed from here?

That looks to me like the separate PME nodes are dying through some
linking problem and the problem is only manifest on node 0 when its
sendrecv doesn't complete. Forcing mdrun -npme 0 may confirm this when
all the nodes die at the first point they refer to a symbol in the FFT
library.

Otherwise, looking at warnings/errors from the linker will be required.
Are you compiling an FFT library version for the back end, or the front end?

Mark
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[gmx-users] problem in equilibration step

2009-06-02 Thread nitu sharma
Dear all,

 I am doing simulation of membrane protein for this I am
following justin's tutorial  In the first equilibration step i am getting
error like this-
---
Program mdrun, VERSION 4.0.3
Source code file: trnio.c, line: 252

File input/output error:
Cannot write trajectory frame; maybe you are out of quota?

Can anyone have idea to solve this problem? If have please let me know.

My command line like this-

mdrun -v -s nvt.tpr -o new_seq-nvt.trr -c new_seq-nvt.gro -e
newe_seq-nvt.edr -g new_seq-nvt.log.

My nvt.mdp file is below-

title   = NVT equilibration for TAP-DMPC
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 25000 ; 2 * 25000 = 50 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrai
ned
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist   = 1 ; short-range neighborlist cutoff (in nm)
rcoulomb= 1 ; short-range electrostatic cutoff (in nm)
rvdw= 1.2   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = cut-off   ; coulombtype cut-off
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein DMPC SOL_NA+  ; three coupling groups - more
accurat
e
tau_t   = 0.1   0.1 0.1 ; time constant, in ps
ref_t   = 323   323 323 ; reference temperature, one for
each
group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 323   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed

Thanks a lot in advance.

Nitu sharma
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Re: [gmx-users] problem in equilibration step

2009-06-02 Thread Mark Abraham

nitu sharma wrote:

Dear all,

 I am doing simulation of membrane protein for this 
I am following justin's tutorial  In the first equilibration step i am 
getting error like this-

---
Program mdrun, VERSION 4.0.3
Source code file: trnio.c, line: 252

File input/output error:
Cannot write trajectory frame; maybe you are out of quota?


So did you check how much disk space you have left?

Mark
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[gmx-users] Problem in fianl step of MD

2009-06-02 Thread rituraj purohit
Hi ..
I am using gromacs 4.0 for simulating a protein molecule. i am getting
following problem during md run[md.mdp  dt =0.002 ; ps ! nsteps = 10
; total 200.0 ps ]

t = 47.530 ps: Water molecule starting at atom 46763 can not be settled.
Check for bad contacts and/or reduce the timestep.

What should i have to do ? please help me..

Rituraj
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Re: [gmx-users] Problem in fianl step of MD

2009-06-02 Thread Mark Abraham

rituraj purohit wrote:

Hi ..
I am using gromacs 4.0 for simulating a protein molecule. i am getting 
following problem during md run[md.mdp  dt =0.002 ; ps ! nsteps = 
10 ; total 200.0 ps ]


t = 47.530 ps: Water molecule starting at atom 46763 can not be settled.
Check for bad contacts and/or reduce the timestep.

What should i have to do ? please help me..


Upgrade to a recent release of GROMACS, and check out 
http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings


Mark
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