Re: [gmx-users] resolved pdm2gmx

[Mark Abraham]

- Original Message -
From: ahmet yıldırım 
Date: Tuesday, October 5, 2010 17:41
Subject: Re: [gmx-users] resolved pdm2gmx
To: Discussion list for GROMACS users 

> Dear Dr. Abraham,
> 
> I have been trying to install gromacs-4.5.1 for a week but I could not it.  I 
> review the installation instructions step by step, but I failed again.
 > 
> 1. I installed fftw-3.2.2 as following
> > a...@ab-desktop:~/Masaüstü/ cd fftw-3.2.2
> a...@ab-desktop:~/Masaüstü/fftw-3.2.2
> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 ./configure --enable-threads 
> --enable-float
> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make
> a...@ab-desktop:~/Masaüstü/fftw-3.2.2 make install
> In this way, Gromacs-4.5.1 installed /usr/local/gromacs directory-(I have 
> root permissions to write there)
 
> 2. I installedgromacs-4.5.1 as folowing   
>   > a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 
> ./configure 
> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 make
> a...@ab-desktop:~/Masaüstü/gromacs-4.5.1 sudo make install

> In this way, FFTW-3.2.2 installed /usr/local/include and  /usr/local/bin 
> directories--(I have root permissions to write there)
 > 
> You said:
> This set of instructions will not use the above FFTW in GROMACS. The  
> configure command is inappropriate. Please see the installation guide  for 
> the proper approach.
> Can you tell me my mistake?

You need (at least) "configure --with-fft=fftw3" and a suitably configured 
environment. See 
http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions

Mark

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Re: [gmx-users] Water molecule starting at atom x can not be settled - minimization step

[Trang]

I checked the initial coordinate file for overlapping atoms, but nothing
found.
I checked the step*.pdb file written after each crash but did not really
understand those coordinates, for the problematic molecules have MORE THAN 1
positions in those files. what does that mean?

I tried to reproduce the error on another computer, and it could be
reproduced.

I think I should check the initial coordinate more thoroughly to find all
likely problematic points. Would you please recommend a way for me to do
that check?

Thanks
Trang

On Thu, Sep 30, 2010 at 5:38 PM, Justin A. Lemkul  wrote:

>
>
> Trang wrote:
>
>> Dear gmx-users,
>> I do a minimization run with this mdp:
>> -
>> constraints =  none
>> ;define  =  -DFLEX_SPC
>> integrator  = cg
>> ;nstcgsteep = 300
>> emtol   =  100.0
>> emstep  =  0.005
>> dt  =  0.001; ps !
>> nsteps  =  20  ; total 200 ps.
>> nstcomm =  100
>> nstxout =  1
>> nstvout =  0
>> nstfout =  0
>> nstlog  =  1
>> nstenergy   =  1000
>> nstlist =  10
>> ns_type =  grid
>> rlist   =  1.0
>> rcoulomb=  1.0
>> rvdw=  1.0
>> coulombtype =  PME ; Reaction-Field
>> fourierspacing  =  0.12
>> pme_order   =  4
>> optimize_fft=  yes
>> ;epsilon_r   =  1.0
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl  =  berendsen
>> tc-grps =  Protein  SOL
>> tau_t   =  0.010.01
>> ref_t   =  310 310
>> ; Energy monitoring
>> energygrps  =  Protein SOL
>> ; Isotropic pressure coupling is now on
>> Pcoupl  = berendsen
>> Pcoupltype  = isotropic
>> tau_p   =  0.25
>> compressibility =  5.4e-5
>> ref_p   =  1.0
>> ; Generate velocites is off at 300 K.
>> gen_vel =  no
>> ;gen_temp=  300.0
>> ;gen_seed=  749261
>>
>> ---
>> and get the error, output like this:
>>
>> Polak-Ribiere Conjugate Gradients:
>>   Tolerance (Fmax)   =  1.0e+02
>>   Number of steps=   20
>>   F-max =  4.69437e+04 on atom 2513
>>   F-Norm=  1.05294e+03
>>
>>
>> step -1: Water molecule starting at atom 43372 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>>
>> ...
>>
>> Fatal error:
>> 1 particles communicated to PME node 4 are more than 2/3 times the cut-off
>> out of the domain decomposition cell of their charge group in dimension y.
>> This usually means that your system is not well equilibrated.
>> --
>>
>> I did a successful run with another equivalent system (same protein
>> sequence, same number of atoms), even with a LARGER TIMESTEP, 0.002 ps
>> I found a lot of people encounter the same error, but in production run
>> step. And in those cases, they're advised to minimize/equilibrate the system
>> more thoroughly. What can I do to resolve this problem in MINIMIZATION step?
>>
>>
> You likely have some unresolvable atomic clash(es) in your system that
> can't be energy-minimized.  Check your structure around the location of the
> problematic water molecule to see if anything is overlapping.
>
> -Justin
>
>  Many thanks
>> Trang
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/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] Re: [gmx-developers] Simulations on GPU

[Szilárd Páll]

I think this mail belongs to the user's list, CC-d will continue the
discussion there.

--
Szilárd



2010/10/5 Igor Leontyev :
> Dear gmx-developers,
> My first attempt to start GPU-version of gromacs has no success. The reason
> is that grompp turns off setting of electrostatics overriding them by
> coulombtype=Cut-off and rcoulomb=1, which are not currently supported in gpu
> version, despite that in mdp-file coulombtype is set to "PME" and
> rcoulomb=1.2. See the log-file bellow. Any suggestions?
>
> 1) Here a precompiled mdrun-gpu binary from the distributed archive
> "gromacs-4.5-GPU-beta2_linux-X86_64.tar.gz" was used along with standard
> installation of gromacs version 4.5-beta2. I tried to follow the
> instructions given at
> http://www.gromacs.org/Downloads/Installation_Instructions/Gromacs_on_GPUs
> The output always points to unsupported method of electrostatics
> disregarding the fact that both tried methods (PME and NoCutoff) should be
> supported.
>
> 2) I also tried upper versions of grompp: 4.5-beta3, 4.5-beta4, 4.5 and
> 4.5.1.
> In 4.5-beta3 version grompp does not switch the electrostatics method but
> mdrun-gpu yet generate an error:
>>
>> The requested platform "CUDA" could not be found
>
> While all upper gmx-versions are not compatible with this mdrun-gpu
> executable
>>
>> Fatal error:
>> reading tpx file (CcO_0hcav_3Dch_E242side_OH-_O2-_PM.tpr) version 73 with
>> version 71
>
> Thanks,
> Igor
>
>
>
> The output of gmx4.5-beta2 is
> --
> Log file opened on Mon Oct  4 21:56:10 2010
> Host: powerpc  pid: 30370  nodeid: 0  nnodes:  1
> The Gromacs distribution was built @TMP_TIME@ by
> ros...@mohawk.cbr.su.se [CMAKE] (@TMP_MACHINE@)
>
>                        :-)  G  R  O  M  A  C  S  (-:
>                     GROwing Monsters And Cloning Shrimps
>                       :-)  VERSION 4.5-GPU-beta2  (-:
>
>     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.
> :-)  /home/leontyev/programs/bin/gromacs/gromacs-4.5-beta2/bin/mdrun-gpu (-:
>
>  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               = 100
>  init_step            = 0
>  nstcalcenergy        = 10
>  ns_type              = Simple
>  nstlist              = 0
>  ndelta               = 2
>  nstcomm              = 1003
>  comm_mode            = Linear
>  nstlog               = 10
>  nstxout              = 5000
>  nstvout              = 1000
>  nstfout              = 0
>  nstenergy            = 1000
>  nstxtcout            = 1
>  init_t               = 0
>  delta_t              = 0.001
>  xtcprec              = 1000
>  nkx                  = 0
>  nky                  = 0
>  nkz                  = 0
>  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
>  nsttcouple           = -1
>  epc                  = No
>  epctype              = Isotropic
>  nstpcouple           = -1
>  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

[gmx-users] Re: [gmx-developers] Simulations on GPU

[Szilárd Páll]

Hi,

The beta versions are all outdated, could you please use the latest
source distribution (4.5.1) instead (or git from the
release-4-5-patches branch)?
The instructions are here:
http://www.gromacs.org/gpu#Compiling_and_custom_installation_of_GROMACS-GPU

>> The requested platform "CUDA" could not be found

AFAIR that is generally the sign of a problem with the mismatch
between the CUDA version of the libraries mdrun and openmm are linked
against with.

Let us know if you succeed!

--
Szilárd
>>
>>
>>
>> The output of gmx4.5-beta2 is
>> --
>> Log file opened on Mon Oct  4 21:56:10 2010
>> Host: powerpc  pid: 30370  nodeid: 0  nnodes:  1
>> The Gromacs distribution was built @TMP_TIME@ by
>> ros...@mohawk.cbr.su.se [CMAKE] (@TMP_MACHINE@)
>>
>>                        :-)  G  R  O  M  A  C  S  (-:
>>                     GROwing Monsters And Cloning Shrimps
>>                       :-)  VERSION 4.5-GPU-beta2  (-:
>>
>>     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.
>> :-)  /home/leontyev/programs/bin/gromacs/gromacs-4.5-beta2/bin/mdrun-gpu (-:
>>
>>  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               = 100
>>  init_step            = 0
>>  nstcalcenergy        = 10
>>  ns_type              = Simple
>>  nstlist              = 0
>>  ndelta               = 2
>>  nstcomm              = 1003
>>  comm_mode            = Linear
>>  nstlog               = 10
>>  nstxout              = 5000
>>  nstvout              = 1000
>>  nstfout              = 0
>>  nstenergy            = 1000
>>  nstxtcout            = 1
>>  init_t               = 0
>>  delta_t              = 0.001
>>  xtcprec              = 1000
>>  nkx                  = 0
>>  nky                  = 0
>>  nkz                  = 0
>>  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
>>  nsttcouple           = -1
>>  epc                  = No
>>  epctype              = Isotropic
>>  nstpcouple           = -1
>>  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
>>  rlistlong            = 1
>>  rtpi                 = 0.05
>>  coulombtype          = Cut-off
>>  rcoulomb_switch      = 0
>>  rcoulomb             = 1
>>  vdwtype              = Cut-off
>>  rvdw_switch          = 0
>>  rvdw                 = 1
>>  epsilon_r

Re: [gmx-users] Water molecule starting at atom x can not be settled - minimization step

[Mark Abraham]

- Original Message -
From: Trang 
Date: Tuesday, October 5, 2010 19:12
Subject: Re: [gmx-users] Water molecule starting at atom x can not be settled   
- minimization step
To: Discussion list for GROMACS users 

> I checked the initial coordinate file for overlapping atoms, but nothing 
> found.

Even for the water at atom index 43372?

> I checked the step*.pdb file written after each crash but did not really 
> understand those coordinates, for the problematic molecules have MORE THAN 1 
> positions in those files. what does that mean?

I don't understand your meaning. A molecule can have more than one position, an 
atom can't.
  
> I tried to reproduce the error on another computer, and it could be 
> reproduced.
> 
> I think I should check the initial coordinate more thoroughly to find all 
> likely problematic points. Would you please recommend a way for me to do that 
> check?

Using constraints during EM is not always a great idea, since the point of the 
procedure is to let atoms move according to the forces to relax bad contacts. 
Once the EM completes, the waters will be close to the geometry enforced by the 
constraint, which your first constraint-activated MD step will then enforce. 
Thus, try uncommenting your "define="-DFLEXSPC" line.

Mark

> 
> Thanks
> Trang
> 
> On Thu, Sep 30, 2010 at 5:38 PM, Justin A. Lemkul  wrote:
 > 
 > 
>  Trang wrote:
 >  Dear gmx-users,
>  I do a minimization run with this mdp:
>  -
>  constraints =  none
>  ;define  =  -DFLEX_SPC
>  integrator  = cg
>  ;nstcgsteep = 300
>  emtol   =  100.0
>  emstep  =  0.005
>  dt  =  0.001; ps !
>  nsteps  =  20  ; total 200 ps.
>  nstcomm =  100
>  nstxout =  1
>  nstvout =  0
>  nstfout =  0
>  nstlog  =  1
>  nstenergy   =  1000
>  nstlist =  10
>  ns_type =  grid
>  rlist   =  1.0
>  rcoulomb=  1.0
>  rvdw=  1.0
>  coulombtype =  PME ; Reaction-Field
>  fourierspacing  =  0.12
>  pme_order   =  4
>  optimize_fft=  yes
>  ;epsilon_r   =  1.0
>  ; Berendsen temperature coupling is on in two groups
>  Tcoupl  =  berendsen
>  tc-grps =  Protein  SOL
>  tau_t   =  0.010.01
>  ref_t   =  310 310
>  ; Energy monitoring
>  energygrps  =  Protein SOL
>  ; Isotropic pressure coupling is now on
>  Pcoupl  = berendsen
>  Pcoupltype  = isotropic
>  tau_p   =  0.25
>  compressibility =  5.4e-5
>  ref_p   =  1.0
>  ; Generate velocites is off at 300 K.
>  gen_vel =  no
>  ;gen_temp=  300.0
>  ;gen_seed=  749261
 > 
>  ---
>  and get the error, output like this:
 > 
>  Polak-Ribiere Conjugate Gradients:
> Tolerance (Fmax)   =  1.0e+02
> Number of steps=   20
> F-max =  4.69437e+04 on atom 2513
> F-Norm=  1.05294e+03
 > 
 > 
>  step -1: Water molecule starting at atom 43372 can not be settled.
>  Check for bad contacts and/or reduce the timestep if appropriate.
 > 
>  ...
 > 
>  Fatal error:
>  1 particles communicated to PME node 4 are more than 2/3 times the cut-off 
> out of the domain decomposition cell of their charge group in dimension y.
>  This usually means that your system is not well equilibrated.
>  --
 > 
>  I did a successful run with another equivalent system (same protein 
> sequence, same number of atoms), even with a LARGER TIMESTEP, 0.002 ps
>  I found a lot of people encounter the same error, but in production run 
> step. And in those cases, they're advised to minimize/equilibrate the system 
> more thoroughly. What can I do to resolve this problem in MINIMIZATION step?
  > 
  > 
>  You likely have some unresolvable atomic clash(es) in your system that can't 
> be energy-minimized.  Check your structure around the location of the 
> problematic water molecule to see if anything is overlapping.
 > 
>  -Justin
 > 
 >  Many thanks
>  Trang
 > 
  > 
>  -- 
>  
 > 
>  Justin A. Lemkul
>  Ph.D. Candidate
>  ICTAS Doctoral Scholar
>  MILES-IGERT Trainee
>  Department of Biochemistry
>  Virginia Tech
>  Blacksburg, VA
>  jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 > 
>  
>  -- 
>  gmx-users mailing listgmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at 
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[gmx-users] Reg:Equilibration

[vinothkumar mohanakrishnan]

Hi all

Suppose say i have a box of decane molecules and i want to equilibrate. say
i have all the necessary files to run mdrun. on what basis i say whether my
equilibration is successful r not after the mdrun. what properties i should
measure to know whether my equilibration was successful.

Regards
Vinoth
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Re: [gmx-users] Reg:Equilibration

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:

Hi all

Suppose say i have a box of decane molecules and i want to equilibrate. 
say i have all the necessary files to run mdrun. on what basis i say 
whether my equilibration is successful r not after the mdrun. what 
properties i should measure to know whether my equilibration was successful.




Beyond making sure your ensemble has converged (i.e. temperature and/or 
pressure), I would suggest you do some homework and find out how others judge 
such systems to be stable and reliable.  What do they measure, and why do they 
do it?  Such an exercise is of greater benefit to you than someone spoon-feeding 
you some instructions (for which there may not be a generalized answer).


-Justin


Regards
Vinoth



--


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


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Re: [gmx-users] Reg:Equilibration

[Anil Mhashal]

 To check ur equilibration, just look at the potential energy and find out
the deviation in the energy if the deviation in the energy is within 10%
then ur equilibration is successful...

On 5 October 2010 14:56, vinothkumar mohanakrishnan wrote:

> Hi all
>
> Suppose say i have a box of decane molecules and i want to equilibrate. say
> i have all the necessary files to run mdrun. on what basis i say whether my
> equilibration is successful r not after the mdrun. what properties i should
> measure to know whether my equilibration was successful.
>
> Regards
> Vinoth
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
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Research fellow
Physical Chemistry Division
National Chemical Laboratory
Pune
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Re: [gmx-users] xpm file

[Carla Jamous]

Thank you Justin,

I used an .m2p file to change the properties of my .xpm.
I got an .eps file that I opened with Gimp. In order to visualize this .eps
file, I have to put 200% in Gimp.
But my problem is that my graph is too large, so I can't seem to print it
out.
I really  to print the .eps file, so please is there a way to do it or do I
have to split my trajectory and generate many .eps ?

Thanks,
Carla

On Fri, Oct 1, 2010 at 2:34 PM, Justin A. Lemkul  wrote:

>
>
> Carla Jamous wrote:
>
>> Hi everyone,
>>
>> Please I need some help visualizing an .xpm file.
>> I tried to open my .xpm file (g_hbond matrix) with Gimp but It gives me
>> red lines that I don't understand.
>> So I converted my .xpm file into an .eps file with xpm2ps. When I try to
>> open my .eps file, I get the legend:
>> Hydrogen bonds
>> white=none
>> red=Present
>>
>> And the legend of my axis: x axis=time(ps)
>>  y axis=Hydrogen Bond index
>>
>> But I can't see the values: It means I see that there is an axis but it's
>> a black bold line instead of values of time or number of atoms in hydrogen
>> bonds.
>>
>>
> You're not going to get any numbers in this plot (aside from hydrogen bond
> indices).  The matrix you're trying to plot is an existence matrix, a red
> pixel if the hydrogen bond is present, a white one if none is present.  You
> can map which hydrogen bond is which from the hbond.ndx file.  That is, once
> you get it rendered properly (see below).
>
>
>  Please how can I visualize correctly my matrix?
>>
>>
> You can alter its properties (proportions, x/y spacing) with a .m2p file.
>  There is an example in the online manual.  If the plot is simply a straight
> line, you'll probably want to decrease the x-spacing and increase the
> y-spacing to make it look normal.
>
> -Justin
>
>  Thank you
>>
>> Carla
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] xpm file

[Erik Marklund]

 You can use the m2p file to tune the size of the datapoint in the x- 
and/or y-dimension.


Erik

Carla Jamous skrev 2010-10-05 13.21:


Thank you Justin,

I used an .m2p file to change the properties of my .xpm.
I got an .eps file that I opened with Gimp. In order to visualize this 
.eps file, I have to put 200% in Gimp.
But my problem is that my graph is too large, so I can't seem to print 
it out.
I really  to print the .eps file, so please is there a way to do it or 
do I have to split my trajectory and generate many .eps ?


Thanks,
Carla

On Fri, Oct 1, 2010 at 2:34 PM, Justin A. Lemkul > wrote:




Carla Jamous wrote:

Hi everyone,

Please I need some help visualizing an .xpm file.
I tried to open my .xpm file (g_hbond matrix) with Gimp but It
gives me red lines that I don't understand.
So I converted my .xpm file into an .eps file with xpm2ps.
When I try to open my .eps file, I get the legend:
Hydrogen bonds
white=none
red=Present

And the legend of my axis: x axis=time(ps)
 y axis=Hydrogen Bond
index

But I can't see the values: It means I see that there is an
axis but it's a black bold line instead of values of time or
number of atoms in hydrogen bonds.


You're not going to get any numbers in this plot (aside from
hydrogen bond indices).  The matrix you're trying to plot is an
existence matrix, a red pixel if the hydrogen bond is present, a
white one if none is present.  You can map which hydrogen bond is
which from the hbond.ndx file.  That is, once you get it rendered
properly (see below).


Please how can I visualize correctly my matrix?


You can alter its properties (proportions, x/y spacing) with a
.m2p file.  There is an example in the online manual.  If the plot
is simply a straight line, you'll probably want to decrease the
x-spacing and increase the y-spacing to make it look normal.

-Justin

Thank you

Carla


-- 



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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--
---
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] Reg:Equilibration

[vinothkumar mohanakrishnan]

hi anil

i get the potential energy at the end of the mdrun. if i want to calulate
the deviation with what i should compare and calculate the deviation.can you
be more specific.

Regards
Vinoth

On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal wrote:

>  To check ur equilibration, just look at the potential energy and find out
> the deviation in the energy if the deviation in the energy is within 10%
> then ur equilibration is successful...
>
> On 5 October 2010 14:56, vinothkumar mohanakrishnan wrote:
>
>> Hi all
>>
>> Suppose say i have a box of decane molecules and i want to equilibrate.
>> say i have all the necessary files to run mdrun. on what basis i say whether
>> my equilibration is successful r not after the mdrun. what properties i
>> should measure to know whether my equilibration was successful.
>>
>> Regards
>> Vinoth
>>
>> --
>>
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Anil R.Mhashal
> Research fellow
> Physical Chemistry Division
> National Chemical Laboratory
> Pune
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Reg:Equilibration

[Anil Mhashal]

Just plot a graph of the potential energy with respect to the time and check
the energy fluctuation, it should be less than 10% of the average potential
energy then u can say that ur protein is equilibrated.



On 5 October 2010 17:16, vinothkumar mohanakrishnan wrote:

> hi anil
>
> i get the potential energy at the end of the mdrun. if i want to calulate
> the deviation with what i should compare and calculate the deviation.can you
> be more specific.
>
> Regards
> Vinoth
>
>
> On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal wrote:
>
>>  To check ur equilibration, just look at the potential energy and find out
>> the deviation in the energy if the deviation in the energy is within 10%
>> then ur equilibration is successful...
>>
>> On 5 October 2010 14:56, vinothkumar mohanakrishnan 
>> wrote:
>>
>>> Hi all
>>>
>>> Suppose say i have a box of decane molecules and i want to equilibrate.
>>> say i have all the necessary files to run mdrun. on what basis i say whether
>>> my equilibration is successful r not after the mdrun. what properties i
>>> should measure to know whether my equilibration was successful.
>>>
>>> Regards
>>> Vinoth
>>>
>>> --
>>>
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>> --
>> Anil R.Mhashal
>> Research fellow
>> Physical Chemistry Division
>> National Chemical Laboratory
>> Pune
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
>
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-- 
Anil R.Mhashal
Research fellow
Physical Chemistry Division
National Chemical Laboratory
Pune
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Re: [gmx-users] Reg:Equilibration

[Justin A. Lemkul]

Anil Mhashal wrote:
Just plot a graph of the potential energy with respect to the time and 
check the energy fluctuation, it should be less than 10% of the average 
potential energy then u can say that ur protein is equilibrated.




I would think that, for most systems, a fluctuation of 10% is quite large.  I 
would expect most stable systems to fluctuate less than 1%, if that.  Even then, 
you can judge very little from potential energy alone.  The simulation may be 
stable at that point, but without more analysis, I'd say it is hard to judge how 
equilibrated the system is.  In my experience, the potential energy generally 
converges within a few ps, but other properties may take substantially longer to 
converge.


-Justin

 

On 5 October 2010 17:16, vinothkumar mohanakrishnan > wrote:


hi anil

i get the potential energy at the end of the mdrun. if i want to
calulate the deviation with what i should compare and calculate the
deviation.can you be more specific.

Regards
Vinoth


On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal
mailto:anil2000.2...@gmail.com>> wrote:

 To check ur equilibration, just look at the potential energy
and find out the deviation in the energy if the deviation in the
energy is within 10% then ur equilibration is successful...

On 5 October 2010 14:56, vinothkumar mohanakrishnan
mailto:kmvin...@gmail.com>> wrote:

Hi all

Suppose say i have a box of decane molecules and i want to
equilibrate. say i have all the necessary files to run
mdrun. on what basis i say whether my equilibration is
successful r not after the mdrun. what properties i should
measure to know whether my equilibration was successful.

Regards
Vinoth

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-- 
Anil R.Mhashal

Research fellow
Physical Chemistry Division
National Chemical Laboratory
Pune 



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--
Anil R.Mhashal
Research fellow
Physical Chemistry Division
National Chemical Laboratory
Pune 



--


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


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Re: [gmx-users] Reg:Equilibration

[Mark Abraham]

- Original Message -
From: Anil Mhashal 
Date: Tuesday, October 5, 2010 23:11
Subject: Re: [gmx-users] Reg:Equilibration
To: Discussion list for GROMACS users 

> Just plot a graph of the potential energy with respect to the time and check 
> the energy fluctuation, it should be less than 10% of the average potential 
> energy then u can say that ur protein is equilibrated.

Well, you can suppose that the potential energy is approximately equilibrated, 
but that might not relate to the equilibration of the properties of interest. 
Different observables relax on different time scales.

Mark

> On 5 October 2010 17:16, vinothkumar mohanakrishnan  
> wrote:
>  hi anil
> 
> i get the potential energy at the end of the mdrun. if i want to calulate the 
> deviation with what i should compare and calculate the deviation.can you be 
> more specific.
> 
> Regards
> Vinoth > 
> 
>  On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal  wrote:
>To check ur equilibration, just look at the potential energy and find out 
> the deviation in the energy if the deviation in the energy is within 10% then 
> ur equilibration is successful... 
> 
  > On 5 October 2010 14:56, vinothkumar mohanakrishnan  
wrote:
 > Hi all
> 
> Suppose say i have a box of decane molecules and i want to equilibrate. say i 
> have all the necessary files to run mdrun. on what basis i say whether my 
> equilibration is successful r not after the mdrun. what properties i should 
> measure to know whether my equilibration was successful.
> 
> Regards
> Vinoth
 > 
> --
>  gmx-users mailing listgmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>  www interface or send it to gmx-users-requ...@gromacs.org.
>  Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> > 
> -- 
>   Anil R.Mhashal
> Research fellow Physical Chemistry Division
> National Chemical Laboratory> Pune > 
 > 
> --
>  gmx-users mailing listgmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> 
 > 
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 > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > 
> -- 
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> Research fellow Physical Chemistry Division
> National Chemical Laboratory> Pune > 
 > -- 
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Re: [gmx-users] Reg:Equilibration

[Anil Mhashal]

Yeah... A equilibration can be complish within the ps n we have to make
ensure that the there should not be more fluctuation in the potential energy
in other words it should be stabilize.

On 5 October 2010 17:47, Justin A. Lemkul  wrote:

>
>
> Anil Mhashal wrote:
>
>> Just plot a graph of the potential energy with respect to the time and
>> check the energy fluctuation, it should be less than 10% of the average
>> potential energy then u can say that ur protein is equilibrated.
>>
>>
> I would think that, for most systems, a fluctuation of 10% is quite large.
>  I would expect most stable systems to fluctuate less than 1%, if that.
>  Even then, you can judge very little from potential energy alone.  The
> simulation may be stable at that point, but without more analysis, I'd say
> it is hard to judge how equilibrated the system is.  In my experience, the
> potential energy generally converges within a few ps, but other properties
> may take substantially longer to converge.
>
> -Justin
>
>
>> On 5 October 2010 17:16, vinothkumar mohanakrishnan 
>> > kmvin...@gmail.com>> wrote:
>>
>>hi anil
>>
>>i get the potential energy at the end of the mdrun. if i want to
>>calulate the deviation with what i should compare and calculate the
>>deviation.can you be more specific.
>>
>>Regards
>>Vinoth
>>
>>
>>On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal
>>mailto:anil2000.2...@gmail.com>> wrote:
>>
>> To check ur equilibration, just look at the potential energy
>>and find out the deviation in the energy if the deviation in the
>>energy is within 10% then ur equilibration is successful...
>>
>>On 5 October 2010 14:56, vinothkumar mohanakrishnan
>>mailto:kmvin...@gmail.com>> wrote:
>>
>>Hi all
>>
>>Suppose say i have a box of decane molecules and i want to
>>equilibrate. say i have all the necessary files to run
>>mdrun. on what basis i say whether my equilibration is
>>successful r not after the mdrun. what properties i should
>>measure to know whether my equilibration was successful.
>>
>>Regards
>>Vinoth
>>
>>--
>>
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
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>>
>>
>>
>>-- Anil R.Mhashal
>>Research fellow
>>Physical Chemistry Division
>>National Chemical Laboratory
>>Pune
>>
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>> --
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>> Pune
>>
>
> --
> 
>
> 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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Research fellow
Physical Chemistry

[gmx-users] about COM pulling and g_dist

[chris . neale]

Dear Zhongjin:

1. You have indeed provided more data, but please try to make some  
progress on your own. E.g. you tell me the order of selections into  
g_dist, but you should try reversing the order.


2. Your figures are difficult to interpret -- I only opened Snap5, but  
I don't know what part of your procedure this is from.


3. I'm not going to download 4 separate files, rename them, look at  
them, and try to figure out what they mean. If you want more help,  
please provide good descriptions on all figures and upload them to  
some file storage site where I can look at them online (e.g.  
photobucket, flikr).


Chris.

-- original message --

--- 10?10?5, zhongjin  ???


???: zhongjin 
??: about COM pulling and g_dist
???: gmx-users at gromacs.org
??: 2010?10?5?,??,??9:53
 Dear Chris,
Snap7.jpg shows distance in one umbrella sampling window.
 Zhongjin He




Dear Zhongjin:

First, I see no reason why you would not expect your g_dist values to
be negative. If you want the positive distances, then reverse the
order of the groups as you pass then to g_dist. Also, what type of
values do you get directly out of mdrun and into the pull_x.xvg file?

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

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

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

Chris.

-- original message --

Hi all,
 I have done a simulation about pulling a K+ throug a (9,9)CNT.
The results may be strange.
 The length of the CNT is 1.477nm,the box is 5*5*5nm.I use the
Umbrella Sampling to calculate PMF ,following the tutorial by Justin
A. Lemkul. I have pulled (along Z direction) a K+ (pulling group)frome
one end (reference group ) of the CNT to another end to generate
Configurations for Umbrella Sampling,both ends of CNT were fixed. Then
I use g_dist to calculate the COM distance between K+ and the
reference group,the result is strange,the Z direction component -dz is
negative,it should be positive,because the Z coordinate of K+ is lager
than that of reference in the .xtc output file. I don't know why. the
pulling distance is not larger than half of the box size.the Z
direction component -dz  is also negative in Umbrella Sampling windows.
Then do Umbrella Sampling,the pulling group and reference group is
as in COM pulling step.pull_geometry = distance,pull_rate = 0. The PMF
is negative and not symmetry about the middle of the CNT.I think it is
wrong.May be it is because the dz is negative,or the choice of
reference is not proper, it should be the middle the CNT as the
reference.Anybody could help? Thanks a lot!
; COM PULLING
; Pull type: no, umbrella, constraint or constant_force
pull = umbrella
; Pull geometry: distance, direction, cylinder or position
pull_geometry= distance
; Select components for the pull vector. default: Y Y Y
pull_dim = N N Y
; Cylinder radius for dynamic reaction force groups (nm)
pull_r1  = 1
; Switch from r1 to r0 in case of dynamic reaction force
pull_r0  = 1
pull_constr_tol  = 1e-06
pull_start   = yes
pull_nstxout = 500
pull_nstfout = 500
; Number of pull groups
pull_ngroups = 1
; Group name, weight (default all 1), vector, init, rate (nm/ps),
kJ/(mol*nm^2)
pull_group0  = refer
pull_weights0=
pull_pbcatom0= 0
pull_group1  = K
pull_weights1=
pull_pbcatom1= 0
pull_vec1= 0 0 0
pull_init1   = 0
pull_rate1   = 0.0
pull_k1  = 1000

Zhongjin He








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[gmx-users] g_h2order for 5 sites water

[Mikhail Stukan]

Dear gmx-users,

I have the following problem with g_h2order tool (4.0.7 and 4.5.1 versions). It 
works perfectly fine when I apply it to a box of SPC/E water, but I have 
something really strange if I try to apply it to SW or SWM4-NDP water models 
(both are 5 sited models). In my index file I have a group which looks like

[ Water ]
1  2  3  6  7  8
  11   12   13 

All shell particles (numbers 5,10 etc) and virtual sites (numbers 4, 9, etc) 
are omitted, O,H,H order is correct. But the results I receive are obviously 
wrong. I have order.xvg file which looks like. What is the most strange is that 
the output  is independent on -d option. What am I doing wrong?

# This file was created Tue Oct  5 15:41:30 2010
# by the following command:
# g_h2order4.5.1 -f sw4.gro -n index.ndx -s sw4.tpr -d Z
#
# g_h2order4.5.1 is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@title "Water orientation with respect to normal"
@xaxis  label "box (nm)"
@yaxis  label "mu_x, mu_y, mu_z (D), cosine with normal"
@TYPE xy
   0.000  208.441  234.9236.737 2.596742e-02
   0.101  218.501  194.438   22.236 7.899551e-02
   0.201  242.260  197.469   33.994 1.243817e-01
   0.302  155.735  211.908   46.930 2.177687e-01
   0.402  248.467  214.602   60.764 1.884665e-01
   0.503  203.367  224.841   75.197 2.791217e-01
   0.603  225.723  207.376   88.851 2.910973e-01
   0.704  214.146  223.984  103.027 3.272970e-01
   0.805  233.803  187.219  116.877 3.938356e-01
   0.905  199.563  245.420  129.262 3.936486e-01
   1.006  188.535  196.094  143.064 4.543617e-01
   1.106  212.706  249.064  156.556 4.418467e-01
   1.207  211.675  205.420  171.057 5.094404e-01
   1.308  246.957  186.864  185.596 5.123689e-01
   1.408  207.272  226.950  197.887 5.508973e-01
   1.509  221.945  185.566  211.389 5.808831e-01
   1.609  224.529  218.854  227.235 5.853382e-01
   1.710  196.245  182.504  238.778 6.468648e-01
   1.810  228.958  253.420  253.580 5.898822e-01
   1.911  186.654  181.046  267.176 6.963417e-01
   2.012  220.318  225.659  278.641 6.373896e-01
   2.112  209.207  205.927  294.242 6.980361e-01
   2.213  223.278  232.911  308.723 6.743686e-01
   2.313  189.832  194.477  320.685 7.507596e-01
   2.414  210.459  248.153  335.703 6.921831e-01
   2.514  223.793  207.197  348.529 7.283705e-01
   2.615  198.909  185.450  362.836 7.815984e-01
   2.716  171.940  219.477  376.684 7.800925e-01
   2.816  236.925  218.644  388.275 7.497334e-01
   2.917  240.590  199.067  403.015 7.664154e-01
   3.017  177.790  196.700  416.747 8.174569e-01


Thank you very much in advance,
Mikhail

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[gmx-users] ffamber94 parameters

[Artur Panczakiewicz]

Dear All,

Do you know what is the unit of kb in ffamber94bon.itp file? I need to
add some missing parameters for my system however I have them in
kcal/mol and it seems that ffamber94 uses another units. For example:
b0 kb
C  O2 10.12500   548940.8 ; 7,(1986),230; GLU,ASP
//taken from ffamber94bon.itp
C  O2 1.250656,0 (kcal/mol)  //JCC, 7, 230, 1986

Thank you in advcance for help!

Regards,
Artur
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[gmx-users] Use the TIP4P water model in the gmx2 force field

[kecy_wu]

 Hello, I want to use the tip4p water model in the  gmx2 force field, but 
it seems that it doesn't have the nobond parameter of the OWT4 in the gmx2 
force field ,does it need add by myself?
 
look  forward to your respond. -- 
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RE: [gmx-users] Use the TIP4P water model in the gmx2 force field

[Berk Hess]

I think you don't want to use the gmx2 force field.
It does say "DEPRECATED" without reason.

Berk

Date: Tue, 5 Oct 2010 21:13:46 +0800
From: kecy...@sina.com
To: gmx-users@gromacs.org
Subject: [gmx-users] Use the TIP4P water model in the gmx2 force field 

 Hello, I want to use the tip4p water model in the  gmx2 force field, but it 
seems that it doesn't have the nobond parameter of the OWT4 in the gmx2 force 
field ,does it need add by myself?

 

look  forward to your respond. 

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Re: [gmx-users] ffamber94 parameters

[Mark Abraham]

As one of the early chapters in the GROMACS manual points out, GROMACS always 
uses energy and distance quantities in particular units. The use of kb depends 
on those conventions, so you should look up the relevant formulae for AMBER and 
GROMACS and see how the conversion should work (hint: there's a factor of 2 
involved as well). Or, you could play around with 4.184J/cal and work it out in 
a minute or two :-)

Mark

- Original Message -
From: Artur Panczakiewicz 
Date: Wednesday, October 6, 2010 0:14
Subject: [gmx-users] ffamber94 parameters
To: gmx-users@gromacs.org

> Dear All,
> 
> Do you know what is the unit of kb in ffamber94bon.itp file? I 
> need to
> add some missing parameters for my system however I have them in
> kcal/mol and it seems that ffamber94 uses another units. For example:
> b0 kb
> C  O2 
> 10.12500   548940.8 ; 7,(1986),230; 
> GLU,ASP//taken from ffamber94bon.itp
> C  
> O2 1.250656,0 (kcal/mol)  //JCC, 7, 230, 1986
> 
> Thank you in advcance for help!
> 
> Regards,
> Artur
> -- 
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RE: [gmx-users] ffamber94 parameters

[Berk Hess]

Hi,

Units are listed in the large table in the topology section of the pdf manual.
(hint: the energy unit everywhere in Gromacs is always kJ/mol and length always 
nm)

Berk


> Date: Tue, 5 Oct 2010 15:14:18 +0200
> From: apanczakiew...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] ffamber94 parameters
> 
> Dear All,
> 
> Do you know what is the unit of kb in ffamber94bon.itp file? I need to
> add some missing parameters for my system however I have them in
> kcal/mol and it seems that ffamber94 uses another units. For example:
> b0 kb
> C  O2 10.12500   548940.8 ; 7,(1986),230; GLU,ASP
> //taken from ffamber94bon.itp
> C  O2 1.250656,0 (kcal/mol)  //JCC, 7, 230, 1986
> 
> Thank you in advcance for help!
> 
> Regards,
> Artur
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] DMSO compressibility

[Sebastian Waltz]

Hi all,
can someone tell which compressibility should be used for
DMSO at 300K?

Thanks a lot

Sebastian 
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[gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2

[rashmi]

Hi All,

I want to install Gromacs 4.5.1 version on a cluster system (high
performance computing facility) in our institute. I don't have access to
root and thus, I have to install gromacs in my home directory.

The problem is that, the cluster has CentOS 5.4 as the operating system
and the gcc version is 4.1.2.

Gromacs site says that gcc 4.1.x and above are broken compilers and
gromacs should not be compiled using them.

So I plan to install a compatible version of gcc, for eg. gcc-4.0.4, in my
home directory and then install gromacs 4.5.1 using this compiler. Will
this be ok?

I am asking this question because the new gcc i will install will be
compiled with the so called broken compiler version gcc 4.1.2 (which i
cannot change). Is this the correct way to ensure that i do not compile
gromcas with a broken compiler.

Please do reply. Thanxs in advance.

Rashmi
IIT Bombay




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RE: [gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2

[Berk Hess]

Hi,

We had issues with 4.1 series compilers, but we are not longer sure if there 
really
are issues in 4.1.2 and 4.1.3. I would surely avoid 4.1.0 and 4.1.1.
But we found that one or two issues in Gromacs only showed up with 4.1.2 and 
4.1.3,
but there were problems in Gromacs, not gcc.
So we are not 100% sure, but version 4.5.1 probably works fine with gcc 4.1.2.

Berk

> Date: Tue, 5 Oct 2010 20:03:41 +0530
> From: ras...@chem.iitb.ac.in
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Installation of gromacs on a cluster with gcc version
> 4.1.2
> 
> Hi All,
> 
> I want to install Gromacs 4.5.1 version on a cluster system (high
> performance computing facility) in our institute. I don't have access to
> root and thus, I have to install gromacs in my home directory.
> 
> The problem is that, the cluster has CentOS 5.4 as the operating system
> and the gcc version is 4.1.2.
> 
> Gromacs site says that gcc 4.1.x and above are broken compilers and
> gromacs should not be compiled using them.
> 
> So I plan to install a compatible version of gcc, for eg. gcc-4.0.4, in my
> home directory and then install gromacs 4.5.1 using this compiler. Will
> this be ok?
> 
> I am asking this question because the new gcc i will install will be
> compiled with the so called broken compiler version gcc 4.1.2 (which i
> cannot change). Is this the correct way to ensure that i do not compile
> gromcas with a broken compiler.
> 
> Please do reply. Thanxs in advance.
> 
> Rashmi
> IIT Bombay
> 
> 
> 
> 
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Re: [gmx-users] Installation of gromacs on a cluster with gcc version 4.1.2

[Jussi Lehtola]

On Tue, 5 Oct 2010 20:03:41 +0530 (IST)
ras...@chem.iitb.ac.in wrote:

> Hi All,
> 
> I want to install Gromacs 4.5.1 version on a cluster system (high
> performance computing facility) in our institute. I don't have access
> to root and thus, I have to install gromacs in my home directory.
> 
> The problem is that, the cluster has CentOS 5.4 as the operating
> system and the gcc version is 4.1.2.
> 
> Gromacs site says that gcc 4.1.x and above are broken compilers and
> gromacs should not be compiled using them.

I haven't had any problems with Gromacs in CentOS 5 compiled with the
system compiler. The people at Red Hat have probably fixed all the bugs
that caused the problems a long time ago.

Another possibility is to ask the admin to install the 4.4 version of
GCC, which is readily available in the distribution.
-- 
--
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.leht...@helsinki.fi
--
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.leht...@helsinki.fi, p. 191 50632
--
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[gmx-users] g_densmap time-position-density output

[Paymon Pirzadeh]

Hello,
Can g_densmap produce 2D plots that one axis is the position in box, and
the other is time? In other words, evolution of box content density with
time on either  axes of the box?
Regards,

Paymon 

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[gmx-users] Simulations on GPU

[Igor Leontyev]

Szilárd wrote:

The beta versions are all outdated, could you please use the latest
source distribution (4.5.1) instead (or git from the
release-4-5-patches branch)?


The result is the same for both the distribution 4.5.1 and git from the 
release-4-5-patches. See the output bellow.

=

PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
LD_LIBRARY_PATH=/usr/local/opt/bin/mpi/openmpi-1.4.2/lib:/home/leontyev/programs/bin/cuda/lib64:
CPPFLAGS=-I//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/include 
-I//usr/local/opt/bin/mpi/openmpi-1.4.2/include
LDFLAGS=-L//usr/local/opt/bin/gromacs/fftw-3.2.2/single_sse/lib 
-L//usr/local/opt/bin/mpi/openmpi-1.4.2/lib
OPENMM_ROOT_DIR=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git/openmm

cmake 
src -DGMX_OPENMM=ON -DGMX_THREADS=OFF -DCMAKE_INSTALL_PREFIX=/home/leontyev/programs/bin/gromacs/gromacs-4.5.1-git

CMake Error at gmxlib/CMakeLists.txt:124 (set_target_properties):
 set_target_properties called with incorrect number of arguments.


CMake Error at gmxlib/CMakeLists.txt:126 (install):
 install TARGETS given no ARCHIVE DESTINATION for static library target
 "gmx".


CMake Error at mdlib/CMakeLists.txt:11 (set_target_properties):
 set_target_properties called with incorrect number of arguments.


CMake Error at mdlib/CMakeLists.txt:13 (install):
 install TARGETS given no ARCHIVE DESTINATION for static library target
 "md".


CMake Error at kernel/CMakeLists.txt:43 (set_target_properties):
 set_target_properties called with incorrect number of arguments.


CMake Error at kernel/CMakeLists.txt:44 (set_target_properties):
 set_target_properties called with incorrect number of arguments.


CMake Error at kernel/gmx_gpu_utils/CMakeLists.txt:18 
(CUDA_INCLUDE_DIRECTORIES):

 Unknown CMake command "CUDA_INCLUDE_DIRECTORIES".


CMake Warning (dev) in CMakeLists.txt:
 No cmake_minimum_required command is present.  A line of code such as

   cmake_minimum_required(VERSION 2.8)

 should be added at the top of the file.  The version specified may be 
lower

 if you wish to support older CMake versions for this project.  For more
 information run "cmake --help-policy CMP".
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Configuring incomplete, errors occurred! 



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[gmx-users] Re : installation of gromacs in windows on cygwin

[bharat gupta]

Hi all

I am trying installing gromacs 4.5.1 in windows using cygwin .. I have fftw3
package also without any error.. but the moment I use ./configure command
given in the installation instruction I am getting the following error :-


se...@selva-pc /fftw-3.2.2/gromacs-4.5.1
$ ./configure
checking build system type... config/config.guess: line 136:  4000 Aborted
   ( test -f /.attbin/uname ) > /dev/null 2>&1
config/config.guess: line 1308:  3184 Aborted ( umask 077 &&
mkd
ir $tmp )
config/config.guess: line 1308:  4060 Aborted ( umask 077 &&
mkd
ir $tmp )
config.guess: cannot create a temporary directory in /tmp
config/config.guess: line 1308:  3248 Aborted ( rm -f
$tmpfiles
2> /dev/null; rmdir $tmp 2> /dev/null )
configure: error: cannot guess build type; you must specify one

se...@selva-pc /fftw-3.2.2/gromacs-4.5.1
$ ./configure --enable-shared LDFLAGS = '-L/usr/local/lib'
configure: WARNING: you should use --build, --host, --target
configure: error: invalid variable name: `'


Can anybody help me out in this regard ...


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
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Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[Justin A. Lemkul]

bharat gupta wrote:

Hi all

I am trying installing gromacs 4.5.1 in windows using cygwin .. I have 
fftw3 package also without any error.. but the moment I use ./configure 
command given in the installation instruction I am getting the following 
error :-



se...@selva-pc /fftw-3.2.2/gromacs-4.5.1
$ ./configure
checking build system type... config/config.guess: line 136:  4000 Aborted
   ( test -f /.attbin/uname ) > /dev/null 2>&1
config/config.guess: line 1308:  3184 Aborted ( umask 
077 && mkd

ir $tmp )
config/config.guess: line 1308:  4060 Aborted ( umask 
077 && mkd

ir $tmp )
config.guess: cannot create a temporary directory in /tmp
config/config.guess: line 1308:  3248 Aborted ( rm -f 
$tmpfiles

2> /dev/null; rmdir $tmp 2> /dev/null )
configure: error: cannot guess build type; you must specify one

se...@selva-pc /fftw-3.2.2/gromacs-4.5.1
$ ./configure --enable-shared LDFLAGS = '-L/usr/local/lib'
configure: WARNING: you should use --build, --host, --target
configure: error: invalid variable name: `'



There should not be spaces within the declaration of LDFLAGS, i.e.:

LDFLAGS='-L/usr/local/lib'

You are also being told that configure cannot guess your build type, so it must 
be specified manually.


-Justin



Can anybody help me out in this regard ...


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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


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Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[bharat gupta]

build type ?? ... actually I am new to cygwin so I don't know .. what
exactly do I have to do for this one ??
-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[Justin A. Lemkul]

bharat gupta wrote:


build type ?? ... actually I am new to cygwin so I don't know .. what 
exactly do I have to do for this one ??


If you installed FFTW, then its configure script must have properly detected 
your build type.  Check the config.log from that process to see what it used. 
It is weird that Gromacs can't detect it, though.


-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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


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Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[bharat gupta]

thanks for ur help.. I have figured out the problem and not installation is
going on .. I want to know one more thing that xmgrace which is required for
plotting the data .. how can we install it as I have searched on google ..
but  I am not able to get the correct link

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
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Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[Justin A. Lemkul]

bharat gupta wrote:
thanks for ur help.. I have figured out the problem and not installation 
is going on .. I want to know one more thing that xmgrace which is 
required for plotting the data .. how can we install it as I have 
searched on google .. but  I am not able to get the correct link 



The first Google result for "xmgrace" is the site you want, I don't know what 
else to tell you.


http://plasma-gate.weizmann.ac.il/Grace/

Follow whatever documentation they provide to install it.

-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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


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RE: [gmx-users] Re : installation of gromacs in windows on cygwin

[#ZHAO LINA#]

sudo apt-get install grace


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, October 06, 2010 11:29 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] Re : installation of gromacs in windows on cygwin

bharat gupta wrote:
> thanks for ur help.. I have figured out the problem and not installation
> is going on .. I want to know one more thing that xmgrace which is
> required for plotting the data .. how can we install it as I have
> searched on google .. but  I am not able to get the correct link
>

The first Google result for "xmgrace" is the site you want, I don't know what
else to tell you.

http://plasma-gate.weizmann.ac.il/Grace/

Follow whatever documentation they provide to install it.

-Justin

> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com 
>

--


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


--
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Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[Justin A. Lemkul]

#ZHAO LINA# wrote:

sudo apt-get install grace


For Linux sure, but I think the Cygwin equivalent is something like cyg-get 
(which is probably not standard) and there may or may not be a "grace" package 
available.


-Justin




From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, October 06, 2010 11:29 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] Re : installation of gromacs in windows on cygwin

bharat gupta wrote:

thanks for ur help.. I have figured out the problem and not installation
is going on .. I want to know one more thing that xmgrace which is
required for plotting the data .. how can we install it as I have
searched on google .. but  I am not able to get the correct link



The first Google result for "xmgrace" is the site you want, I don't know what
else to tell you.

http://plasma-gate.weizmann.ac.il/Grace/

Follow whatever documentation they provide to install it.

-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


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


--
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--


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


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[gmx-users] Reg: Energy minimisation of hexane

[vinothkumar mohanakrishnan]

Hi all

I am trying to simulate 150 molecules of hexane in a triclinic box
(8.319*3.01*3.01 nm^3) using OPLSAA force field.I got the .gro file from
PRODRG and generated the topology using X2top command. when i run energy
minimisation for hexane my potential energy is positve. is this right?. what
i should correct to get the potential energy as negative. below is my
result. any help is highly appreciated.

Steepest Descents converged to Fmax < 100 in 10454 steps
Potential Energy  =  3.4133051e+04
Maximum force =  9.8812309e+01 on atom 635
Norm of force =  7.9230022e+00

Below is my contents of my em.mdp file

integrator= cg
emtol = 100.0
emstep  = 0.01
nsteps   = 5
nstcgsteep = 1000
nstlist = 1
ns_type  = grid
rlist= 1.0
coulombtype   = PME
fourierspacing = 0.12
rcoulomb= 1.0
rvdw  = 1.0
pbc   = xyz

Regards
Vinoth
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Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[Roland Schulz]

I recommend to use Linux inside a Virtualbox (http://www.virtualbox.org/)
over Cygwin. Cygwin is rather slow.

We should have a Virtual Appliance with GROMACS installed ...

On Tue, Oct 5, 2010 at 11:42 PM, Justin A. Lemkul  wrote:

>
>
> #ZHAO LINA# wrote:
>
>> sudo apt-get install grace
>>
>
> For Linux sure, but I think the Cygwin equivalent is something like cyg-get
> (which is probably not standard) and there may or may not be a "grace"
> package available.
>
> -Justin
>
>
>
>> 
>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
>> behalf of Justin A. Lemkul [jalem...@vt.edu]
>> Sent: Wednesday, October 06, 2010 11:29 AM
>> To: Gromacs Users' List
>> Subject: Re: [gmx-users] Re : installation of gromacs in windows on cygwin
>>
>> bharat gupta wrote:
>>
>>> thanks for ur help.. I have figured out the problem and not installation
>>> is going on .. I want to know one more thing that xmgrace which is
>>> required for plotting the data .. how can we install it as I have
>>> searched on google .. but  I am not able to get the correct link
>>>
>>>
>> The first Google result for "xmgrace" is the site you want, I don't know
>> what
>> else to tell you.
>>
>> http://plasma-gate.weizmann.ac.il/Grace/
>>
>> Follow whatever documentation they provide to install it.
>>
>> -Justin
>>
>>  --
>>> Bharat
>>> Ph.D. Candidate
>>> Room No. : 7202A, 2nd Floor
>>> Biomolecular Engineering Laboratory
>>> Division of Chemical Engineering and Polymer Science
>>> Pusan National University
>>> Busan -609735
>>> South Korea
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>> Mobile no. - 010-5818-3680
>>> E-mail : monu46...@yahoo.com 
>>>
>>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/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
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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Re: [gmx-users] Reg: Energy minimisation of hexane

[Mark Abraham]

- Original Message -
From: vinothkumar mohanakrishnan 
Date: Wednesday, October 6, 2010 15:20
Subject: [gmx-users] Reg: Energy minimisation of hexane
To: Discussion list for GROMACS users 

> Hi all
> 
> I am trying to simulate 150 molecules of hexane in a triclinic box 
> (8.319*3.01*3.01 nm^3) using OPLSAA force field.I got the .gro file from 
> PRODRG and generated the topology using X2top command. when i run energy 
> minimisation for hexane my potential energy is positve. is this right?. what 
> i should correct to get the potential energy as negative. below is my result. 
> any help is highly appreciated.
 > 
> Steepest Descents converged to Fmax < 100 in 10454 steps
> Potential Energy  =  3.4133051e+04
> Maximum force =  9.8812309e+01 on atom 635
> Norm of force =  7.9230022e+00

So something is unhappy, and the minimizer can't deal with it. Probably you 
have some massive steric clash, like two molecules overlying each other. Look 
at the contents of your simulation cell before and after EM.

Mark
 
> Below is my contents of my em.mdp file
 > 
> integrator= cg
> emtol = 100.0  
> emstep  = 0.01
> nsteps   = 5 
> nstcgsteep = 1000
> nstlist = 1   
> ns_type  = grid
>  rlist= 1.0   
> coulombtype   = PME   
> fourierspacing = 0.12
> rcoulomb= 1.0   
> rvdw  = 1.0   
> pbc   = xyz 
> 
> Regards
> Vinoth   
> 
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Re: [gmx-users] Reg: Energy minimisation of hexane

[vinothkumar mohanakrishnan]

Hi Mark

I saw both the .gro file of hexane before and after EM in VMD as well
checked their coordinates. I am not able to make anything out of it. it will
better if one knows how to find the steric clash between two molecules?.

Regards
Vinoth

On Wed, Oct 6, 2010 at 11:08 AM, Mark Abraham wrote:

>
>
> - Original Message -
> From: vinothkumar mohanakrishnan 
> Date: Wednesday, October 6, 2010 15:20
> Subject: [gmx-users] Reg: Energy minimisation of hexane
> To: Discussion list for GROMACS users 
>
> > Hi all
> >
> > I am trying to simulate 150 molecules of hexane in a triclinic box
> (8.319*3.01*3.01 nm^3) using OPLSAA force field.I got the .gro file from
> PRODRG and generated the topology using X2top command. when i run energy
> minimisation for hexane my potential energy is positve. is this right?. what
> i should correct to get the potential energy as negative. below is my
> result. any help is highly appreciated.
> >
> > Steepest Descents converged to Fmax < 100 in 10454 steps
> > Potential Energy  =  3.4133051e+04
> > Maximum force =  9.8812309e+01 on atom 635
> > Norm of force =  7.9230022e+00
>
> So something is unhappy, and the minimizer can't deal with it. Probably you
> have some massive steric clash, like two molecules overlying each other.
> Look at the contents of your simulation cell before and after EM.
>
> Mark
>
>
> > Below is my contents of my em.mdp file
> >
> > integrator= cg
> > emtol = 100.0
> > emstep  = 0.01
> > nsteps   = 5
> > nstcgsteep = 1000
> > nstlist = 1
> > ns_type  = grid
> > rlist= 1.0
> > coulombtype   = PME
> > fourierspacing = 0.12
> > rcoulomb= 1.0
> > rvdw  = 1.0
> > pbc   = xyz
> >
> > Regards
> > Vinoth
> >
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Reg: Energy minimisation of hexane

[Mark Abraham]

- Original Message -
From: vinothkumar mohanakrishnan 
Date: Wednesday, October 6, 2010 17:18
Subject: Re: [gmx-users] Reg: Energy minimisation of hexane
To: Discussion list for GROMACS users 

> Hi Mark
> 
> I saw both the .gro file of hexane before and after EM in VMD as well checked 
> their coordinates. I am not able to make anything out of it. it will better 
> if one knows how to find the steric clash between two molecules?.

  It's best avoided rather than searched for. Consider whether your box  size 
is suitable for your coordinates. Construct a simpler version that  is easier 
to check by hand.

VMD is a good tool for seeking steric clashes, because its bond-creating  
heuristics when you load in a .gro file will normally indicate where  atoms are 
too close together. From VMD's Tk console you can use "pbc  box" to view the 
box wrt the coordinates.

Mark 


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