date:20090824

Re: [gmx-users] problems with rerun

2009-08-24 Thread Mark Abraham


rsf wrote:

Mark
Thanks for your reply, I do prepare a .tpr file for each run. I run the
original md run and then I run grompp using the files with my modified
topology I need and then run with the -rerun option as you said. I am
using gromacs 4.0.5 since I saw in the notes for the release it had been
fixed. I think the problem should be what you said about the neighbour
list, etc.


I should add to what I said earlier - the neighbour searching only 
affects the nonbonded interactions, and I was seeing small differences 
in the bonded interaction energies. This suggests that you are not 
comparing like with like. Thus you might be imposing a second round of 
constraints, or taking structures from a limited precision .gro file, or 
such like.





You also need to choose sensible combinations of unconstrained_start,
gen_vel, extracting a trajectory frame for which velocities were
written, and not accidentally taking coordinates from a .gro file.


What would be a sensible combination for these? Thanks so much for your
help, I think I have a better idea of what I'm doing wrong.


Read about these options in section 7.3 of the manual, then experiment 
with varying one or two of them in a manner that seems sensible. You'll 
learn much better this way than me prescribing something that may or may 
not suit your actual needs, since I don't know what they are!


http://oldwiki.gromacs.org/index.php/Doing_Restarts may have a bit of 
help, but it is not intended for GROMACS 4.


Mark


rsf wrote:

Hi I have a molecule described by two sets of parameters (in atom
connectivity and coupe values of bond interactions) and I need to get
the
energy difference between those two descriptions. I have been having
problems with the rerun capability (I am using the latest version of
gromacs)

I did the following tests, I will include only the energy components for
the first step of the trajectory for each state after a steepest descent
run for each state.

Proper procedure would be to obtain a trajectory file with the
structures of interest, and then to construct a .tpr file suitable for
each model physics, and then to use -rerun on the same trajectory file
with each .tpr file.


Running an md calculation with state 1:
result during md simulation
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.
LJ-14
2.81497e+029.71604e+021.09286e+032.84503e+02
1.34015e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb
(LR)
1.69155e+042.28027e+04   -2.23828e+03   -2.79565e+05
-3.31702e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total
Energy
   -1.11970e+040.0e+00   -2.53835e+052.27203e+01
-2.53812e+05
Temperature Pressure (bar)
1.64402e-01   -1.23399e+04

result extracting the configuration from .trr file and runing a single
step md
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.
LJ-14
2.81948e+029.72103e+021.09285e+032.84608e+02
1.33985e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb
(LR)
1.69153e+042.28365e+04   -2.23835e+03   -2.79562e+05
-3.31715e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total
Energy
   -1.11970e+040.0e+00   -2.53797e+052.39171e+01
-2.53773e+05
Temperature Pressure (bar)
1.73062e-01   -1.22928e+04

using rerun
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.
LJ-14
2.81497e+029.71604e+021.09286e+032.84503e+02
1.34015e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb
(LR)
1.69155e+042.28027e+04   -2.23828e+03   -2.79565e+05
-3.31702e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total
Energy
   -1.11970e+040.0e+00   -2.53835e+052.27203e+01
-2.53812e+05
Temperature Pressure (bar)
1.64402e-01   -1.23399e+04


For state 2:
result during md run
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.
LJ-14
1.64555e+029.37861e+021.09286e+032.82162e+02
1.44514e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb
(LR)
1.65633e+042.27962e+04   -2.23852e+03   -2.79767e+05
-3.27838e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total
Energy
   -1.12594e+040.0e+00   -2.54562e+051.69486e+01
-2.54545e+05
Temperature Pressure (bar)
1.22639e-01   -1.22600e+04

result extracting the configuration from .trr file and runing a single
step md
  Step   Time Lambda
  0

[gmx-users] Re: Something about getting started

2009-08-24 Thread Justin A. Lemkul




DreamCatcher wrote:


Dear Justin,
I did make the rtp and hdb files in accordance with the tutorial 
onthe website 
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html 
,but 
the problem cann't be settle,what can I do?


The [atoms] sections you presented are incorrect.  They lack both charge and 
charge group information.



   Looking forward for your reply!
   Thanks,
   
dreamcatcher


Please take note of the following:


When replying, please edit your Subject line so it is more specific
than "Re: Contents of gmx-users digest..."


-Justin

--


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-users Digest, Vol 64, Issue 156

2009-08-24 Thread DreamCatcher

t;CB   HB2
> >CBCA
> >CA   HA1
> >CA   OH
> >OH   HO
> >CACG
> >CG   HG1
> >CG   HG2
> >CG   CD
> >CDHD
> >CD   OD
> >OD   HOD
> >CD   +CB
> >
> > [VAE]
> >  [ atoms ]
> >CB  opls_136
> >HB1  opls_140
> >HB2  opls_140
> > CA  opls_157
> >HA1  opls_140
> >HA2  opls_140
> >OH  opls_154
> >HO  opls_155
> >
> >  [ bonds ]
> >CB  -CD
> >CB  HB1
> >CB  HB2
> >CB   CA
> >CA  HA1
> >CA  HA2
> >CA   OH
> >OH   HO
> >
> >  in .hdb file:
> > ; H add type H i j k
> > VAB3
> > 3 4 HB  CB  CA  +CB
> > 1 5 HA  CA  CB  +CB
> > 1 2 HO  OH  CA  +CB
> > VA  6
> > 2 6 HB  CB  CA  -CA
> > 1 5 HA  CA  CB   CG
> > 1 2 HOA OA  CA   CG
> > 2 6 HG  CG  CA   CD
> > 1 5 HD  CD  CG  +CB
> > 1 1 HOD OD  CD  CG
> > VAE 3
> > 2 6 HB  CB  CA  -CD
> > 2 6 HA  CA  CB  +CB
> > 1 2 HO  OH  CA  +CB
> >
> >
> > 
> >
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
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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
>
> 
>
>
> --
>
> Message: 4
> Date: Mon, 24 Aug 2009 14:57:39 -0400
> From: Jamie Seyed 
> Subject: Re: [gmx-users] correlation function
> To: jalem...@vt.edu, Discussion list for GROMACS users
>
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Sun, Aug 23, 2009 at 7:32 PM, Justin A. Lemkul  wrote:
>
> >
> >
> >
> >Actually when I open autocorr.xvg I can see from data/feature
> >>extraction/  the last set is S1295 (N=101, autocorr.xvg) which means
> >>they are 1296 graphs each with poor statistics start at 1 and coming
> >>down. To have a ACF for a system I expect to get one graph with good
> >>statistic... I hope I make it clear now.
> >>
> >
> > What did you extract with g_traj?  All the coordinates of all the
> > molecules? The command line you gave would be helpful here.  It would
> seem
> > that 1296/216 = 6, therefore (and this is just a guess) then g_analyze is
> > trying to calculate some sort of ACF between all coordinates: x-x, y-y,
> z-z,
> > x-y, x-z, y-z.  That way, you'd be getting these ACF's for each
> individual
> > molecule.  Again, just a guess.
>
>
> Hi Justin,
> I think that I extract only the coordinates for my desired atoms using this
> command:
> g_traj  -f  f.xtc  -s f.tpr  -n f.ndx  -ox coord.xvg
> and then
> g_analyze  -f coord.xvg  -ac autocorr.xvg
>
> Is that the way to get ACF or I am doing something wrong here?? Many Thanks
> in Advance/Jamie
>
>
> >
> >
> > -Justin
> >
> > --
> > 
> >
> > 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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> End of gmx-users Digest, Vol 64, Issue 156
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Re: [gmx-users] problems with rerun

2009-08-24 Thread rsf

Mark
Thanks for your reply, I do prepare a .tpr file for each run. I run the
original md run and then I run grompp using the files with my modified
topology I need and then run with the -rerun option as you said. I am
using gromacs 4.0.5 since I saw in the notes for the release it had been
fixed. I think the problem should be what you said about the neighbour
list, etc.

> You also need to choose sensible combinations of unconstrained_start,
> gen_vel, extracting a trajectory frame for which velocities were
> written, and not accidentally taking coordinates from a .gro file.

What would be a sensible combination for these? Thanks so much for your
help, I think I have a better idea of what I'm doing wrong.




> rsf wrote:
>> Hi I have a molecule described by two sets of parameters (in atom
>> connectivity and coupe values of bond interactions) and I need to get
>> the
>> energy difference between those two descriptions. I have been having
>> problems with the rerun capability (I am using the latest version of
>> gromacs)
>>
>> I did the following tests, I will include only the energy components for
>> the first step of the trajectory for each state after a steepest descent
>> run for each state.
>
> Proper procedure would be to obtain a trajectory file with the
> structures of interest, and then to construct a .tpr file suitable for
> each model physics, and then to use -rerun on the same trajectory file
> with each .tpr file.
>
>> Running an md calculation with state 1:
>> result during md simulation
>>Step   Time Lambda
>>   00.00.0
>>
>>Energies (kJ/mol)
>> G96Bond   G96AngleProper Dih.  Improper Dih.
>> LJ-14
>> 2.81497e+029.71604e+021.09286e+032.84503e+02
>> 1.34015e+02
>>  Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb
>> (LR)
>> 1.69155e+042.28027e+04   -2.23828e+03   -2.79565e+05
>> -3.31702e+03
>>RF excl. Position Rest.  PotentialKinetic En.   Total
>> Energy
>>-1.11970e+040.0e+00   -2.53835e+052.27203e+01
>> -2.53812e+05
>> Temperature Pressure (bar)
>> 1.64402e-01   -1.23399e+04
>>
>> result extracting the configuration from .trr file and runing a single
>> step md
>>Step   Time Lambda
>>   00.00.0
>>
>>Energies (kJ/mol)
>> G96Bond   G96AngleProper Dih.  Improper Dih.
>> LJ-14
>> 2.81948e+029.72103e+021.09285e+032.84608e+02
>> 1.33985e+02
>>  Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb
>> (LR)
>> 1.69153e+042.28365e+04   -2.23835e+03   -2.79562e+05
>> -3.31715e+03
>>RF excl. Position Rest.  PotentialKinetic En.   Total
>> Energy
>>-1.11970e+040.0e+00   -2.53797e+052.39171e+01
>> -2.53773e+05
>> Temperature Pressure (bar)
>> 1.73062e-01   -1.22928e+04
>>
>> using rerun
>>Step   Time Lambda
>>   00.00.0
>>
>>Energies (kJ/mol)
>> G96Bond   G96AngleProper Dih.  Improper Dih.
>> LJ-14
>> 2.81497e+029.71604e+021.09286e+032.84503e+02
>> 1.34015e+02
>>  Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb
>> (LR)
>> 1.69155e+042.28027e+04   -2.23828e+03   -2.79565e+05
>> -3.31702e+03
>>RF excl. Position Rest.  PotentialKinetic En.   Total
>> Energy
>>-1.11970e+040.0e+00   -2.53835e+052.27203e+01
>> -2.53812e+05
>> Temperature Pressure (bar)
>> 1.64402e-01   -1.23399e+04
>>
>>
>> For state 2:
>> result during md run
>>Step   Time Lambda
>>   00.00.0
>>
>>Energies (kJ/mol)
>> G96Bond   G96AngleProper Dih.  Improper Dih.
>> LJ-14
>> 1.64555e+029.37861e+021.09286e+032.82162e+02
>> 1.44514e+02
>>  Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb
>> (LR)
>> 1.65633e+042.27962e+04   -2.23852e+03   -2.79767e+05
>> -3.27838e+03
>>RF excl. Position Rest.  PotentialKinetic En.   Total
>> Energy
>>-1.12594e+040.0e+00   -2.54562e+051.69486e+01
>> -2.54545e+05
>> Temperature Pressure (bar)
>> 1.22639e-01   -1.22600e+04
>>
>> result extracting the configuration from .trr file and runing a single
>> step md
>>   Step   Time Lambda
>>   00.00.0
>>
>>Energies (kJ/mol)
>> G96Bond   G96AngleProper Dih.  Improper Dih.
>> LJ-14
>> 1.64743e+029.38358e+021.09285e+032.82134e+02
>> 1.44485e+02
>>  Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb
>> (LR)
>> 1.65631e+042.27975e+04   -2.23859e+03   -2.79766e+05
>> -3.27859e+03
>>RF excl. Position Rest.  PotentialKinetic En.   Total
>> Energy
>>-1.12594e+040.0e+00

Re: [gmx-users] problems with rerun

2009-08-24 Thread Mark Abraham


rsf wrote:

Hi I have a molecule described by two sets of parameters (in atom
connectivity and coupe values of bond interactions) and I need to get the
energy difference between those two descriptions. I have been having
problems with the rerun capability (I am using the latest version of
gromacs)

I did the following tests, I will include only the energy components for
the first step of the trajectory for each state after a steepest descent
run for each state.


Proper procedure would be to obtain a trajectory file with the 
structures of interest, and then to construct a .tpr file suitable for 
each model physics, and then to use -rerun on the same trajectory file 
with each .tpr file.



Running an md calculation with state 1:
result during md simulation
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
2.81497e+029.71604e+021.09286e+032.84503e+021.34015e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.69155e+042.28027e+04   -2.23828e+03   -2.79565e+05   -3.31702e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.11970e+040.0e+00   -2.53835e+052.27203e+01   -2.53812e+05
Temperature Pressure (bar)
1.64402e-01   -1.23399e+04

result extracting the configuration from .trr file and runing a single
step md
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
2.81948e+029.72103e+021.09285e+032.84608e+021.33985e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.69153e+042.28365e+04   -2.23835e+03   -2.79562e+05   -3.31715e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.11970e+040.0e+00   -2.53797e+052.39171e+01   -2.53773e+05
Temperature Pressure (bar)
1.73062e-01   -1.22928e+04

using rerun
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
2.81497e+029.71604e+021.09286e+032.84503e+021.34015e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.69155e+042.28027e+04   -2.23828e+03   -2.79565e+05   -3.31702e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.11970e+040.0e+00   -2.53835e+052.27203e+01   -2.53812e+05
Temperature Pressure (bar)
1.64402e-01   -1.23399e+04


For state 2:
result during md run
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
1.64555e+029.37861e+021.09286e+032.82162e+021.44514e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.65633e+042.27962e+04   -2.23852e+03   -2.79767e+05   -3.27838e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.12594e+040.0e+00   -2.54562e+051.69486e+01   -2.54545e+05
Temperature Pressure (bar)
1.22639e-01   -1.22600e+04

result extracting the configuration from .trr file and runing a single
step md
  Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
1.64743e+029.38358e+021.09285e+032.82134e+021.44485e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.65631e+042.27975e+04   -2.23859e+03   -2.79766e+05   -3.27859e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.12594e+040.0e+00   -2.54560e+051.70085e+01   -2.54543e+05
Temperature Pressure (bar)
1.23072e-01   -1.22427e+04
using rerun
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
1.64555e+029.37861e+021.09286e+032.82162e+021.44514e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.65633e+042.27962e+04   -2.23852e+03   -2.79767e+05   -3.27838e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.12594e+040.0e+00   -2.54562e+051.69486e+01   -2.54545e+05
Temperature Pressure (bar)
1.22639e-01   -1.22600e+04


Now, taking the trajectory from state one and running with state two I get:
result extracting the configuration from .trr file and runing a single
step md
   Step   Time Lambda
  0

Re: [gmx-users] [Fwd: Please solve my problem]

2009-08-24 Thread Mark Abraham


ceste...@unsl.edu.ar wrote:

Hi All
I have similar problem using gromacs 4.0.2.
The MD simulation (5 ns) on single processor is complited in 5 days, but
the same MD can`t be complited on cluster on 4 or 8 processors. The MD
simulation is stopped without any error message.


If there actually is no error message on stdout, stderr or the .log 
file, then it's often an MPI problem.


Mark
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Re: [gmx-users] Parameters for membrane stability

2009-08-24 Thread Justin A. Lemkul




Ragnarok sdf wrote:
I've just generated a 512 DPPC bilayer using genconf with a 128 DPPC 
from tieleman's website as a starting structure. I've run a short 1 ns 
semi-isotropic simulation at 323 K and monitored the area per lipid as a 
stability parameter for my membrane simulation. If the area per lipid 
maintains the same, can I consider my membrane as being stable? Would 
there be better parameters for it?


Many membrane parameters are inter-related, but if you are trying to make a 
strong argument for stability (and ultimately equilibrium behavior), I would 
think a much more thorough analysis would include: deuterium order parameters, 
membrane thickness, and lateral diffusion of lipids, if not a few more.


-Justin


Thank you in advance
Fabrício Bracht




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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] problems with rerun

2009-08-24 Thread rsf


Hi I have a molecule described by two sets of parameters (in atom
connectivity and coupe values of bond interactions) and I need to get the
energy difference between those two descriptions. I have been having
problems with the rerun capability (I am using the latest version of
gromacs)

I did the following tests, I will include only the energy components for
the first step of the trajectory for each state after a steepest descent
run for each state.


Running an md calculation with state 1:
result during md simulation
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
2.81497e+029.71604e+021.09286e+032.84503e+021.34015e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.69155e+042.28027e+04   -2.23828e+03   -2.79565e+05   -3.31702e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.11970e+040.0e+00   -2.53835e+052.27203e+01   -2.53812e+05
Temperature Pressure (bar)
1.64402e-01   -1.23399e+04

result extracting the configuration from .trr file and runing a single
step md
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
2.81948e+029.72103e+021.09285e+032.84608e+021.33985e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.69153e+042.28365e+04   -2.23835e+03   -2.79562e+05   -3.31715e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.11970e+040.0e+00   -2.53797e+052.39171e+01   -2.53773e+05
Temperature Pressure (bar)
1.73062e-01   -1.22928e+04

using rerun
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
2.81497e+029.71604e+021.09286e+032.84503e+021.34015e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.69155e+042.28027e+04   -2.23828e+03   -2.79565e+05   -3.31702e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.11970e+040.0e+00   -2.53835e+052.27203e+01   -2.53812e+05
Temperature Pressure (bar)
1.64402e-01   -1.23399e+04


For state 2:
result during md run
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
1.64555e+029.37861e+021.09286e+032.82162e+021.44514e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.65633e+042.27962e+04   -2.23852e+03   -2.79767e+05   -3.27838e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.12594e+040.0e+00   -2.54562e+051.69486e+01   -2.54545e+05
Temperature Pressure (bar)
1.22639e-01   -1.22600e+04

result extracting the configuration from .trr file and runing a single
step md
  Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
1.64743e+029.38358e+021.09285e+032.82134e+021.44485e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.65631e+042.27975e+04   -2.23859e+03   -2.79766e+05   -3.27859e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.12594e+040.0e+00   -2.54560e+051.70085e+01   -2.54543e+05
Temperature Pressure (bar)
1.23072e-01   -1.22427e+04
using rerun
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
1.64555e+029.37861e+021.09286e+032.82162e+021.44514e+02
 Coulomb-14LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)
1.65633e+042.27962e+04   -2.23852e+03   -2.79767e+05   -3.27838e+03
   RF excl. Position Rest.  PotentialKinetic En.   Total Energy
   -1.12594e+040.0e+00   -2.54562e+051.69486e+01   -2.54545e+05
Temperature Pressure (bar)
1.22639e-01   -1.22600e+04


Now, taking the trajectory from state one and running with state two I get:
result extracting the configuration from .trr file and runing a single
step md
   Step   Time Lambda
  00.00.0

   Energies (kJ/mol)
G96Bond   G96AngleProper Dih.  Improper Dih.  LJ-14
1.67952e+029.49784e+021.09257e+032.99138e+021.44148e+02
 Coulomb-14LJ (SR)L

[gmx-users] Parameters for membrane stability

2009-08-24 Thread Ragnarok sdf

I've just generated a 512 DPPC bilayer using genconf with a 128 DPPC from
tieleman's website as a starting structure. I've run a short 1 ns
semi-isotropic simulation at 323 K and monitored the area per lipid as a
stability parameter for my membrane simulation. If the area per lipid
maintains the same, can I consider my membrane as being stable? Would there
be better parameters for it?
Thank you in advance
Fabrício Bracht
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Re: [gmx-users] correlation function

2009-08-24 Thread Justin A. Lemkul




Jamie Seyed wrote:



On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul > wrote:




Jamie Seyed wrote:

with a lot of x-y sets seperated by & character. I think I did
not get the key point here. So my question is what is the right
way to get  using this tool?? Many Thanks/Jamie


Well, as far as g_analyze is concerned, it's done its job.  If you
feed g_analyze a whole bunch of data sets, it will give you a whole
bunch of ACF's. So you essentially got an ACF for each molecule's x,
y, and z coordinates.  I guess I just don't understand what you're
really after, because as I said, g_analyze did its job. 

 
Thanks a lot Justin,
Actually I tried to use xmgrace to make a <> of all bunch of ACF and I 
find under data/feature extraction/Feature Y average to do the job. I 
did not find out how it works yet, but do you think is this correct??
 


I think, if you average the ACF, you will get zero.


--another question related to g_rotacf. Before I used it like this:
first I made a ndx file and then extract xtc and tpr file for ndx and 
then used this command:
 
1)   g_rotacf -f f.xtc -s tpxout.tpr -n f.ndx -o rotacf.xvg -d 
and I saw strange result (as I mentioned before like y=2x)

Then I tried to use original files (xtc and tpr) insted of filtered files:
 
2)   g_rotacf  -f traj.xtc  -s f.tpr  -n f.ndx  -o rotacf.xvg -d 
and I got completely different but very expected result. So now I 
believe that the right way is the second one... Do you have any idea or 
comment on this? or what is the result of first method?


Filtered trajectories are for visualization purposes only.  When doing analysis, 
always use the original trajectory.


-Justin


Many Thanks/Jamie

-Justin

--


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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--


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] correlation function

2009-08-24 Thread Jamie Seyed

On Mon, Aug 24, 2009 at 3:44 PM, Justin A. Lemkul  wrote:

>
>
> Jamie Seyed wrote:
>
> with a lot of x-y sets seperated by & character. I think I did not get the
>> key point here. So my question is what is the right way to get 
>> using this tool?? Many Thanks/Jamie
>>
>
> Well, as far as g_analyze is concerned, it's done its job.  If you feed
> g_analyze a whole bunch of data sets, it will give you a whole bunch of
> ACF's. So you essentially got an ACF for each molecule's x, y, and z
> coordinates.  I guess I just don't understand what you're really after,
> because as I said, g_analyze did its job.


Thanks a lot Justin,
Actually I tried to use xmgrace to make a <> of all bunch of ACF and I find
under data/feature extraction/Feature Y average to do the job. I did not
find out how it works yet, but do you think is this correct??

--another question related to g_rotacf. Before I used it like this:
first I made a ndx file and then extract xtc and tpr file for ndx and then
used this command:

1)   g_rotacf -f f.xtc -s tpxout.tpr -n f.ndx -o rotacf.xvg -d
and I saw strange result (as I mentioned before like y=2x)
Then I tried to use original files (xtc and tpr) insted of filtered files:

2)   g_rotacf  -f traj.xtc  -s f.tpr  -n f.ndx  -o rotacf.xvg -d
and I got completely different but very expected result. So now I believe
that the right way is the second one... Do you have any idea or comment on
this? or what is the result of first method?
Many Thanks/Jamie

-Justin

-- 


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] correlation function

2009-08-24 Thread Justin A. Lemkul




Jamie Seyed wrote:

with a lot of x-y sets seperated by & character. I think I did not get 
the key point here. So my question is what is the right way to get 
 using this tool?? Many Thanks/Jamie


Well, as far as g_analyze is concerned, it's done its job.  If you feed 
g_analyze a whole bunch of data sets, it will give you a whole bunch of ACF's. 
So you essentially got an ACF for each molecule's x, y, and z coordinates.  I 
guess I just don't understand what you're really after, because as I said, 
g_analyze did its job.


-Justin

--


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] correlation function

2009-08-24 Thread Jamie Seyed

On Sun, Aug 23, 2009 at 7:32 PM, Justin A. Lemkul  wrote:

>
>
>
>Actually when I open autocorr.xvg I can see from data/feature
>>extraction/  the last set is S1295 (N=101, autocorr.xvg) which means
>>they are 1296 graphs each with poor statistics start at 1 and coming
>>down. To have a ACF for a system I expect to get one graph with good
>>statistic... I hope I make it clear now.
>>
>
> What did you extract with g_traj?  All the coordinates of all the
> molecules? The command line you gave would be helpful here.  It would seem
> that 1296/216 = 6, therefore (and this is just a guess) then g_analyze is
> trying to calculate some sort of ACF between all coordinates: x-x, y-y, z-z,
> x-y, x-z, y-z.  That way, you'd be getting these ACF's for each individual
> molecule.  Again, just a guess.


Hi Justin,
I think that I extract only the coordinates for my desired atoms using this
command:
g_traj  -f  f.xtc  -s f.tpr  -n f.ndx  -ox coord.xvg
and then
g_analyze  -f coord.xvg  -ac autocorr.xvg

Is that the way to get ACF or I am doing something wrong here?? Many Thanks
in Advance/Jamie


>
>
> -Justin
>
> --
> 
>
> 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] Something about getting started

2009-08-24 Thread Justin A. Lemkul




DreamCatcher wrote:

Dear gmx-users,
  I am a freshman of gmx and I wanna use gromacs for 
polyvinyl-alcohol simulation.But I don't even know how to start it.


Then start simple with some tutorial material:

http://oldwiki.gromacs.org/index.php/Tutorials

  Is it necessary to start my simulation with a .pdb files?If 


You need some sort of structure to start with; .pdb files are generally the 
starting point.


so,What should I do before this?I can make an pdb file for a chain of 
syndiotatic polyvinyl-alcohols via Material Studio or some other 
packages,but the residue cann't be recognize,so I have to modify some 
top files to correct it.I just modify the .hdb and rtp files endeavor to 
make it.But it seems not an easy work.


Indeed, it is not.  I again suggest you start with some basic tutorials with 
robust systems so you learn the workflow of a Gromacs simulation.  Once you've 
got a handle on how everything flows, then attempt your system.


For polymers, you may find this thread useful:

http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html

-Justin

 the message the package sent to me is as follows,appreciate if 
somebody can help me to handle this!
*** (this is an previous version.when i try to use pdb2gmx to get its 
.top file,a fatal error reminds:

 "source code file : resall.c line:279 ()
   Fatal errors:
in .rtp file at line :"
 when I add the charge and chargegroupndx of the atoms,there comes a 
similar error  ):

My attempt is as follows:
###  in rtp file
[ VAB ]
 [ atoms ]
  CB  opls_135
  HB1  opls_140
  HB2  opls_140
  HB3  opls_140
   CA  opls_158
  HA1  opls_140
   OH  opls_154
   HO  opls_155
  
 [ bonds ]

   CB  HB1
   CB  HB2
   CB  HB3
   CB   CA
   CA  HA1
   CA   OH
   OH   HO
   CA  +CB
  
[VA ]

 [ atoms ]
CB  opls_136
   HB1  opls_140
   HB2  opls_140
CA  opls_158 
   HA1  opls_140

   OA  opls_154
  HOA  opls_155
   CG  opls_136
  HG1  opls_140
  HG2  opls_140
   CD  opls_158
   HD  opls_140
   OD  opls_154
  HOD  opls_155

 [ bonds ]

   CB-CA
   CB   HB1
   CB   HB2
   CBCA
   CA   HA1
   CA   OH
   OH   HO
   CACG
   CG   HG1
   CG   HG2
   CG   CD
   CDHD
   CD   OD
   OD   HOD
   CD   +CB
  
[VAE]

 [ atoms ]
   CB  opls_136
   HB1  opls_140
   HB2  opls_140
CA  opls_157
   HA1  opls_140
   HA2  opls_140
   OH  opls_154
   HO  opls_155
   
 [ bonds ]

   CB  -CD
   CB  HB1
   CB  HB2
   CB   CA
   CA  HA1
   CA  HA2
   CA   OH
   OH   HO
 
 in .hdb file:

; H add type H i j k
VAB3
3 4 HB  CB  CA  +CB
1 5 HA  CA  CB  +CB
1 2 HO  OH  CA  +CB
VA  6
2 6 HB  CB  CA  -CA
1 5 HA  CA  CB   CG
1 2 HOA OA  CA   CG
2 6 HG  CG  CA   CD
1 5 HD  CD  CG  +CB
1 1 HOD OD  CD  CG
VAE 3
2 6 HB  CB  CA  -CD
2 6 HA  CA  CB  +CB
1 2 HO  OH  CA  +CB




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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] Something about getting started

2009-08-24 Thread DreamCatcher

Dear gmx-users,
  I am a freshman of gmx and I wanna use gromacs for polyvinyl-alcohol
simulation.But I don't even know how to start it.
  Is it necessary to start my simulation with a .pdb files?If so,What
should I do before this?I can make an pdb file for a chain of syndiotatic
polyvinyl-alcohols via Material Studio or some other packages,but the
residue cann't be recognize,so I have to modify some top files to correct
it.I just modify the .hdb and rtp files endeavor to make it.But it seems not
an easy work.
 the message the package sent to me is as follows,appreciate if somebody
can help me to handle this!
*** (this is an previous version.when i try to use pdb2gmx to get its .top
file,a fatal error reminds:
 "source code file : resall.c line:279 ()
   Fatal errors:
in .rtp file at line :"
 when I add the charge and chargegroupndx of the atoms,there comes a
similar error  ):
My attempt is as follows:
###  in rtp file
[ VAB ]
 [ atoms ]
  CB  opls_135
  HB1  opls_140
  HB2  opls_140
  HB3  opls_140
   CA  opls_158
  HA1  opls_140
   OH  opls_154
   HO  opls_155

 [ bonds ]
   CB  HB1
   CB  HB2
   CB  HB3
   CB   CA
   CA  HA1
   CA   OH
   OH   HO
   CA  +CB

[VA ]
 [ atoms ]
CB  opls_136
   HB1  opls_140
   HB2  opls_140
CA  opls_158
   HA1  opls_140
   OA  opls_154
  HOA  opls_155
   CG  opls_136
  HG1  opls_140
  HG2  opls_140
   CD  opls_158
   HD  opls_140
   OD  opls_154
  HOD  opls_155

 [ bonds ]
   CB-CA
   CB   HB1
   CB   HB2
   CBCA
   CA   HA1
   CA   OH
   OH   HO
   CACG
   CG   HG1
   CG   HG2
   CG   CD
   CDHD
   CD   OD
   OD   HOD
   CD   +CB

[VAE]
 [ atoms ]
   CB  opls_136
   HB1  opls_140
   HB2  opls_140
CA  opls_157
   HA1  opls_140
   HA2  opls_140
   OH  opls_154
   HO  opls_155

 [ bonds ]
   CB  -CD
   CB  HB1
   CB  HB2
   CB   CA
   CA  HA1
   CA  HA2
   CA   OH
   OH   HO

 in .hdb file:
; H add type H i j k
VAB3
3 4 HB  CB  CA  +CB
1 5 HA  CA  CB  +CB
1 2 HO  OH  CA  +CB
VA  6
2 6 HB  CB  CA  -CA
1 5 HA  CA  CB   CG
1 2 HOA OA  CA   CG
2 6 HG  CG  CA   CD
1 5 HD  CD  CG  +CB
1 1 HOD OD  CD  CG
VAE 3
2 6 HB  CB  CA  -CD
2 6 HA  CA  CB  +CB
1 2 HO  OH  CA  +CB
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Re: [gmx-users] [Fwd: Please solve my problem]

2009-08-24 Thread cesteban

Hi again
the MPI coding is OPEN MPI 1.2.7 that is  found in the ROCKS CLUSTER 5.1
distribution
thanks
Carmen
>
> ceste...@unsl.edu.ar wrote:
>> Hi All
>> I have similar problem using gromacs 4.0.2.
>> The MD simulation (5 ns) on single processor is complited in 5 days, but
>> the same MD can`t be complited on cluster on 4 or 8 processors. The MD
>> simulation is stopped without any error message.
>> Any help would be appreciated
>
> Which MPI implementation are you using?  Some are known to be buggy.
> Also, to
> rule out any other potentially buggy behavior, upgrade to version 4.0.5;
> 4.0.2
> is several months old.
>
> -Justin
>
>> Carmen
>>> To,
>>>David van der Spoel
>>>
>>> Dear Sir,
>>>
>>> I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a
>>> problem.
>>> I am giving job for 50 steps step size 0.002ps (total 1ns) but my
>>> job is stopped after 47 steps. when i run this on 4 processors.
>>>
>>> But the same job is completed on 2 processors.Why this happing i am not
>>> able to understand.
>>>
>>> Another thing is that job for 150 steps step size 0.002ps (total
>>> 3ns) is stopped after 375000 steps on 2 processors
>>> and after 587000 steps on 4 processors, without any error message.
>>>
>>> What could be the problem and how to solve it, please help me.
>>>
>>> even i tried the 2 same jobs for 100 steps step size 0.002ps (total
>>> 2ns), one on single processor it is completed in 8 days
>>> but the same job is stop after 55 steps on 4 processors.
>>>
>>> Is there any change is required in MPI coding or in .mdp files. Sir if
>>> you need any other please let me know.
>>>
>>> Please solve my problem, I will be highly obliged.
>>>
>>>
>>> DvdS:
>>>
>>> Please upgrade to a recent version. 3.2.1 is more than five years old.
>>>
>>>
>>>
>>> With warm regards.
>>> Shikhar
>>>
>>>
>>>
>>> --
>>> 
>>> Shikhar Gupta
>>> Senior Research Fellow
>>> Pharmacoinformatics Department
>>> Block- A (Room No.- 208)
>>> National Institute of Pharmaceutical Education & Research( NIPER )
>>> Sec- 67, S.A.S Nagar
>>> Mohali, Punjab (India)
>>> Web-Site: www.niper.ac.in 
>>> PIN- 160062
>>> Email:shik_...@rediffmail.com
>>> ,shik...@gmail.com
>>> 
>>>
>>>
>>>
>>>
>>> --
>>> 
>>> Shikhar Gupta
>>> Senior Research Fellow
>>> Pharmacoinformatics Department
>>> Block- A (Room No.- 208)
>>> National Institute of Pharmaceutical Education & Research( NIPER )
>>> Sec- 67, S.A.S Nagar
>>> Mohali, Punjab (India)
>>> Web-Site: www.niper.ac.in 
>>> PIN- 160062
>>> Email:shik_...@rediffmail.com
>>> ,shik...@gmail.com
>>> 
>>>
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
>>> University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
>>> sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
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>>
>>
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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] [Fwd: Please solve my problem]

2009-08-24 Thread Justin A. Lemkul




ceste...@unsl.edu.ar wrote:

Hi All
I have similar problem using gromacs 4.0.2.
The MD simulation (5 ns) on single processor is complited in 5 days, but
the same MD can`t be complited on cluster on 4 or 8 processors. The MD
simulation is stopped without any error message.
Any help would be appreciated


Which MPI implementation are you using?  Some are known to be buggy.  Also, to 
rule out any other potentially buggy behavior, upgrade to version 4.0.5; 4.0.2 
is several months old.


-Justin


Carmen

To,
   David van der Spoel

Dear Sir,

I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a
problem.
I am giving job for 50 steps step size 0.002ps (total 1ns) but my
job is stopped after 47 steps. when i run this on 4 processors.

But the same job is completed on 2 processors.Why this happing i am not
able to understand.

Another thing is that job for 150 steps step size 0.002ps (total
3ns) is stopped after 375000 steps on 2 processors
and after 587000 steps on 4 processors, without any error message.

What could be the problem and how to solve it, please help me.

even i tried the 2 same jobs for 100 steps step size 0.002ps (total
2ns), one on single processor it is completed in 8 days
but the same job is stop after 55 steps on 4 processors.

Is there any change is required in MPI coding or in .mdp files. Sir if
you need any other please let me know.

Please solve my problem, I will be highly obliged.


DvdS:

Please upgrade to a recent version. 3.2.1 is more than five years old.



With warm regards.
Shikhar



--

Shikhar Gupta
Senior Research Fellow
Pharmacoinformatics Department
Block- A (Room No.- 208)
National Institute of Pharmaceutical Education & Research( NIPER )
Sec- 67, S.A.S Nagar
Mohali, Punjab (India)
Web-Site: www.niper.ac.in 
PIN- 160062
Email:shik_...@rediffmail.com
,shik...@gmail.com





--

Shikhar Gupta
Senior Research Fellow
Pharmacoinformatics Department
Block- A (Room No.- 208)
National Institute of Pharmaceutical Education & Research( NIPER )
Sec- 67, S.A.S Nagar
Mohali, Punjab (India)
Web-Site: www.niper.ac.in 
PIN- 160062
Email:shik_...@rediffmail.com
,shik...@gmail.com



--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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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] spc model of water

2009-08-24 Thread Justin A. Lemkul




abhijit kayal wrote:

Hi,
Myself Abhijit Kayal.Please anyone can give me the right 
topology,grompp and conf file of spc model of water.


The coordinate and topolgy file for SPC water is provided in the /share/top 
subdirectory of your Gromacs installation.  There is no standard grompp input 
file; you must choose the parameters for the system you are trying to simulate.


-Justin

  
Abhijit Kayal
IIT 
Delhi





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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] results of tpi

2009-08-24 Thread Berk Hess


Hi,

Did you try to load the file into xmgrace?
That will give you more readable output.

I don't know what you mean with Psi.
s2 is , where U is the interaction energy between the inserted
molecule and the system. V is the volume of that frame.
The entry s4 gives the average potential energy: .
The entries s5 and higher give energy components: .

Berk

> From: rolf.is...@rwth-aachen.de
> To: gmx-users@gromacs.org
> Date: Mon, 24 Aug 2009 15:35:46 +0200
> Subject: [gmx-users] results of tpi
> 
> Hi everybody,
> 
> I'm doing calculations with results, that I receive from tpi insertions. As I 
> don't get the results I am heading for, I starded to wonder weather I 
> interpretate the values in the columns of the xvg file correct.
> 
> Hear is the head of the xvg files and next to it my interpretation of its 
> meaning
> 
> @ s0 legend "-kT log(/)"  = the total average of 
> -kT*ln(/)
> /@ s1 legend "f. -kT log" = 
> -kT*ln()   of one frame
> @ s2 legend "f. "=  of 
> one frame  ***
> @ s3 legend "f. V" = V of one 
> frame  ***
> @ s4 legend "f. "  =  no idea
> @ s5 legend "f. "= no idea
> 
> The values that I need are these branded with "***". Were my suggesstions 
> right?
> 
> Regards, Rolf
> 
> 
> ___
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Re: [gmx-users] [Fwd: Please solve my problem]

2009-08-24 Thread cesteban

Hi All
I have similar problem using gromacs 4.0.2.
The MD simulation (5 ns) on single processor is complited in 5 days, but
the same MD can`t be complited on cluster on 4 or 8 processors. The MD
simulation is stopped without any error message.
Any help would be appreciated
Carmen
>
> To,
>David van der Spoel
>
> Dear Sir,
>
> I am using Gromacs 3.2.1 for the MD simulation on clusters but facing a
> problem.
> I am giving job for 50 steps step size 0.002ps (total 1ns) but my
> job is stopped after 47 steps. when i run this on 4 processors.
>
> But the same job is completed on 2 processors.Why this happing i am not
> able to understand.
>
> Another thing is that job for 150 steps step size 0.002ps (total
> 3ns) is stopped after 375000 steps on 2 processors
> and after 587000 steps on 4 processors, without any error message.
>
> What could be the problem and how to solve it, please help me.
>
> even i tried the 2 same jobs for 100 steps step size 0.002ps (total
> 2ns), one on single processor it is completed in 8 days
> but the same job is stop after 55 steps on 4 processors.
>
> Is there any change is required in MPI coding or in .mdp files. Sir if
> you need any other please let me know.
>
> Please solve my problem, I will be highly obliged.
>
>
> DvdS:
>
> Please upgrade to a recent version. 3.2.1 is more than five years old.
>
>
>
> With warm regards.
> Shikhar
>
>
>
> --
> 
> Shikhar Gupta
> Senior Research Fellow
> Pharmacoinformatics Department
> Block- A (Room No.- 208)
> National Institute of Pharmaceutical Education & Research( NIPER )
> Sec- 67, S.A.S Nagar
> Mohali, Punjab (India)
> Web-Site: www.niper.ac.in 
> PIN- 160062
> Email:shik_...@rediffmail.com
> ,shik...@gmail.com
> 
>
>
>
>
> --
> 
> Shikhar Gupta
> Senior Research Fellow
> Pharmacoinformatics Department
> Block- A (Room No.- 208)
> National Institute of Pharmaceutical Education & Research( NIPER )
> Sec- 67, S.A.S Nagar
> Mohali, Punjab (India)
> Web-Site: www.niper.ac.in 
> PIN- 160062
> Email:shik_...@rediffmail.com
> ,shik...@gmail.com
> 
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755.
> sp...@xray.bmc.uu.se  sp...@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] spc model of water

2009-08-24 Thread abhijit kayal

Hi,
Myself Abhijit Kayal.Please anyone can give me the right topology,grompp
and conf file of spc model of water.
  Abhijit
Kayal
IIT
Delhi
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[gmx-users] results of tpi

2009-08-24 Thread Rolf Erwin Isele-Holder

Hi everybody,

I'm doing calculations with results, that I receive from tpi insertions. As I 
don't get the results I am heading for, I starded to wonder weather I 
interpretate the values in the columns of the xvg file correct.

Hear is the head of the xvg files and next to it my interpretation of its 
meaning

@ s0 legend "-kT log(/)"  = the total average of 
-kT*ln(/)
/@ s1 legend "f. -kT log" = -kT*ln()  
 of one frame
@ s2 legend "f. "=  of 
one frame  ***
@ s3 legend "f. V" = V of one frame 
 ***
@ s4 legend "f. "  =  no idea
@ s5 legend "f. "= no idea

The values that I need are these branded with "***". Were my suggesstions right?

Regards, Rolf


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RE: [gmx-users] RE: Re: Pull to separate dimer

2009-08-24 Thread Berk Hess

 >  > pull_dim  =  Y N N

> >  > pull_nstxout  =  10

> >  > pull_nstfout  =  1

> >  > pull_ngroups  =  1

> >  > pull_group0  = DPPC

> >  > pull_group1 = r_31-60

> >  > pull_vec1  =  1 0 0

> >  > pull_init1  =  0.0

> >  > pull_rate1  =  0

> >

> > With a pull rate of 0, nothing is going to get pulled apart.  With

> > umbrella

> > pulling and a pull rate of 0, the distance between the two groups is

> > going to be

> > restrained at its initial value, as I understand it.

> >

> >  > pull_k1  =  1000

> >  >

> >  > Since I am trying to separate the two structures I thought about

> > using

> >  > the DPPC membrane as a reference structure for the pull, since my

> >

> > With DPPC as the reference, then pulling would occur between the COM

> > of the

> > pulled group and the COM of the bilayer.  If they lie at the same

> > place (i.e.,

> > protein dimer centered within the bilayer), I don't think this will

> > work.

> >

> >  > attemps with the monomer as a reference struture went with nothing

> >  > happening whatsoever. Is it correct to use such a long series of

> >  > aminoacids as a pull reference, i.e., gromacs will understand

> > that tha

> >  > pull should be in the center of mass, right? What does the manual

> > mean

> >

> > COM pulling should indeed be applied to the center of mass of

> > whatever you are

> > trying to pull on.

> >

> > If you're trying to separate a dimer, I would try setting

> > pull_group0 = Protein1

> > and pull_group1 = Protein2 (and apply a pull rate > 0).  Just a

> > guess worth

> > trying; I'm still figuring my way through the pull code for a few

> > things, too :)

> >

> > -Justin

> >

> >  > with "grompp normalizes the vector"? Is this how I should procede to

> >  > separate my dimer?

> >  > Thank you in advance

> >  > Fabrício Bracht

> >  >

> >  >

> >

> >

> >

> > 

> >

> > ___

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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] topology file

2009-08-24 Thread Justin A. Lemkul




abhijit kayal wrote:

Hi,
Myself Abhijit Kayal,student at IITD.Is it possible to create a 
topology file by Amber or some other molecular dynamics software for 
nonstandard molecules such as n-butane and can these topology files be 
used in gromacs?please reply.
 


Yes.  There are scripts in the User Contributions section of the website that 
will do exactly that.


-Justin


Abhijit Kayal
 
IIT Delhi
  






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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] topology file

2009-08-24 Thread abhijit kayal

Hi,
Myself Abhijit Kayal,student at IITD.Is it possible to create a topology
file by Amber or some other molecular dynamics software for nonstandard
molecules such as n-butane and can these topology files be used in
gromacs?please reply.

Abhijit Kayal
 IIT
Delhi
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[gmx-users] RE: Re: Pull to separate dimer

2009-08-24 Thread Ragnarok sdf

 N
> > >  > pull_nstxout  =  10
> > >  > pull_nstfout  =  1
> > >  > pull_ngroups  =  1
> > >  > pull_group0  = DPPC
> > >  > pull_group1 = r_31-60
> > >  > pull_vec1  =  1 0 0
> > >  > pull_init1  =  0.0
> > >  > pull_rate1  =  0
> > >
> > > With a pull rate of 0, nothing is going to get pulled apart.  With
> > > umbrella
> > > pulling and a pull rate of 0, the distance between the two groups
> is
> > > going to be
> > > restrained at its initial value, as I understand it.
> > >
> > >  > pull_k1  =  1000
> > >  >
> > >  > Since I am trying to separate the two structures I thought about
> > > using
> > >  > the DPPC membrane as a reference structure for the pull, since
> my
> > >
> > > With DPPC as the reference, then pulling would occur between the
> COM
> > > of the
> > > pulled group and the COM of the bilayer.  If they lie at the same
> > > place (i.e.,
> > > protein dimer centered within the bilayer), I don't think this will
> > > work.
> > >
> > >  > attemps with the monomer as a reference struture went with
> nothing
> > >  > happening whatsoever. Is it correct to use such a long series of
> > >  > aminoacids as a pull reference, i.e., gromacs will understand
> > > that tha
> > >  > pull should be in the center of mass, right? What does the
> manual
> > > mean
> > >
> > > COM pulling should indeed be applied to the center of mass of
> > > whatever you are
> > > trying to pull on.
> > >
> > > If you're trying to separate a dimer, I would try setting
> > > pull_group0 = Protein1
> > > and pull_group1 = Protein2 (and apply a pull rate > 0).  Just a
> > > guess worth
> > > trying; I'm still figuring my way through the pull code for a few
> > > things, too :)
> > >
> > > -Justin
> > >
> > >  > with "grompp normalizes the vector"? Is this how I should
> procede to
> > >  > separate my dimer?
> > >  > Thank you in advance
> > >  > Fabrício Bracht
> > >  >
> > >  >
> > >
> > >
> > >
> > >
> 
> > >
> > > ___
> > > gmx-users mailing listgmx-users@gromacs.org
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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] p-lincs use

2009-08-24 Thread Berk Hess


Hi,

I don't understand what you want or why you want this.
If it is necessary (you have constraint in your molecule between different
charge groups and you run in parallel with domain decomposition)
Gromacs will automatically use P-LINCS.

Berk

> Date: Mon, 24 Aug 2009 19:24:32 +0800
> From: dcp...@sina.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] p-lincs use
> 
>  Dear Gromacs developers,
> 
> I am using the Gromacs 4.05 and I want use the P-LINCS
>  in my work.  But I donot know how to use it.
>  Could you please give me a detailed description of using it, as I cannot
>  find its use method in the Manual4.0
> 
>  Thank you very much in advance,
> >
>  James, Wang  (Dr.)
> > Dalian University of Techonology
> > dcp...@163.com
> > 2009-08-24
> >
> 
> 
> 
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[gmx-users] p-lincs use

2009-08-24 Thread YH

 Dear Gromacs developers,

I am using the Gromacs 4.05 and I want use the P-LINCS
 in my work.  But I donot know how to use it.
 Could you please give me a detailed description of using it, as I cannot
 find its use method in the Manual4.0

 Thank you very much in advance,
>
 James, Wang  (Dr.)
> Dalian University of Techonology
> dcp...@163.com
> 2009-08-24
>



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RE: [gmx-users] Re: Pull to separate dimer

2009-08-24 Thread Berk Hess




> Date: Sat, 22 Aug 2009 20:01:19 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Re: Pull to separate dimer
> 
> 
> 
> Ragnarok sdf wrote:
> > Hi Justin, yes the intention is to pull the dimer apart within the
> > plane of the bilayer. I've ran a few more tests changing a few of
> > the parameters and got to one set that pulls my dimer apart
> > apparently in a "friendly" way, I mean, using g_dist to monitor the
> > COM distances I got an increment of 0.4 nm for a 500ps simulation.
> > Below is my set of parameters. I have a few questions though. I
> > don't seem to understand the relation between pull_k1 and
> > pull_rate1. I am sorry if that sounds like a silly question, but I
> > thought that the rate of pulling would be determined by the force
> > constant applied and the vector selected. 
> > 
> 
> The pull rate is how fast the applied force moves; pull_k1 is the force 
> constant 
> of the spring doing the pulling.
> 
> > One other question is regarding a future application. I intend to 
> > calculate the free energy of dimerization of my dimer. Using g_wham I 
> > would be able to get that, right? Then I got a little confused again, 
> 
> Yes.
> 
> > for in a tutorial that exaplains this procedure but using two argon 
> > molecules, there is a constraint set between both atoms, and that is 
> > coupled to the lambda value. I kind of understand that way of 
> > calculating free energy, since it is similar to fep, where is calculate 
> > along reaction coordinates. Well, I would really appreciate if someone 
> > could give me a reference or any indication on reading material. Anyway, 
> > my set of parameters:
> 
> I've yet to find a good tutorial for this purpose.  If anyone else knows of 
> one, 
> I'd be curious.  I've been doing some pulling lately to calculate PMF for 
> various ligand-binding events.  The way I think things need to go is:
> 
> 1. Generate a trajectory of configurations along the reaction coordinate.
> 2. Use different configurations as the starting points for independent 
> simulations in each sampling window.
> 3. Use umbrella sampling to restrain these configurations within the windows.
> 4. Calculate PMF from these simulations.
> 
> If anyone else has a better or more complete explanation, I'd like to see it, 
> too; the documentation on the subject is a bit thin.
> 
> -Justin
> 

I personally prefer using a constraint instead of an umbrella potential.
This avoids choosing a force constant and avoid the WHAM procedure.

You can also start the re/constrained simulation from the last configuration
at the previous distance. But this is not convenient if you want to run multiple
simulations simultaneously.
In both methods checking the convergence of the re/constraint force is critical.

Berk

> >  ; Pull Code
> > pull  =  umbrella
> > pull-geometry  =  direction
> > pull_dim  =  Y Y N
> > pull_nstxout  =  10
> > pull_nstfout  =  1
> > pull_ngroups  =  1
> > pull_group0  = r_1-30
> > pull_group1 = r_31-60
> > pull_vec1  =  1 1 0
> > pull_init1  =  0.0
> > pull_rate1  =  0.05
> > pull_k1  =  30
> > pull_constr_tol  =  1e-06
> > pull_pbcatom0  =  0
> > pull_pbcatom1  =  0
> > 
> > Fabrício Bracht
> > 
> > 
> > Ragnarok sdf wrote:
> >  > I am trying to learn how to use the pull code to separate a dimer. I
> >  > have read gromacs 4 manual and a tutorial I found on CSC, but it
> > seems I
> >  > still haven´t got the knack.
> >  > My system is consisted of a dimer inserted into a membrane lipid
> >  > bilayer. I have included the following lines into my mdp
> > parameter file.
> >  >
> > 
> > So the goal is to pull the dimer apart, within the plane of the bilayer?
> > 
> >  > pull  =  umbrella
> >  > pull-geometry  =  direction
> >  > pull_dim  =  Y N N
> >  > pull_nstxout  =  10
> >  > pull_nstfout  =  1
> >  > pull_ngroups  =  1
> >  > pull_group0  = DPPC
> >  > pull_group1 = r_31-60
> >  > pull_vec1  =  1 0 0
> >  > pull_init1  =  0.0
> >  > pull_rate1  =  0
> > 
> > With a pull rate of 0, nothing is going to get pulled apart.  With
> > umbrella
> > pulling and a pull rate of 0, the distance between the two groups is
> > going to be
> > restrained at its initial value, as I understand it.
> > 
> >  > pull_k1  =  1000
> >  >
> >  > Since I am trying to separate the two structures I thought about
> > using
> >  > the DPPC membrane as a reference structure for the pull, since my
> > 
> > With DPPC as the reference, then pulling would occur between the COM
> > of the
> > pulled group and the COM of the bilayer.  If they lie at the same
> > place (i.e.,
> > protein dimer centered within the bilayer), I don't think this will
> > work.
> > 
> >  > attemps with the monomer as a reference struture went with nothing
> >  > happening whatsoever. Is it correct

Re: [gmx-users] problems with rerun

[gmx-users] Re: Something about getting started

[gmx-users] Re: gmx-users Digest, Vol 64, Issue 156

Re: [gmx-users] problems with rerun

Re: [gmx-users] problems with rerun

Re: [gmx-users] [Fwd: Please solve my problem]

Re: [gmx-users] Parameters for membrane stability

[gmx-users] problems with rerun

[gmx-users] Parameters for membrane stability

Re: [gmx-users] correlation function

Re: [gmx-users] correlation function

Re: [gmx-users] correlation function

Re: [gmx-users] correlation function

Re: [gmx-users] Something about getting started

[gmx-users] Something about getting started

Re: [gmx-users] [Fwd: Please solve my problem]

Re: [gmx-users] [Fwd: Please solve my problem]

Re: [gmx-users] spc model of water

RE: [gmx-users] results of tpi

Re: [gmx-users] [Fwd: Please solve my problem]

[gmx-users] spc model of water

[gmx-users] results of tpi

RE: [gmx-users] RE: Re: Pull to separate dimer

Re: [gmx-users] topology file

[gmx-users] topology file

[gmx-users] RE: Re: Pull to separate dimer

RE: [gmx-users] p-lincs use

[gmx-users] p-lincs use

RE: [gmx-users] Re: Pull to separate dimer

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