date:20130614

at md stage, 

can we set refcoord_scaling = com  as follows, 

; Pressure coupling is on 
pcoupl   = Parrinello-Rahman; Pressure coupling on in NPT 
pcoupltype  = isotropic ; uniform scaling of box vectors 
tau_p= 2.0   ; time constant, in ps 
ref_p= 1.0   ; reference pressure, in bar 
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 
refcoord_scaling = com 

at lysozyme tutorial there is no  refcoord_scaling set.  I'm not sure if it
could do that set refcoord_scaling = com at md stage 

Thank you very much! 

maggin



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[gmx-users] Steepest Descents in vacuo

Before do Steepest with water,   we first do Steepest Descents in vacuo, if
such way will better to only do  Steepest with water ? 

Thank you very much! 

maggin



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[gmx-users] Re: distance_restraints

Hi, Tsjerk,

I have one question that in what situation people do constraint ?

Thank you very much!

maggin 



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Re: [gmx-users] Re: distance_restraints

2013-06-14 Thread Tsjerk Wassenaar

Hi Maggin,

The constraints are typically used during MD simulation to allow larger
time steps.

Cheers,

Tsjerk


On Fri, Jun 14, 2013 at 9:39 AM, maggin  wrote:

> Hi, Tsjerk,
>
> I have one question that in what situation people do constraint ?
>
> Thank you very much!
>
> maggin
>
>
>
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Re: [gmx-users] RE: About the binary identical results by restarting from the checkpoint file

On Fri, Jun 14, 2013 at 12:52 AM, Cuiying Jian wrote:

> Hi GROMACS Users,
>
> I am sorry if you are bothered by my second post about this topic. But the
> fact is that I tested restarting simulations with .cpt files by GROMACS
> 4.6.1.  and I still cannot get binary identical results from restarted
> simulations with those from continuous simulations. The command I used for
> restarting is as the following (e.g., only one processor is used during the
> simulations.):
> mdrun -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod
>

I answered you 11 days ago and you are re-posting with nothing new. Why?

Mark


>
>
> For further information, I attach my original .mdp file below:
> constraints  =  all-bonds ; convert all bonds to
> constraints.
> integrator =  md
> dt  =  0.002  ; ps !
> nsteps  =  1 ; total 2 ns.
> nstcomm =  10; frequency for center of
> mass motion removal.
> nstxout=  5  ; collect data every 10.0
> ps.
> nstxtcout =  5  ; frequency to write
> coordinate to xtc trajectory.
> nstvout=  5  ; frequency to write
> velocities to output trajectory.
> nstfout =  5  ; frequency to write
> forces to output trajectory.
> nstlog   =  5  ; frequency to write
> energies to log file.
> nstenergy=  5  ; frequency to write
> energies to energy file.
> nstlist   =  1   ; frequency to update
> the neighbor list.
> ns_type   =  grid
> rlist   =  1.4
> coulombtype  =  PME
> rcoulomb=  1.4
> vdwtype  =  cut-off
> rvdw =  1.4
> pme_order  =  8 ; use 6,8 or 10
> when running in parallel
> ewald_rtol   =  1e-5
> optimize_fft=  yes
> DispCorr   =  no ; don't apply any
> correction
> ;open LINCS
> constraint_algorithm = LINCS
> lincs_order   = 4   ;highest order in the
> expansion of the constraint coupling matrix
> lincs_warnangle  = 30 ;maximum angle that a bond can
> rotate before LINCS will complain
> lincs_iter  = 1;number of iterations
> to correct for a rotational lengthening in LINCS
> ; Temperature coupling is on
> Tcoupl  = v-rescale
> tau_t = 0.1
> tc-grps  = HEP
> ref_t  =  300
> ; Pressure  coupling is on
> Pcoupl  = parrinello-rahman
> Pcoupltype  = isotropic
> tau_p= 1.0
> compressibility   = 4.5e-5
> ref_p = 1.0
> ; generate velocity is on at 300 K.
> gen_vel  = yes
> gen_temp  = 300.0
> gen_seed   = -1
>
> Is there something wrong with my .mdp file or my command? Thanks a lot.
>
> Cheers,
> Cuiying
>
> From: cuiying_j...@hotmail.com
> To: gmx-users@gromacs.org
> Subject: RE: About the binary identical results by restarting from the
> checkpoint file
> Date: Mon, 3 Jun 2013 16:59:31 +
>
>
>
>
> Hi Mark,
>
> Thanks for your reply. I tested restarting simulations with .cpt files by
> GROMACS 4.6.1.  and the problems are still there, i.e. I cannot get binary
> identical results from restarted simulations with those from continuous
> simulations. The command I used for restarting is as the following (Only
> one processor is used during the simulations.):
> mdrun -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod
>
>
> For further information, I attach my original .mdp file below:
> constraints  =  all-bonds ; convert all bonds to
> constraints.
> integrator =  md
> dt  =  0.002  ; ps !
> nsteps  =  1 ; total 2 ns.
> nstcomm =  10; frequency for center of
> mass motion removal.
> nstxout=  5  ; collect data every 10.0
> ps.
> nstxtcout =  5  ; frequency to write
> coordinate to xtc trajectory.
> nstvout=  5  ; frequency to write
> velocities to output trajectory.
> nstfout =  5  ; frequency to write
> forces to output trajectory.
> nstlog   =  5  ; frequency to write
> energies to log file.
> nstenergy=  5  ; frequency to write
> energies to energy file.
> nstlist   =  1   ; frequency to update
> the neighbor list.
> ns_type   =  grid
> rlist   =  1.4
>

Re: [gmx-users] System equilibrium problems

On Thu, Jun 13, 2013 at 11:59 PM, Parker de Waal
wrote:

> Hi everyone,
>
> I recently tried to perform an 25 ns simulation on 12 nodes and was greeted
> with this error around 3.2 ns into the run.
>
> '3 particles communicated to PME node 9 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.'
>
> To my knowledge the system has reached equilibrium as shown by energy
> minimization, nvt and npt runs prior to the md run. The only thing that
> concerns me is the Pressure average of 1.9
>

This is normal, see
http://www.gromacs.org/Documentation/Terminology/Pressure


>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Potential   -921529  3200094074.9-214425
>  (kJ/mol)
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Temperature 300.033   0.161.57434  -0.790469  (K)
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Pressure1.94649   0.3291.45451.28586  (bar)
> Density 1012.96  0.037   0.778484 -0.0126246
>  (kg/m^3)
>
> Additionally here is a link to my md.mdp file
> https://gist.github.com/ParkerdeWaal/d472bac58aa9cebfc23e#file-gistfile1-sh


Seems fine, apart from fourierspacing being rather more lax than normal. Be
sure your settings are compatible with those used for your force field.

Mark


>
>
> Any input would be greatly appreciated!
> Parker
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[gmx-users] Re: distance_restraints

Hi, Tsjerk, 

Oh, so that's it . Thank you very much!

maggin




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Re: [gmx-users] refcoord_scaling = com




On 6/14/13 2:58 AM, maggin wrote:

at md stage,

can we set refcoord_scaling = com  as follows,

; Pressure coupling is on
pcoupl   = Parrinello-Rahman; Pressure coupling on in NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p= 2.0   ; time constant, in ps
ref_p= 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of water, bar^-1
refcoord_scaling = com

at lysozyme tutorial there is no  refcoord_scaling set.  I'm not sure if it
could do that set refcoord_scaling = com at md stage



The refcoord_scaling option is only relevant when running an NPT ensemble with 
position restraints.  It is, in fact, used in the tutorial during NPT 
equilibration.  It is unnecessary during the other steps.


-Justin

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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] Steepest Descents in vacuo




On 6/14/13 3:33 AM, maggin wrote:

Before do Steepest with water,   we first do Steepest Descents in vacuo, if
such way will better to only do  Steepest with water ?



Steepest descents is a fairly robust method, and as such, I rarely (if ever) do 
in vacuo minimization before minimizing my whole system.  On occasion, I have 
done it if some component has known bad geometry to start with.


-Justin

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Blacksburg, VA
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[gmx-users] Failed to lock: md.log.

2013-06-14 Thread zhaowh

Hi everyone,

When I restart the simulation as the following: "mdrun -s tpxout -cpi", a fatal 
error is arised (Fatal error: Failed to lock: md.log. Already running 
simulation?). But I have the files: md.log, traj.xtc, ender.edr, etc.

Thank you for your attention and answer.




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[gmx-users] Re: refcoord_scaling = com

Hi, Justin,

At md step, protein run out of box, if it will better that set position
constraint, let protein at center of box?

Thank you very much!

maggin  





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Re: [gmx-users] Failed to lock: md.log.

2013-06-14 Thread Jianguo Li



You can try move "md.log" to some folder and then copy back such as:
1) mv  md.log /some_folder 
2) cp  /some_folder/md.log .


It works for me


Jianguo 


- Original Message -
From: zhaowh 
To: gmx-users ; gmx-users ; 
gmx-users ; gmx-users ; gmx-users 
; gmx-users 
Cc: 
Sent: Friday, 14 June 2013, 17:35
Subject: [gmx-users] Failed to lock: md.log. 

Hi everyone,

When I restart the simulation as the following: "mdrun -s tpxout -cpi", a fatal 
error is arised (Fatal error: Failed to lock: md.log. Already running 
simulation?). But I have the files: md.log, traj.xtc, ender.edr, etc.

Thank you for your attention and answer.




zhaowh
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[gmx-users] Re: Steepest Descents in vacuo

Hi, Justin,

Thank you very much for your help!

Another question is when we do steep minimization, if it will be better
first do steep with constraint, then do steep without constraint?

Thank you very much!

maggin 



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Re: [gmx-users] Re: Steepest Descents in vacuo

Constraints make the job of the minimizer more difficult. If the starting
configuration is bad enough that the EM step might be really useful, give
the potential energy surface a free run without constraints. And then in
such cases do a preliminary NVT with dt=0.0005 and no constraints to get
things relaxed further. Only once things are close to correct do you want
to think about constraints so you can increase the time step.

Mark


On Fri, Jun 14, 2013 at 12:38 PM, maggin  wrote:

> Hi, Justin,
>
> Thank you very much for your help!
>
> Another question is when we do steep minimization, if it will be better
> first do steep with constraint, then do steep without constraint?
>
> Thank you very much!
>
> maggin
>
>
>
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Re: [gmx-users] Issues with energy when running in the microcanonical ensemble

On Wed, Jun 12, 2013 at 11:26 AM, C.M.Sampson  wrote:

> Dear all,
>
> I'm using Gromacs 4.5.5 with the amber ff99SB forcefield to run NVE
> simulations on ethane in 725 TIP3P water molecules.  I used antechamber
> to parametrise my ethane.
>
> I have 2 issues;
>
> Firstly the energy conservation of my simulations seems to get worse as
> I lower my timestep, here is an example .mdp file that I'm using:
>
>
> integrator  = md-vv
> gen_vel = no
> nsteps  = 100
> dt  = 0.001
> nstlist = 10
> rlist   = 1.3
> coulombtype = pme
> rcoulomb= 1.0
> vdw-type= Shift
> rvdw= 1.0
> tcoupl  = no
> pcoupl  = no
> nstenergy   = 100
>
> I found a link describing that it could be an issue with the precision
> and that Gromacs can be installed with double precision:
>
> http://www.gromacs.org/Documentation/Terminology/Conserving_Energy
>
> but is this the only way to ensure energy conservation?
>

Many issues with md-vv have been fixed since 4.5.5. Please update and try
again.


>
> My second issue is with the calculation of the kinetic energy, I have
> 2183 atoms in my simulation box which means the kinetic energy should be
> (roughly)
>
> 0.5 * 3*2183-3(degrees of freedom) * 0.001987204118(kB) * 300(T) *
> 4.184(conversion from kcal/mol to kJ/mol) = 8163.97
>
> however, when I look in my simulation the kinetic energy Gromacs outputs
> is 5498.20
>
>Step   Time Lambda
>   00.00.0
>
>Energies (kJ/mol)
>Bond  Angle Ryckaert-Bell.  LJ-14 Coulomb-14
> 5.95743e+001.96046e+014.71247e-015.73520e-013.92661e+00
> LJ (SR)   Coulomb (SR)   Coul. recip.  PotentialKinetic En.
> 5.12842e+03   -3.20604e+04   -2.67111e+03   -2.95726e+045.49820e+03
> Total EnergyTemperature Pressure (bar)
>-2.40744e+043.02575e+02   -1.82251e+03
>
> By running in NVE I'm not using a thermostat and can't find any reason
> in the manual to scale the kinetic energy.  Is there an a reason I'm
> missing as to why my kinetic energy seems lower than it should be?
>

I couldn't follow your equation above, but the most likely issue would be
the use of some algorithm that reduces the number of degrees of freedom,
e.g. rigid water/bonds.

Mark
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[gmx-users] Re: Steepest Descents in vacuo

Hi, Justin,

If I use Pymol to set up a mutation of 1dx0.pdb, If it best do Steepest
Descents in vacuo first ?

Thank you very much!

maggin



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Re: [gmx-users] System equilibrium problems

Hi Mark,

Thanks for your response,

Currently I'm using the gromos53a6 force field because it is compatible
with heme cofactor found within P450.
I'll look through the literature again to double check my settings for my
NvT, NpT and energy minimization steps
as well, however any further insight would be greatly appreciated!

Parker


On Fri, Jun 14, 2013 at 4:13 AM, Mark Abraham wrote:

> On Thu, Jun 13, 2013 at 11:59 PM, Parker de Waal
> wrote:
>
> > Hi everyone,
> >
> > I recently tried to perform an 25 ns simulation on 12 nodes and was
> greeted
> > with this error around 3.2 ns into the run.
> >
> > '3 particles communicated to PME node 9 are more than 2/3 times the
> cut-off
> > out of the domain decomposition cell of their charge group in dimension
> y.'
> >
> > To my knowledge the system has reached equilibrium as shown by energy
> > minimization, nvt and npt runs prior to the md run. The only thing that
> > concerns me is the Pressure average of 1.9
> >
>
> This is normal, see
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
>
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> >
> ---
> > Potential   -921529  3200094074.9-214425
> >  (kJ/mol)
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> >
> ---
> > Temperature 300.033   0.161.57434  -0.790469  (K)
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> >
> ---
> > Pressure1.94649   0.3291.45451.28586
>  (bar)
> > Density 1012.96  0.037   0.778484 -0.0126246
> >  (kg/m^3)
> >
> > Additionally here is a link to my md.mdp file
> >
> https://gist.github.com/ParkerdeWaal/d472bac58aa9cebfc23e#file-gistfile1-sh
>
>
> Seems fine, apart from fourierspacing being rather more lax than normal. Be
> sure your settings are compatible with those used for your force field.
>
> Mark
>
>
> >
> >
> > Any input would be greatly appreciated!
> > Parker
> > --
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[gmx-users] question about g_mindist

2013-06-14 Thread Mahin Saberi

I appreciate you for your useful guidance
I want to determine the minimum distances between COM (center of mass)
of a surfactant molecule and that of number of other surfactants but
g_mindist compute the distances between one group and a number of
other groups.  It is not quite clear for me that g_mindist can do
it?please guide me about it.
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[gmx-users] Re: System equilibrium problems

Hi, Parker,

gromos53a6 force field,  rvdw=1,  if it right ? please check. 

Your ref_p = 1.0, So, Pressure average of 1.9 is come from which step? NVT,
NPT, md ?

Actually, we use:  g_energy -f npt.edr -o pressure.xvg 
to see if NPT has reached equilibrium. 

g_energy -f nvt.edr
to see if NVT has reached equilibrium.

maggin



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Re: [gmx-users] Re: System equilibrium problems

HI Maggin,

The Pressure came from NPT simulation, I apologize for the lack of
annotation. Here are some of the outputs of your suggested checks of
equilibrium
https://docs.google.com/spreadsheet/ccc?key=0Ao2bINpUakZ-dHpiZG9SOXhkX0JGNXlqTHBfQ1kwbnc&usp=sharing

I'm currently looking into the rvdw value as you suggested as well as the
fourierspacing as Mark suggested.

However to help with this problem I've uploaded all of .mdp files as well
as my bash script here ->
https://gist.github.com/ParkerdeWaal/8a7a73682e04a4878902
Maybe there is a problem with my choice of box size? -bt cubic -d 1?
Viewing the boxed and solvated system showed a distance of ~10A between the
protein and the box which should be ample.

Additionally a full output log of the run can be found here ->
http://research.parkerdewaal.com/slurm-940372.out
which seems to be error free until the final md run.

Thanks Everyone,
Parker

On Fri, Jun 14, 2013 at 9:56 AM, maggin  wrote:

> Hi, Parker,
>
> gromos53a6 force field,  rvdw=1,  if it right ? please check.
>
> Your ref_p = 1.0, So, Pressure average of 1.9 is come from which step? NVT,
> NPT, md ?
>
> Actually, we use:  g_energy -f npt.edr -o pressure.xvg
> to see if NPT has reached equilibrium.
>
> g_energy -f nvt.edr
> to see if NVT has reached equilibrium.
>
> maggin
>
>
>
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Re: [gmx-users] Re: refcoord_scaling = com




On 6/14/13 6:33 AM, maggin wrote:

Hi, Justin,

At md step, protein run out of box, if it will better that set position
constraint, let protein at center of box?


There is no such thing as "outside" of an infinite system using periodic 
boundary conditions.


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

-Justin

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Re: [gmx-users] Failed to lock: md.log.




On 6/14/13 6:35 AM, Jianguo Li wrote:



You can try move "md.log" to some folder and then copy back such as:
1) mv  md.log /some_folder
2) cp  /some_folder/md.log .



Otherwise use -noappend in the mdrun command.  All the important files can be 
concatenated after the run, anyway.


-Justin

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Blacksburg, VA
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: Steepest Descents in vacuo




On 6/14/13 7:22 AM, maggin wrote:

Hi, Justin,

If I use Pymol to set up a mutation of 1dx0.pdb, If it best do Steepest
Descents in vacuo first ?



I have no idea.  There are many ways you can probably dream up to proceed with 
any system.  For normal proteins in water, I never waste time with an in vacuo 
minimization, unless, like I said before, I know some element of the structure 
is really bad.


-Justin

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Re: [gmx-users] Re: System equilibrium problems

On 6/14/13 10:45 AM, Parker de Waal wrote:

HI Maggin,

The Pressure came from NPT simulation, I apologize for the lack of
annotation. Here are some of the outputs of your suggested checks of
equilibrium
https://docs.google.com/spreadsheet/ccc?key=0Ao2bINpUakZ-dHpiZG9SOXhkX0JGNXlqTHBfQ1kwbnc&usp=sharing

I'm currently looking into the rvdw value as you suggested as well as the
fourierspacing as Mark suggested.

However to help with this problem I've uploaded all of .mdp files as well
as my bash script here ->
https://gist.github.com/ParkerdeWaal/8a7a73682e04a4878902
Maybe there is a problem with my choice of box size? -bt cubic -d 1?
Viewing the boxed and solvated system showed a distance of ~10A between the
protein and the box which should be ample.

Additionally a full output log of the run can be found here ->
http://research.parkerdewaal.com/slurm-940372.out
which seems to be error free until the final md run.

The cutoffs are wrong for 53A6. Standard usage:

rcoulomb = 0.9
rlist = 0.9
rvdw = 1.4

The values of rcoulomb and rlist are fairly flexible when using PME. The value
of rvdw generally should not be toyed with.

-Justin

Justin A. Lemkul, Ph.D.
Research Scientist
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: About the binary identical results by restarting from the checkpoint file

2013-06-14 Thread Cuiying Jian




Hi Mark,
 
Sorry for my carelessness. I check my email again and see your reply. I get 
your point that my problem may be (at least part of) caused by RNG of the 
thermostat. 
 
Thanks again and sorry for my careless bothering. 
 
Cheers,
Cuiying
 
> On Fri, Jun 14, 2013 at 12:52 AM, Cuiying Jian 
> wrote:
> 
> > Hi GROMACS Users,
> >
> > I am sorry if you are bothered by my second post about this topic. But the
> > fact is that I tested restarting simulations with .cpt files by GROMACS
> > 4.6.1.  and I still cannot get binary identical results from restarted
> > simulations with those from continuous simulations. The command I used for
> > restarting is as the following (e.g., only one processor is used during the
> > simulations.):
> > mdrun -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod
> >
> 
> I answered you 11 days ago and you are re-posting with nothing new. Why?
> 
> Mark
> 
> 
> >
> >
> > For further information, I attach my original .mdp file below:
> > constraints  =  all-bonds ; convert all bonds to
> > constraints.
> > integrator =  md
> > dt  =  0.002  ; ps !
> > nsteps  =  1 ; total 2 ns.
> > nstcomm =  10; frequency for center of
> > mass motion removal.
> > nstxout=  5  ; collect data every 10.0
> > ps.
> > nstxtcout =  5  ; frequency to write
> > coordinate to xtc trajectory.
> > nstvout=  5  ; frequency to write
> > velocities to output trajectory.
> > nstfout =  5  ; frequency to write
> > forces to output trajectory.
> > nstlog   =  5  ; frequency to write
> > energies to log file.
> > nstenergy=  5  ; frequency to write
> > energies to energy file.
> > nstlist   =  1   ; frequency to update
> > the neighbor list.
> > ns_type   =  grid
> > rlist   =  1.4
> > coulombtype  =  PME
> > rcoulomb=  1.4
> > vdwtype  =  cut-off
> > rvdw =  1.4
> > pme_order  =  8 ; use 6,8 or 10
> > when running in parallel
> > ewald_rtol   =  1e-5
> > optimize_fft=  yes
> > DispCorr   =  no ; don't apply any
> > correction
> > ;open LINCS
> > constraint_algorithm = LINCS
> > lincs_order   = 4   ;highest order in the
> > expansion of the constraint coupling matrix
> > lincs_warnangle  = 30 ;maximum angle that a bond can
> > rotate before LINCS will complain
> > lincs_iter  = 1;number of iterations
> > to correct for a rotational lengthening in LINCS
> > ; Temperature coupling is on
> > Tcoupl  = v-rescale
> > tau_t = 0.1
> > tc-grps  = HEP
> > ref_t  =  300
> > ; Pressure  coupling is on
> > Pcoupl  = parrinello-rahman
> > Pcoupltype  = isotropic
> > tau_p= 1.0
> > compressibility   = 4.5e-5
> > ref_p = 1.0
> > ; generate velocity is on at 300 K.
> > gen_vel  = yes
> > gen_temp  = 300.0
> > gen_seed   = -1
> >
> > Is there something wrong with my .mdp file or my command? Thanks a lot.
> >
> > Cheers,
> > Cuiying
> >
> > From: cuiying_j...@hotmail.com
> > To: gmx-users@gromacs.org
> > Subject: RE: About the binary identical results by restarting from the
> > checkpoint file
> > Date: Mon, 3 Jun 2013 16:59:31 +
> >
> >
> >
> >
> > Hi Mark,
> >
> > Thanks for your reply. I tested restarting simulations with .cpt files by
> > GROMACS 4.6.1.  and the problems are still there, i.e. I cannot get binary
> > identical results from restarted simulations with those from continuous
> > simulations. The command I used for restarting is as the following (Only
> > one processor is used during the simulations.):
> > mdrun -v -s md.tpr -cpt 0 -cpi md.cpt -deffnm md -reprod
> >
> >
> > For further information, I attach my original .mdp file below:
> > constraints  =  all-bonds ; convert all bonds to
> > constraints.
> > integrator =  md
> > dt  =  0.002  ; ps !
> > nsteps  =  1 ; total 2 ns.
> > nstcomm =  10; frequency for center of
> > mass motion removal.
> > nstxout=  5  ; collect data every 10.0
> > ps.
> > nstxtcout =  5  ; frequency to write
> > coordinate to xtc trajectory.
> > nstvout=  5  ; frequency to write
> > velocities to

[gmx-users] Re: Enthalpy Confusion

2013-06-14 Thread Jeffery Perkins

 or should i be doing < U+*ref_p > = ? 
>> 
>>> More specifically,  + *ref_p = H 
>> 
>>>  isn't really meaningful thing.  I mean, you can define something 
>>> such that  = H, but that's not really thermodynamics. 
>> 
>> sorry I always have issues deciding how to talk about this stuff, so
>> thanks 
>> for putting up with my terrible notation =) 
>> 
 example system gives  = -1168 kJ/mol and i find  = -725 kJ/mol 
 either 
>> 
>>> Interesting.  What material at what phase conditions?  For liquids, 
>>> the PV contribution should be very small. 
>> 
>> I hadn't really thought about that... but the system is a monatomic 
>> Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass
>> = 
>> 40 amu) which should be a liquid at the conditions I was looking at,
>> P=1000 
>> bar, T = 300 K using phase diagram in: Equation of state for the 
>> Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL.
>> 37, 
>> No. 5, 1429-1454 
>> 
>> the  is -1600 and the p is 880 when manually done, around 400 from 
>> g_energy 
>Here's the code: 
> /* This is pV (in kJ/mol).  The pressure is the reference
> pressure, 
>not the instantaneous pressure */ 
> pv = vol*md->ref_p/PRESFAC; 
>
> add_ebin(md->ebin, md->ipv, 1, &pv, bSum); 
> enthalpy = pv + enerd->term[F_ETOT]; 
>
>What is your volume? 
>What is Etot?

a bit messy but this is data from g_energy for the system with increasing
temperature (300 K-1000 K), and constant pressure of 1000 bar (so 100 000
000 Pascals):

Temperature VolumeEnthalpy  Potential   Total EnergypV  
Kinetic En.
K nm^3   kJ/molkJ/mol
kJ/mol   kJ/mol kJ/mol
299.914 14.7226  -1168.83   -2565.44-1611.63442.791 
953.817
399.901 17.462   -339.795   -2080.31-808.501468.706 
1271.81
499.898 21.0263   421.763   -1666.7 -76.8794498.643 
  
1589.83
599.899 25.1149   1088.79   -1348.14559.718 529.07  
1907.86
699.914 29.4219   1668.2-1115.471110.46 557.733 
2225.94
799.925 33.7642184.31   -943.6131600.39 583.922 
2544
899.923 38.0865  2660.3 -809.5722052.45 607.847 
2862.03
999.931 42.2798  3101.56-707.9082472.17 629.383 
3180.08

all uncorrected for the number of particles in the box (so Etot is in kJ/256
mol of particles)

when i use this data to get H myself i get:

H
kJ/mol
-725.32948
242.7114
1188.90386
2071.63498
2881.65838
3632.9828
4345.2573
5017.41396

again uncorrected for the number of particles in the box

Thoughts?



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[gmx-users] lipid parmaters

2013-06-14 Thread Revthi Sanker

Dear all,
I am trying to perform all-atom simulations of a protein+lipid system with 
charmm27 forcefield in gromacs . Can anyone suggest me from where I could 
obtain the paramaters( *.itp file)  from? I tried searching the lipid-book but 
in vain.cGENFF and swissparam are exclusively for small molecules and not for 
biomolecules. I need parameters for cholesteryl oleate and dioleyl phosphotidyl 
choline. 
Kindly provide your valuable suggestions.
Thank you all in advance.

Regards,
Revathi
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Re: [gmx-users] Re: Enthalpy Confusion

2013-06-14 Thread David van der Spoel


On 2013-06-14 19:28, Jeffery Perkins wrote:

or should i be doing < U+*ref_p > = ?



More specifically,  + *ref_p = H



 isn't really meaningful thing.  I mean, you can define something
such that  = H, but that's not really thermodynamics.


sorry I always have issues deciding how to talk about this stuff, so
thanks
for putting up with my terrible notation =)


example system gives  = -1168 kJ/mol and i find  = -725 kJ/mol
either



Interesting.  What material at what phase conditions?  For liquids,
the PV contribution should be very small.


I hadn't really thought about that... but the system is a monatomic
Lennard-Jones particle (uncharged sigma = 0.35 nm epsilon = 2 kJ/mol mass
=
40 amu) which should be a liquid at the conditions I was looking at,
P=1000
bar, T = 300 K using phase diagram in: Equation of state for the
Lennard-Jones fluid, J. J. Nicolas et al., MOLECULAR PHYSICS, 1979, VOL.
37,
No. 5, 1429-1454

the  is -1600 and the p is 880 when manually done, around 400 from
g_energy

Here's the code:
 /* This is pV (in kJ/mol).  The pressure is the reference
pressure,
not the instantaneous pressure */
 pv = vol*md->ref_p/PRESFAC;

 add_ebin(md->ebin, md->ipv, 1, &pv, bSum);
 enthalpy = pv + enerd->term[F_ETOT];

What is your volume?
What is Etot?


a bit messy but this is data from g_energy for the system with increasing
temperature (300 K-1000 K), and constant pressure of 1000 bar (so 100 000
000 Pascals):

Temperature VolumeEnthalpy  Potential   Total EnergypV  
Kinetic En.
K nm^3   kJ/molkJ/mol
kJ/mol   kJ/mol kJ/mol
299.914 14.7226  -1168.83   -2565.44-1611.63442.791 
953.817
399.901 17.462   -339.795   -2080.31-808.501468.706 
1271.81
499.898 21.0263   421.763   -1666.7 -76.8794498.643
1589.83
599.899 25.1149   1088.79   -1348.14559.718 529.07  
1907.86
699.914 29.4219   1668.2-1115.471110.46 557.733 
2225.94
799.925 33.7642184.31   -943.6131600.39 583.922 
2544
899.923 38.0865  2660.3 -809.5722052.45 607.847 
2862.03
999.931 42.2798  3101.56-707.9082472.17 629.383 
3180.08

all uncorrected for the number of particles in the box (so Etot is in kJ/256
mol of particles)

when i use this data to get H myself i get:

H
kJ/mol
-725.32948
242.7114
1188.90386
2071.63498
2881.65838
3632.9828
4345.2573
5017.41396

again uncorrected for the number of particles in the box

Thoughts?


Your calculation seems correct. Which gmx version did you use?
The correlation between the numbers is almost 100% so there must be a 
simple explanation.





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[gmx-users] Re: Enthalpy Confusion

2013-06-14 Thread Jeffery Perkins

>Your calculation seems correct. Which gmx version did you use? 
>The correlation between the numbers is almost 100% so there must be a 
>simple explanation.

gmx version is 4.5.4, and yeah the correlation is odd, in the code you
listed:

>>  pv = vol*md->ref_p/PRESFAC; 
>> 
>>  add_ebin(md->ebin, md->ipv, 1, &pv, bSum); 
>>  enthalpy = pv + enerd->term[F_ETOT]

so pv = vol * md->ref_p/PRESFAC; is the vol * ref_p/conversion factor,
right?
the only thing there that seems like it could be off is if PRESFAC isn't
correct for some reason

(correct me if I'm wrong of course!)

Jeffery



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[gmx-users] choosing box vectors

Dear All,

I have two different membrane systems (membrane with waters only) already
with me. So I dont need to add solvent molecules.

So to start with simulation I need box size (last line in gro file). I used
following command (for both cases):

editconf -f del.pdb -o del.gro -c -bt cubic


First case details:

system size : 10.707 11.077  7.493 (nm)
diameter: 14.737   (nm)
center  :  6.928  6.932  6.936 (nm)
box vectors : 10.707 11.077  7.493 (nm)
box angles  :  90.00  90.00  90.00 (degrees)
box volume  : 888.68   (nm^3)
shift   : -1.574 -1.394 -3.190 (nm)
new center  :  5.353  5.538  3.747 (nm)



Second case details:

system size : 10.065 11.826  9.911 (nm)
diameter: 16.459   (nm)
center  :  9.229  9.229  9.229 (nm)
box vectors : 18.459 18.459 18.459 (nm)
box angles  :  90.00  90.00  90.00 (degrees)
box volume  :6289.31   (nm^3)
shift   :  0.000  0.000  0.001 (nm)
new center  :  9.229  9.229  9.229 (nm)



As I have solvents already so my box size as a rule should be (Maximum X -
Minimum X), (Maximum Y - Minimum Y), (Maximum Z - Minimum Z). This indeed I
found to be correct for my first case in which box dimensions in gro file =
10.707 11.077  7.493

But why in my second case box dimension in gro file = 18.459 18.459 18.459.
Surprisingly its is equal to Maximum X + Minimum X of my system and all are
same being 18.459. Rather it should be (Maximum X - Minimum X), (Maximum Y
- Minimum Y), (Maximum Z - Minimum Z) as in first case.

Also in VMD I saw gro files. In first case pbc box completely fits the
membrane water system but in second case pbc box is un-necessarily large as
it is using 18.459 18.459 18.459


I am confused why in second case it chose Maximum X + Minimum X unlike in
first case?

please suggest,

thanks,
Jiom
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Re: [gmx-users] choosing box vectors




On 6/14/13 4:58 PM, gromacs query wrote:

Dear All,

I have two different membrane systems (membrane with waters only) already
with me. So I dont need to add solvent molecules.

So to start with simulation I need box size (last line in gro file). I used
following command (for both cases):

editconf -f del.pdb -o del.gro -c -bt cubic


First case details:

 system size : 10.707 11.077  7.493 (nm)
 diameter: 14.737   (nm)
 center  :  6.928  6.932  6.936 (nm)
 box vectors : 10.707 11.077  7.493 (nm)
 box angles  :  90.00  90.00  90.00 (degrees)
 box volume  : 888.68   (nm^3)
 shift   : -1.574 -1.394 -3.190 (nm)
new center  :  5.353  5.538  3.747 (nm)



I don't see how this is possible.  You used -bt cubic, but you clearly (1) don't 
want that, because the system is rectangular and (2) a cubic box is not 
produced.  Why even use editconf?  Clearly the input .pdb file has correct box 
vectors in it already and does not require any modification.





Second case details:

 system size : 10.065 11.826  9.911 (nm)
 diameter: 16.459   (nm)
 center  :  9.229  9.229  9.229 (nm)
 box vectors : 18.459 18.459 18.459 (nm)
 box angles  :  90.00  90.00  90.00 (degrees)
 box volume  :6289.31   (nm^3)
 shift   :  0.000  0.000  0.001 (nm)
new center  :  9.229  9.229  9.229 (nm)



Here, there are probably erroneously large vectors written in the .pdb file 
already.

-Justin




As I have solvents already so my box size as a rule should be (Maximum X -
Minimum X), (Maximum Y - Minimum Y), (Maximum Z - Minimum Z). This indeed I
found to be correct for my first case in which box dimensions in gro file =
10.707 11.077  7.493

But why in my second case box dimension in gro file = 18.459 18.459 18.459.
Surprisingly its is equal to Maximum X + Minimum X of my system and all are
same being 18.459. Rather it should be (Maximum X - Minimum X), (Maximum Y
- Minimum Y), (Maximum Z - Minimum Z) as in first case.

Also in VMD I saw gro files. In first case pbc box completely fits the
membrane water system but in second case pbc box is un-necessarily large as
it is using 18.459 18.459 18.459


I am confused why in second case it chose Maximum X + Minimum X unlike in
first case?

please suggest,

thanks,
Jiom



--


Justin A. Lemkul, Ph.D.
Research Scientist
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] autocorrelation output g_hbond

2013-06-14 Thread learnmd

Hi,

I have run a 5 ns simulation with a small protein in water [SPCE]. I am
interested in the rate of breakage (sense of how quickly / slowly hbonds are
broken and formed) of hbonds between protein and solvent. I ran g_hbond -ac
for the trajectory and received the following output:

Normalization for c(t) = 0.0204961 for gh(t) = 4.55478e-07
Hydrogen bond thermodynamics at T = 298.15 K
Fitting parameters chi^2 =  0.0335188
Q =  0
--
Type  Rate (1/ps) Time (ps)  DG (kJ/mol)  Chi^2
Forward 0.022 46.303  14.035   0.0335188
Backward   -0.080-12.447-666.000
One-way 0.068 14.603  11.175
Integral0.020 48.944  14.173
Relaxation  0.052 19.211  11.854

My question is that the 46 ps that is shown for "forward" can be interpreted
in the sense that I have described above?  Or am I missing the point,
completely. I am grateful for any pointers. 

Thanks




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Re: [gmx-users] Re: System equilibrium problems

Thanks Justin!

I've updated the values accordingly. However can I ask where you found
these? I'm curious if there is a site that I missed while searching.

Best,
Parker


On Fri, Jun 14, 2013 at 12:04 PM, Justin Lemkul  wrote:

>
>
> On 6/14/13 10:45 AM, Parker de Waal wrote:
> > HI Maggin,
> >
> > The Pressure came from NPT simulation, I apologize for the lack of
> > annotation. Here are some of the outputs of your suggested checks of
> > equilibrium
> >
> https://docs.google.com/spreadsheet/ccc?key=0Ao2bINpUakZ-dHpiZG9SOXhkX0JGNXlqTHBfQ1kwbnc&usp=sharing
> >
> >
> > I'm currently looking into the rvdw value as you suggested as well as the
> > fourierspacing as Mark suggested.
> >
> > However to help with this problem I've uploaded all of .mdp files as well
> > as my bash script here ->
> > https://gist.github.com/ParkerdeWaal/8a7a73682e04a4878902
> > Maybe there is a problem with my choice of box size? -bt cubic -d 1?
> > Viewing the boxed and solvated system showed a distance of ~10A between
> the
> > protein and the box which should be ample.
> >
> > Additionally a full output log of the run can be found here ->
> > http://research.parkerdewaal.com/slurm-940372.out
> > which seems to be error free until the final md run.
> >
>
> The cutoffs are wrong for 53A6.  Standard usage:
>
> rcoulomb = 0.9
> rlist = 0.9
> rvdw = 1.4
>
> The values of rcoulomb and rlist are fairly flexible when using PME.  The
> value
> of rvdw generally should not be toyed with.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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: System equilibrium problems




On 6/14/13 7:03 PM, Parker de Waal wrote:

Thanks Justin!

I've updated the values accordingly. However can I ask where you found
these? I'm curious if there is a site that I missed while searching.



Cutoff values are described in the primary literature for the force field of 
interest.


-Justin

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Research Scientist
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] choosing box vectors

Dear Justin,

Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I
dont want to use as I think they are wrong). In my case if I have already
water molecules in my system then if I use:

editconf -f del.pdb -o del.gro -c -d 0.0 -bt cubic

even now also I see pbc box (in vmd) its quite big than system as you can
see from output

system size : 10.707 11.077  7.493 (nm)
diameter: 14.737   (nm)
center  :  6.928  6.932  6.936 (nm)
box vectors :  0.000  0.000  0.000 (nm)
box angles  :   0.00   0.00   0.00 (degrees)
box volume  :   0.00   (nm^3)
shift   :  0.441  0.436  0.432 (nm)
new center  :  7.369  7.369  7.369 (nm)
new box vectors : 14.737 14.737 14.737 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :3200.60   (nm^3)


What should I do?

regards,



On Sat, Jun 15, 2013 at 1:37 AM, Justin Lemkul  wrote:

>
>
> On 6/14/13 4:58 PM, gromacs query wrote:
>
>> Dear All,
>>
>> I have two different membrane systems (membrane with waters only) already
>> with me. So I dont need to add solvent molecules.
>>
>> So to start with simulation I need box size (last line in gro file). I
>> used
>> following command (for both cases):
>>
>> editconf -f del.pdb -o del.gro -c -bt cubic
>>
>>
>> First case details:
>>
>>  system size : 10.707 11.077  7.493 (nm)
>>  diameter: 14.737   (nm)
>>  center  :  6.928  6.932  6.936 (nm)
>>  box vectors : 10.707 11.077  7.493 (nm)
>>  box angles  :  90.00  90.00  90.00 (degrees)
>>  box volume  : 888.68   (nm^3)
>>  shift   : -1.574 -1.394 -3.190 (nm)
>> new center  :  5.353  5.538  3.747 (nm)
>>
>>
> I don't see how this is possible.  You used -bt cubic, but you clearly (1)
> don't want that, because the system is rectangular and (2) a cubic box is
> not produced.  Why even use editconf?  Clearly the input .pdb file has
> correct box vectors in it already and does not require any modification.
>
>
>
>>
>> Second case details:
>>
>>  system size : 10.065 11.826  9.911 (nm)
>>  diameter: 16.459   (nm)
>>  center  :  9.229  9.229  9.229 (nm)
>>  box vectors : 18.459 18.459 18.459 (nm)
>>  box angles  :  90.00  90.00  90.00 (degrees)
>>  box volume  :6289.31   (nm^3)
>>  shift   :  0.000  0.000  0.001 (nm)
>> new center  :  9.229  9.229  9.229 (nm)
>>
>>
> Here, there are probably erroneously large vectors written in the .pdb
> file already.
>
> -Justin
>
>
>
>>
>> As I have solvents already so my box size as a rule should be (Maximum X -
>> Minimum X), (Maximum Y - Minimum Y), (Maximum Z - Minimum Z). This indeed
>> I
>> found to be correct for my first case in which box dimensions in gro file
>> =
>> 10.707 11.077  7.493
>>
>> But why in my second case box dimension in gro file = 18.459 18.459
>> 18.459.
>> Surprisingly its is equal to Maximum X + Minimum X of my system and all
>> are
>> same being 18.459. Rather it should be (Maximum X - Minimum X), (Maximum Y
>> - Minimum Y), (Maximum Z - Minimum Z) as in first case.
>>
>> Also in VMD I saw gro files. In first case pbc box completely fits the
>> membrane water system but in second case pbc box is un-necessarily large
>> as
>> it is using 18.459 18.459 18.459
>>
>>
>> I am confused why in second case it chose Maximum X + Minimum X unlike in
>> first case?
>>
>> please suggest,
>>
>> thanks,
>> Jiom
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] choosing box vectors




On 6/14/13 7:37 PM, gromacs query wrote:

Dear Justin,

Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I
dont want to use as I think they are wrong). In my case if I have already
water molecules in my system then if I use:

editconf -f del.pdb -o del.gro -c -d 0.0 -bt cubic

even now also I see pbc box (in vmd) its quite big than system as you can
see from output

 system size : 10.707 11.077  7.493 (nm)
 diameter: 14.737   (nm)
 center  :  6.928  6.932  6.936 (nm)
 box vectors :  0.000  0.000  0.000 (nm)
 box angles  :   0.00   0.00   0.00 (degrees)
 box volume  :   0.00   (nm^3)
 shift   :  0.441  0.436  0.432 (nm)
new center  :  7.369  7.369  7.369 (nm)
new box vectors : 14.737 14.737 14.737 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :3200.60   (nm^3)


What should I do?



You're specifying a cubic box, but for most membrane systems, that's probably 
wrong.  What editconf is doing is determining what box vectors are necessary, 
then since you're telling it to make the box cubic, it's forcing all of the 
vectors to be the same.  Apparently you have at least one dimension that, in 
this case, is 14.737 nm in length, and then all other vectors are then set to 
the same value.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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Aw: Re: [gmx-users] Re:Problems with extending runs

2013-06-14 Thread lloyd riggs

 
 
I have a bizzar problem.  I did 21 simulation for 4 ns each.  These were equ'd for 4ns prior, then taken from an assembly run over 4ns so between 300 pico and 4ns additional each.  A reviewer wants a couple extnded ends added,say like 4 extra ns, which I can only do 1-4 at most due to time limits (they take several days with 4-5 nodes, 8cpu quad core amd)  Now I just simply took the end run .mdp files, added these on, generated .tpr file, and a short check to generate a checkpoint .cpt.  I ran one on the cluster here in bern, one on a home PC and submitted one to the dutch/euro grid system.  The one on the grid in bern works fine, the one on my PC as well (intel 8 core), however it only reaches 75,000 of 20 million time steps necessary in 8 hours, I could never go beyonda 0.0005 time step (well 0.0008 but kept it at the former due to ease of changing file parmeters), any case, when I submit it to the Eu/dutch grid it crashes at at step 5000 with a PME, non-equilibrated error.  My question is why does it run on one, the exact same tpr tested, but not the other?

I looked at versions 4.5.5 my pc, 4.5.7 at unibe and a altered version of 4.5.3 on the dutch/eu grid.  Other than that, I can not find a problem, but woundered, as use of an extra que would have helped but most likely not now, as I have a response time.  I can not fathom why it would give such large changes however in bonds/angles in one but not the other as the versions are not that different?  Was there a large change between these versions, or other possibilities?

Stephan Watkins


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Re: [gmx-users] choosing box vectors

Dear Justin,

I saw your tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
)

But my case is different. I can not even generate tpr file (trjconv as
tutorial says) as it need box info

Can you please suggest what can be the best possible way? If I just use
system size dimension (X, Y Z) and do mimization it break my system in
parts!


How to choose optimum box vector in such case?

regards,



On Sat, Jun 15, 2013 at 2:49 AM, Justin Lemkul  wrote:

>
>
> On 6/14/13 7:37 PM, gromacs query wrote:
>
>> Dear Justin,
>>
>> Thanks for reply. Yes sorry indeed its taking box vector from pdb (which I
>> dont want to use as I think they are wrong). In my case if I have already
>> water molecules in my system then if I use:
>>
>> editconf -f del.pdb -o del.gro -c -d 0.0 -bt cubic
>>
>> even now also I see pbc box (in vmd) its quite big than system as you can
>> see from output
>>
>>  system size : 10.707 11.077  7.493 (nm)
>>  diameter: 14.737   (nm)
>>  center  :  6.928  6.932  6.936 (nm)
>>  box vectors :  0.000  0.000  0.000 (nm)
>>  box angles  :   0.00   0.00   0.00 (degrees)
>>  box volume  :   0.00   (nm^3)
>>  shift   :  0.441  0.436  0.432 (nm)
>> new center  :  7.369  7.369  7.369 (nm)
>> new box vectors : 14.737 14.737 14.737 (nm)
>> new box angles  :  90.00  90.00  90.00 (degrees)
>> new box volume  :3200.60   (nm^3)
>>
>>
>> What should I do?
>>
>>
> You're specifying a cubic box, but for most membrane systems, that's
> probably wrong.  What editconf is doing is determining what box vectors are
> necessary, then since you're telling it to make the box cubic, it's forcing
> all of the vectors to be the same.  Apparently you have at least one
> dimension that, in this case, is 14.737 nm in length, and then all other
> vectors are then set to the same value.
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] choosing box vectors




On 6/14/13 8:08 PM, gromacs query wrote:

Dear Justin,

I saw your tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
)

But my case is different. I can not even generate tpr file (trjconv as
tutorial says) as it need box info

Can you please suggest what can be the best possible way? If I just use
system size dimension (X, Y Z) and do mimization it break my system in
parts!


How to choose optimum box vector in such case?



Omit "-bt cubic" from your command and it should work fine.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] choosing box vectors

Dear Justin,

Thanks a lot. I used this and it works fine:

editconf -f final.pdb -o final.gro -c -d 0.0

regards,
Jiomm


On Sat, Jun 15, 2013 at 3:09 AM, Justin Lemkul  wrote:

>
>
> On 6/14/13 8:08 PM, gromacs query wrote:
>
>> Dear Justin,
>>
>> I saw your tutorial (
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/**
>> gmx-tutorials/membrane_**protein/03_solvate.html
>>
>> )
>>
>> But my case is different. I can not even generate tpr file (trjconv as
>> tutorial says) as it need box info
>>
>> Can you please suggest what can be the best possible way? If I just use
>> system size dimension (X, Y Z) and do mimization it break my system in
>> parts!
>>
>>
>> How to choose optimum box vector in such case?
>>
>>
> Omit "-bt cubic" from your command and it should work fine.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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
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[gmx-users] 53A6 Heme bound Cys