from:"Johnny Lu"

Dear Users,

I was trying to run NVE simulation of alanine peptide in vacuum with double
precision gromacs 5.1. [plot of energy at
http://postimg.org/image/6b6kksax7/]
The total energy of the simulation still has fluctuation about 1kcal/mol.
There should be no fluctuation of total energy in an ideal world.

What are the possible source of this fluctuation? I'm testing the error
contributed by the integrator by halving the time-step.

How big is the error caused by integrator, error caused by h-bond
constraint, and fluctuation caused by thermostat relative to each other?

Previously I used the same mdp file, except with 1fs time step and with
H-bond constraint, to simulate alanine peptide in water. The total energy
of the whole system seemed conserved. I now wonder if that conservation is
actually a cancellation of different numerical errors.

When I run alanine peptide in vacuum, H-bond constraint made the energy
drop quickly. I set constraint to none, and the energy drop was lower.

The question I'm interested in is verification of a theory. It is affected
by the shape and pattern of these errors. Without knowing the pattern of
these errors, I hope the errors are small enough.

Thank you again.

The mdp file is below. the box size is large enough such that the distance
between mirror image of the molecules is larger than the cut off for vdw
and coulomb forces.

title= Alanine
; Run parameters
integrator= md; leap-frog integrator
nsteps= 3; 300 ns
dt= 0.0005; 0.5 fs

; Output control
nstxout= 10; save coordinates every 1.0 ps
nstvout= 10; save velocities every 1.0 ps
nstfout= 10

nstenergy= 500; save energies every 1.0 ps
nstlog= 500; update log file every 1.0 ps

; Bond parameters
continuation= no; Restarting after NPT equilibration 1
constraint_algorithm= lincs; holonomic constraints
constraints= none; all bonds (even heavy atom-H bonds)
constrained
lincs_iter= 2; accuracy of LINCS
lincs_order= 4; also related to accuracy

; Neighborsearching
cutoff-scheme   = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 20; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; short-range van der Waals cutoff (in nm)

; Electrostatics
coulombtype= PME; Particle Mesh Ewald for long-range
electrostatics
pme_order= 4; cubic interpolation
fourierspacing= 0.1; grid spacing for FFT

tcoupl= no; no thermostat
pcoupl= no; no barostat


; Periodic boundary conditions
pbc= xyz; 3-D PBC

; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme

; Velocity generation
gen_vel= yes; Velocity generation is off

verlet-buffer-drift = 0.0005
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Re: [gmx-users] Split Trajectory file into parts

The file system seemed to have no quota, after checking with that command.
The problem seems to be that the simulation I set up save too quickly for
the file system.
Splitting the trajectory into parts only alleviated but not solved the
problem.
in the end I ran the simulation at another place.

On Mon, Aug 31, 2015 at 3:50 AM, Peter Kroon <p.c.kr...@rug.nl> wrote:

>
>
> On 29/08/15 16:22, Justin Lemkul wrote:
> >
> >
> > On 8/29/15 9:10 AM, Johnny Lu wrote:
> >> Dear Users,
> >>
> >> Simulation writes to a Lustre file system (a distributed file system
> >> made
> >> of many hard drives).
> >> About 100 Gb was written in 1 hrs. After a while, gromacs 5.1 says it
> >> can't
> >> write the trajectory file.
> >> The file system still has lots of space. Not sure if that was because
> >> one
> >> of the many hard drives filled up.
> Does your cluster implement filesystem quotas? Did you reach it? On our
> cluster (which also uses Lustre) I use `lfs quota /home` to see my quota
> and usage on the partition /home.
>
> Peter
> >>
> >> Is it possible to ask gromacs to automatically split the trajectory
> >> files
> >> into parts?
> >
> > No.
> >
> >> Or, I have to write a shell script to make gromacs restart the
> >> simulation
> >> every 15 minutes?
> >>
> >
> > Yes.  Or, heed what grompp tells you about how much data will be
> > generated and simply construct a very trivial loop to execute mdrun
> > for N steps, invoke convert-tpr, mdrun -cpi -noappend, etc.
> >
> > -Justin
> >
>
>
>
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Re: [gmx-users] charge neutralization in vacuum simulations

was that for mass spectrometry?

On Tue, Sep 1, 2015 at 1:30 PM, Vitaly V. Chaban  wrote:

> To get a neutral protein, protonate all residues...
>
> Another question is what's your simulation goal, since protonated and
> deprotonated residues behave obviously in a different way.
>
>
>
>
> On Tue, Sep 1, 2015 at 6:57 AM, tasneem kausar
>  wrote:
> > Dear Gromacs users
> >
> > I am trying to neutralized the protein having two chains with four
> negative
> > charge.
> > I ran the command line as : pdb2gmx -c prtn.pdb -p -o -glu -asp.
> > I have  chosen one protonated glu and one protonated asp for each protein
> > chain.
> > The net charge is now zero.
> > Am I going through the right step for the neutralization?
> > If there is any other way to neutralize protein, please suggest.
> >
> > Thanks in advance
> > --
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Re: [gmx-users] OPLS/AA parameters for 2-propanol

Not sure if those are for 2-propanol as a liquid or interaction between
2-propanol and protein.
from googling "2 propanol opls/aa"

1. Development and Testing of the OPLS All-Atom Force Field on
Conformational Energetics and Properties of Organic Liquids
  The parameters are in the supporting info.
  Seems not exactly 2-propanol. But it has parameter for organic
liquids.
  "OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols"
  http://pubs.acs.org/doi/abs/10.1021/ja9621760

2. A statistical model of hydrogen bond networks in liquid alcohols
  http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf

3. Parameterization of OPLS–AA Force Field for the Conformational Analysis
of Macrocyclic Polyketides
  https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf

On Tue, Sep 1, 2015 at 9:41 PM, Ebert Maximilian 
wrote:

> Dear list,
>
> I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA
> format. Before deriving my own I thought it would be best to ask first. I
> saw some posts that people used 2-propanol in OPLS but couldn’t find any
> reference in google scholar.
>
> Thank you very much,
>
> Max
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Re: [gmx-users] OPLS/AA parameters for 2-propanol

that was by google. I haven't parametrized forcefields.
did they just put the pieces in
http://pubs.acs.org/doi/abs/10.1021/ja9621760 together and say it can work
for 2-propanol?


On Tue, Sep 1, 2015 at 11:34 PM, Johnny Lu <johnny.lu...@gmail.com> wrote:

> Not sure if those are for 2-propanol as a liquid or interaction between
> 2-propanol and protein.
> from googling "2 propanol opls/aa"
>
> 1. Development and Testing of the OPLS All-Atom Force Field on
> Conformational Energetics and Properties of Organic Liquids
>   The parameters are in the supporting info.
>   Seems not exactly 2-propanol. But it has parameter for organic
> liquids.
>   "OPLS-AA Non-Bonded Parameters for Hydrocarbons and Alcohols"
>   http://pubs.acs.org/doi/abs/10.1021/ja9621760
>
> 2. A statistical model of hydrogen bond networks in liquid alcohols
>
> http://publications.lib.chalmers.se/records/fulltext/local_157930.pdf
>
> 3. Parameterization of OPLS–AA Force Field for the Conformational Analysis
> of Macrocyclic Polyketides
>   https://labs.chem.ucsb.edu/bruice/thomas/tcb_pdf/522.pdf
>
> On Tue, Sep 1, 2015 at 9:41 PM, Ebert Maximilian <m.eb...@umontreal.ca>
> wrote:
>
>> Dear list,
>>
>> I wanted to know if anybody has parameters for 2-propanol in the OPLS/AA
>> format. Before deriving my own I thought it would be best to ask first. I
>> saw some posts that people used 2-propanol in OPLS but couldn’t find any
>> reference in google scholar.
>>
>> Thank you very much,
>>
>> Max
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
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>> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
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Re: [gmx-users] extend a simulation just with xtc file

can extend simulation if the number of steps were reached.
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

That said, does extending the simulation avoid the problems that you found
in the simulation?

On Tue, Sep 1, 2015 at 11:54 PM, Johnny Lu <johnny.lu...@gmail.com> wrote:

> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
>
>
>
> On Tue, Sep 1, 2015 at 11:53 PM, Johnny Lu <johnny.lu...@gmail.com> wrote:
>
>> the position in xtc is not accurate enough for restarting simulation. xtc
>> has no velocity.
>>
>> restart need position, velocity, and variables for the thermostat and
>> barostat.
>>
>> Do you have any cpt file? may be you can run a restart using cpt and tpr
>> files.
>>
>> On Mon, Aug 31, 2015 at 10:21 PM, Adriana Garro <adrianagarr...@gmail.com
>> > wrote:
>>
>>> :-(  ok
>>> Thanks, I will have to run this simulation again.
>>> Bye
>>>
>>> Adriana
>>>
>>> ***
>>> Dra. Adriana D. Garro
>>> Química Medicinal
>>> Facultad de Química, Bioquímica y Farmacia
>>> Universidad Nacional de San Luis
>>> IMASL-CONICET
>>> San Luis, Argentina
>>>
>>> Tel..:+54 266 4424689 int 6153
>>> e-mail...: adga...@unsl.edu.ar
>>> e-mail...:  adrianagarr...@gmail.com
>>>
>>>
>>> **
>>>
>>> 2015-08-31 23:17 GMT-03:00 Justin Lemkul <jalem...@vt.edu>:
>>>
>>> >
>>> >
>>> > On 8/31/15 11:52 AM, Adriana Garro wrote:
>>> >
>>> >> Dear Gromacs users,
>>> >>
>>> >> My 100 ns simulation finish but in a wrong way, I knew it when I
>>> tried to
>>> >> use an analizing tool and the message was the next one
>>> >>
>>> >> Fatal error:
>>> >> Magic Number Error in XTC file (read 0, should be 1995)
>>> >>
>>> >> It seems that this kind of error is  related to the network file
>>> system.
>>> >> My first attempt was restart (I am using gromacs 4.5.5)
>>> >> mdrun -s topol.tpr -cpi state.cpt
>>> >> but of course it finished immediately then I realized that the number
>>> of
>>> >> steps was reached.
>>> >>
>>> >> I did a copy of the md.xtc file  while it was running in order to see
>>> how
>>> >> things were going on, aproximately at 85 ns, so I would like to know
>>> if it
>>> >> is possible to extend my simulation using this 85ns xtc file. (without
>>> >> having cpt file)
>>> >>
>>> >>
>>> > The .xtc has nothing useful about the state of the simulation.  A set
>>> of
>>> > coordinates is inadequate for properly continuing a simulation.
>>> >
>>> > -Justin
>>> >
>>> > --
>>> > ==
>>> >
>>> > Justin A. Lemkul, Ph.D.
>>> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> >
>>> > Department of Pharmaceutical Sciences
>>> > School of Pharmacy
>>> > Health Sciences Facility II, Room 629
>>> > University of Maryland, Baltimore
>>> > 20 Penn St.
>>> > Baltimore, MD 21201
>>> >
>>> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> > http://mackerell.umaryland.edu/~jalemkul
>>> >
>>> > ==
>>> > --
>>> > Gromacs Users mailing list
>>> >
>>> > * Please search the archive at
>>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> > posting!
>>> >
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>>> >
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>>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> > send a mail to gmx-users-requ...@gromacs.org.
>>> >
>>> --
>>> Gromacs Users mailing list
>>>
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>>>
>>
>>
>
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Re: [gmx-users] Gromacs-5.1 XLC Seg. Fault.

what is the computer you are using?
i tried to build gromacs 4.6.7 on IBM System p7 755.
It was very tedious. I had to build cmake. I think I even tried to build
gnu gcc compiler.
The end result was that gromacs ran very slow.

On Tue, Aug 25, 2015 at 4:08 PM, Carlos Aguni  wrote:

> Hello guys.
>
> I've compiled Gromacs-5.1 with XLC 13.1.2 + ESSL and FFTW (altivec enabled)
> but
> I'm getting seg. fault while trying to run it.
> I'm testing it with .96 workload. Here's its input:
> http://pastebin.com/Ezp95b2B
>
> Here's the error I'm getting:
>
> [ubuntu:19418] *** Process received signal ***
>
> [ubuntu:19418] Signal: Segmentation fault (11)
>
> [ubuntu:19418] Signal code: Address not mapped (1)
>
> [ubuntu:19418] Failing at address: 0x1beefdebd
>
> [ubuntu:19418] [ 0] [0x3fff99cc0478]
>
> [ubuntu:19418] [ 1]
> /lib/powerpc64le-linux-gnu/libpthread.so.0(pthread_mutex_lock+0x20)
> [0x3fff961fb6b0]
>
> [ubuntu:19418] [ 2] mdrun_mpi() [0x10266830]
>
> [ubuntu:19418] [ 3] mdrun_mpi(tMPI_Thread_mutex_lock+0x30) [0x1044f9f0]
>
> [ubuntu:19418] [ 4] mdrun_mpi(gmx_detect_hardware+0x44) [0x1035b974]
>
> [ubuntu:19418] [ 5] mdrun_mpi(mdrunner+0x2cc) [0x100d6bfc]
>
> [ubuntu:19418] [ 6] mdrun_mpi(_Z9gmx_mdruniPPc+0x14b0) [0x100e0540]
>
> [ubuntu:19418] [ 7] mdrun_mpi() [0x101271fc]
>
> [ubuntu:19418] [ 8]
> mdrun_mpi(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x2f4) [0x1011bae4]
>
> [ubuntu:19418] [ 9]
>
> mdrun_mpi(_ZN3gmx24CommandLineModuleManager21runAsMainSingleModuleEiPPcPNS_26CommandLineModuleInterfaceE+0x9c)
> [0x1011bf4c]
>
> [ubuntu:19418] [10]
>
> mdrun_mpi(_ZN3gmx24CommandLineModuleManager14runAsMainCMainEiPPcPFiiS2_E+0x70)
> [0x1011c0e0]
>
> [ubuntu:19418] [11] mdrun_mpi(main+0x24) [0x100d0374]
>
> [ubuntu:19418] [12] /lib/powerpc64le-linux-gnu/libc.so.6(+0x24e80)
> [0x3fff96054e80]
>
> [ubuntu:19418] [13]
> /lib/powerpc64le-linux-gnu/libc.so.6(__libc_start_main+0xc4)
> [0x3fff96055074]
>
> [ubuntu:19418] *** End of error message ***
>
> --
>
> And here's the md.log:
>
> http://pastebin.com/GCkY136Q
>
>
> Is there anything I can do to help clarify this problem?
>
> Thanks in advance!
>
> Carlos.
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Re: [gmx-users] extend a simulation just with xtc file

the position in xtc is not accurate enough for restarting simulation. xtc
has no velocity.

restart need position, velocity, and variables for the thermostat and
barostat.

Do you have any cpt file? may be you can run a restart using cpt and tpr
files.

On Mon, Aug 31, 2015 at 10:21 PM, Adriana Garro 
wrote:

> :-(  ok
> Thanks, I will have to run this simulation again.
> Bye
>
> Adriana
>
> ***
> Dra. Adriana D. Garro
> Química Medicinal
> Facultad de Química, Bioquímica y Farmacia
> Universidad Nacional de San Luis
> IMASL-CONICET
> San Luis, Argentina
>
> Tel..:+54 266 4424689 int 6153
> e-mail...: adga...@unsl.edu.ar
> e-mail...:  adrianagarr...@gmail.com
>
>
> **
>
> 2015-08-31 23:17 GMT-03:00 Justin Lemkul :
>
> >
> >
> > On 8/31/15 11:52 AM, Adriana Garro wrote:
> >
> >> Dear Gromacs users,
> >>
> >> My 100 ns simulation finish but in a wrong way, I knew it when I tried
> to
> >> use an analizing tool and the message was the next one
> >>
> >> Fatal error:
> >> Magic Number Error in XTC file (read 0, should be 1995)
> >>
> >> It seems that this kind of error is  related to the network file system.
> >> My first attempt was restart (I am using gromacs 4.5.5)
> >> mdrun -s topol.tpr -cpi state.cpt
> >> but of course it finished immediately then I realized that the number of
> >> steps was reached.
> >>
> >> I did a copy of the md.xtc file  while it was running in order to see
> how
> >> things were going on, aproximately at 85 ns, so I would like to know if
> it
> >> is possible to extend my simulation using this 85ns xtc file. (without
> >> having cpt file)
> >>
> >>
> > The .xtc has nothing useful about the state of the simulation.  A set of
> > coordinates is inadequate for properly continuing a simulation.
> >
> > -Justin
> >
> > --
> > ==
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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Re: [gmx-users] extend a simulation just with xtc file

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts



On Tue, Sep 1, 2015 at 11:53 PM, Johnny Lu <johnny.lu...@gmail.com> wrote:

> the position in xtc is not accurate enough for restarting simulation. xtc
> has no velocity.
>
> restart need position, velocity, and variables for the thermostat and
> barostat.
>
> Do you have any cpt file? may be you can run a restart using cpt and tpr
> files.
>
> On Mon, Aug 31, 2015 at 10:21 PM, Adriana Garro <adrianagarr...@gmail.com>
> wrote:
>
>> :-(  ok
>> Thanks, I will have to run this simulation again.
>> Bye
>>
>> Adriana
>>
>> ***
>> Dra. Adriana D. Garro
>> Química Medicinal
>> Facultad de Química, Bioquímica y Farmacia
>> Universidad Nacional de San Luis
>> IMASL-CONICET
>> San Luis, Argentina
>>
>> Tel..:+54 266 4424689 int 6153
>> e-mail...: adga...@unsl.edu.ar
>> e-mail...:  adrianagarr...@gmail.com
>>
>>
>> **
>>
>> 2015-08-31 23:17 GMT-03:00 Justin Lemkul <jalem...@vt.edu>:
>>
>> >
>> >
>> > On 8/31/15 11:52 AM, Adriana Garro wrote:
>> >
>> >> Dear Gromacs users,
>> >>
>> >> My 100 ns simulation finish but in a wrong way, I knew it when I tried
>> to
>> >> use an analizing tool and the message was the next one
>> >>
>> >> Fatal error:
>> >> Magic Number Error in XTC file (read 0, should be 1995)
>> >>
>> >> It seems that this kind of error is  related to the network file
>> system.
>> >> My first attempt was restart (I am using gromacs 4.5.5)
>> >> mdrun -s topol.tpr -cpi state.cpt
>> >> but of course it finished immediately then I realized that the number
>> of
>> >> steps was reached.
>> >>
>> >> I did a copy of the md.xtc file  while it was running in order to see
>> how
>> >> things were going on, aproximately at 85 ns, so I would like to know
>> if it
>> >> is possible to extend my simulation using this 85ns xtc file. (without
>> >> having cpt file)
>> >>
>> >>
>> > The .xtc has nothing useful about the state of the simulation.  A set of
>> > coordinates is inadequate for properly continuing a simulation.
>> >
>> > -Justin
>> >
>> > --
>> > ==
>> >
>> > Justin A. Lemkul, Ph.D.
>> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> >
>> > Department of Pharmaceutical Sciences
>> > School of Pharmacy
>> > Health Sciences Facility II, Room 629
>> > University of Maryland, Baltimore
>> > 20 Penn St.
>> > Baltimore, MD 21201
>> >
>> > jalem...@outerbanks.umaryland.edu | (410) 706-7441
>> > http://mackerell.umaryland.edu/~jalemkul
>> >
>> > ==
>> > --
>> > Gromacs Users mailing list
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>> > posting!
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Re: [gmx-users] regarding box volume

2015-08-29 Thread Johnny Lu

I am new to simulation and haven't done any simulation for finding free
energy. The following is my guess.

How big are the molecules?
If the box size is small then the concentration of the molecules is higher.

May be the dissociation part is fine if:
the hybrid can't see its mirror image (the intermolecular force between the
hybrid and its mirror image is very weak).
the partially dissociated hybrid can't see its mirror image.

The rebinding part is fine if:
Once the hybrid completely dissociated (AB -- A+B), both A and B have
enough space such that A can't see B for a while.

What do you want to know?
If you want to know the free energy of the dissociation, may be the
following tutorial can help:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/02_topology.html
I guess that tutorial only require the hybrid can't see its mirror image.

Might need thermodynamic cycle:
http://openi.nlm.nih.gov/detailedresult.php?img=3203851_1741-7007-9-71-4req=4

On Sat, Aug 29, 2015 at 7:14 AM, soumadwip ghosh soumadwipgh...@gmail.com
wrote:

Ignore the previous mail.

Hi,
please excuse me if my question appears very silly to you. I have a
hybrid of a Carbon nanotube and a polymer and I want to study the
unwrapping dynamics of the polymer in presence of a polymer binding agent.
I kept the hybrid inside a triclinic box and am doing simulations in
presence of that binder for 100 ns. The size of the box is around 277 nm3.
Is there a possibility that once the hybrid dissociates the polymer may not
have enough volume to go apart from the CNT and hence affecting the correct
dynamics picture? Should I perform such kind of simulations in a bigger
box? I might be missing out something very fundamental. Your help would be
appreciated.

Sorry if I am asking for much.
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Re: [gmx-users] adding hydrogens to pdb file

2015-08-29 Thread Johnny Lu

Hi.

reduce.exe seems not part of gromacs.

http://kinemage.biochem.duke.edu/software/reduce.php

On Thu, Aug 27, 2015 at 1:59 AM, elham tazikeh elham.tazi...@gmail.com
wrote:

 Dear GMX users
 i want to *adding Hydrogens* to my lig.pdb (for making lig.itp file by ATB
 server) in cmd program in Windowds, but i dont know the way of that?
 i know the below command is used for that:
 reduce.exe -BUILD lig.pdb  lig_h.pdb
 but i cant do it in cmd program
 i really appricite for any help
 elham
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[gmx-users] Split Trajectory file into parts

2015-08-29 Thread Johnny Lu

Dear Users,

Simulation writes to a Lustre file system (a distributed file system made
of many hard drives).
About 100 Gb was written in 1 hrs. After a while, gromacs 5.1 says it can't
write the trajectory file.
The file system still has lots of space. Not sure if that was because one
of the many hard drives filled up.

Is it possible to ask gromacs to automatically split the trajectory files
into parts?
Or, I have to write a shell script to make gromacs restart the simulation
every 15 minutes?

Thank you.
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[gmx-users] Restart -append

2015-08-26 Thread Johnny Lu

Dear Users,

Simulation crashed.
Gromacs 5.1 wrote last check point at about 4 min before the crash.

Restart with mdrun -cpi (last check point file) -append

Will the -append option get rid of the data for those 4 min between the
last check point written and the crash?

Thank you.
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Re: [gmx-users] How do I calculate the difference between two energy values?

2015-08-26 Thread Johnny Lu

Let x(t) be coulomb decoupling at time t.
Let y(t) be VdW decoupling at time t.

I guess the most safe way to get the answer is:
calculate z(t) = x(t) + y(t)
then, calculate standard deviation of z(t).

If x(t) and y(t) are independent and both x(t) and y(t) are normally
distributed, then I guess using the error propagation rule is fine.
(https://en.wikipedia.org/wiki/Sum_of_normally_distributed_random_variables)



On Tue, Aug 25, 2015 at 2:15 PM, Peter Stern peter.st...@weizmann.ac.il
wrote:

 I believe that this is a statistics question and not a gromacs question
 :-).

 51.4 +/- 1.33 kJ/mol

 Sent from my iPad

  On 25 באוג׳ 2015, at 14:44, minky son minky0...@gmail.com wrote:
 
  Dear GROMACS users,
 
  I have been studying free energy calculation in Justin tutorial.
 
  I performed VDW decoupling and coulomb decoupling simulations separately.
 
  I obtained the free energy values for each simulation using gmx bar.
 
  coulomb decoupling simulation = 60.88 +/- 0.23 kJ/mol
  VDW decoupling simulation= -9.48 +/- 1.31 kJ/mol
 
  So, I want to calculate the sum of the two energy values,
 
  specially the second term (51.4  +/- ???).
 
 
  Please give me any advice to solve this.
 
  Regards,
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[gmx-users] Thread, Multiple gpu, and sharing node

2015-08-18 Thread Johnny Lu

Dear Users,

Hi.

The system has about 3k atoms, and I used a rhombic dodecahedron box.

The node in the cluster has 2 sockets and 12 cores per socket. (24 sockets
in total)
It also has 4 gpu.

Will I waste cpu time, if I run with all 24 cores and assign 1 gpu to 3
cores?

Should I compile for mpi?

Alternatively, I can run with just 12 cores and assign 1 gpu to every 3
cores.
The remaining 12 cores and 2 gpu will be used by another user.

Which way is a more efficient use of time per cpu core?

Thank you.
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[gmx-users] box size and neighbor list cut-off

Dear Users,

Hi.

Box vector length:
  3.448, 3.448, 3.448 nm dodecahedron.
  (Box volume is 28.98 nm^3)

Diameter of tripeptide:
  1.248 nm

Volume of tripeptide:
  0.35503 nm^3 (from genbox output)

Short range Neighbor list cut-off:
  1.1 nm (set manually by rlist=1.1)

Other short range cut off (VdW and electrostatic):
  1.0 nm

According to 5.2 manual (manual-5.2-dev.pdf),
  This means that the length of each box vector must exceed the length
of the macromolecule in the direction of that edge plus two times the
cut-off radius R_c

Box vector length = Diameter of peptide + 2 x cut-off
  3.448 = 1.248 + 2 x 1.1

Do I have to leave any leeway in the box size? (say, a box size of 3.5 nm)

I will run a NPT simulation (Berendsen barostat). Then continue the
simulation with a NVT simulation. And finally continue the NVT simulation
with a NVE simulation.

Last time when I ran a double precision NVE simulation, I set rlist=1.3 and
used a 4.848^3 nm^3 dodecahedron box. The energy conservation was good. If
I use a 1.1nm rlist, will I get an energy conservation that is nearly as
good as the rlist = 1.3nm simulation?

Thank you again.
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Re: [gmx-users] Respect waters in crystallographic pdb file?

I haven't tried that before.
May be you can open the .gro files before and after genbox with a text
editor.
Then, check those water molecules?
Those water molecules might have the same residue id.


On Mon, Aug 17, 2015 at 1:42 PM, Jorge Fernandez de Cossio Diaz 
cos...@cim.sld.cu wrote:

 Hi all,
 I have a crystallographic PDB file which comes some waters molecules. I
 want to run an MD simulation which includes those water molecules. After
 generating the topology file (which includes the waters) and defining the
 box shape, I fill the box with solvent using genbox. At this point it
 becomes impossible to track down visually where the water molecules are. My
 question is if the file that genbox outputs still contains the
 crystallographic water molecules? Or are they replaced by the molecules
 added by genbox?
 Thanks in advance. Best, cossio
 ---

 [http://5.cim.co.cu/cim.gif]
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Re: [gmx-users] box size and neighbor list cut-off

Sorry, I mean:
If I use double precision gmx mdrun and constraint h-bonds, can I expect
1.135 rlist to give a drift in total energy as small as the one in the
table?

On Mon, Aug 17, 2015 at 5:07 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Thank you for the advices.

 I tried setting different varlet buffer drift in the 1st equilibration run
 (nvt) for 5 seconds.
 From the log file of mdrun, I get:

 rlistverlet-buffer-drift
 1.090.05
 1.1140.005
 1.1350.0005 =

 1.1730.05
 1.2340.05
 1.2840.05


 Are these numbers real?

 The wiki says the constraints already causes 0.0001kj/mol/atom in single
 precision gmx mdrun.
 (
 http://www.gromacs.org/Documentation/Cut-off_schemes#How_to_use_the_Verlet_scheme
 )

 If I use double precision gmx mdrun and constraint h-bonds, can I expect
 1.135 rlist to give a verlet-buffer-drift as small as the one in the table?

 Thank you again.

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Re: [gmx-users] box size and neighbor list cut-off

Thank you for the advices.

I tried setting different varlet buffer drift in the 1st equilibration run
(nvt) for 5 seconds.
From the log file of mdrun, I get:

rlistverlet-buffer-drift
1.090.05
1.1140.005
1.1350.0005 =

1.1730.05
1.2340.05
1.2840.05


Are these numbers real?

The wiki says the constraints already causes 0.0001kj/mol/atom in single
precision gmx mdrun.
(
http://www.gromacs.org/Documentation/Cut-off_schemes#How_to_use_the_Verlet_scheme
)

If I use double precision gmx mdrun and constraint h-bonds, can I expect
1.135 rlist to give a verlet-buffer-drift as small as the one in the table?

Thank you again.
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[gmx-users] refcoord-scaling without pressure coupling

2015-04-13 Thread Johnny Lu

Dear GMX users,

If I set refcoord-scaling = com and also pcoupl = no, will that
refcoord-scaling = com do anything (like introducing additional numerical
error in a NVE simulation) ?

Thank you.
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Re: [gmx-users] MD on protein-RNA complex

2015-03-06 Thread Johnny Lu

I guess:
multi-chain means the system has multiple chains of polymer (such as
peptide, or DNA/RNA). Some proteins have several peptide chains connected
together.
heterogeneous system: protein and RNA are different, and so protein + RNA
is a heterogeneous system.

Gromacs can simulate protein + RNA + water well, if the force field used
can accurately describe the three components and the interaction between
them.
I don't know how accurate is the force-field that you use, in describing
your system.

In a perfect world, we have a force field that can accurately describe
everything. Then, we can nearly simulate everything accurately.

On Fri, Mar 6, 2015 at 4:16 AM, Brett brettliu...@163.com wrote:

 Dear Justin,

 What do you mean for Multi-chain and heterogeneous systems work out of
 the box?

 I am looking forward to getting your reply.

 Brett





 At 2015-03-04 10:50:10, Justin Lemkul jalem...@vt.edu wrote:
 
 
 On 3/3/15 9:34 PM, Brett wrote:
  Dear Justin,
 
 
  I mean is any difficulty or special for gromacs to recognize the RNA in
 the PDB file?
 
 
 Multi-chain and heterogeneous systems work out of the box.  As with
 anything,
 the force field has to support everything and the nomenclature has to
 match the
 force field's expectations, but pdb2gmx will take care of everything.
 
 -Justin
 
 --
 ==
 
 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201
 
 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul
 
 ==
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[gmx-users] Test if Trajectories are Independent

2015-01-22 Thread Johnny Lu

Hi.

Is there a good way to test if a set of trajectories are independent from
each other?

I was thinking about

a) show that the initial structures of the trajectories are sufficiently
different.

b) calculate rmsd between corresponding frames of two trajectories.
If the trajectories are independent, the rmsd should be random and possibly
have an autocorrelation with a fast decay to zero.

I'm working with three 100 ns trajectories of alanine tripeptide.

Thank you again.
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Re: [gmx-users] Element naming format in .pdb file

2014-12-20 Thread Johnny Lu

may be try both ways in a small file.
feed it to pdb2gmx
and then check the topol.top file to see if it uses the correct forcefield
name?

On Sat, Dec 20, 2014 at 12:12 AM, Rajan Kumar kumarrajan...@gmail.com
wrote:

 Dear all,

 I am trying to study wetting of Graphene oxide. I have prepared a structure
 file using material studio, which I will simulate in GROMACS.

 My structure contain some epoxy and hydroxyl functional group in Graphene
 sheet. However, the structure file generated does not differentiate between
 carbon atoms with and without functional group in the Name column of .pdb
 file. Also there is no differentiation in naming format of oxygen atom in
 epoxy and hydroxyl group.

 Since, these atoms will have different atom type in atomtype.atp file of
 force filed.(I will be using OPLS-AA for simulation). Do I have to make
 edits in .pdb file for different atomtypes as well.


 Thanks

 Rajan Kumar
 Department of Chemical Engineering
 Indian Institute of Technology, Guwahati
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Re: [gmx-users] Ions drifting

2014-12-18 Thread Johnny Lu

If the Na or Cl ion don't strongly bind to the protein, as described by the
force field, then they might not always bind to and stay with the protein
in the simulation.
If that is what you want, I guess you can artificially add a restraint to
make the ion to stay closer to the protein ... I'm not sure about the
consequence.

On Thu, Dec 18, 2014 at 5:53 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 12/17/14 11:47 PM, jani vinod wrote:

 Dear Johnny,
 I  want to make the Na or Cl- ion always stay with the protein.
 I tried -pbc mol option ans selecting group as Protein_ion but it didn't
 work.


 This should be simple to do with trjconv -center -pbc mol -ur compact

 Choose Protein for centering and System for output.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==
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Re: [gmx-users] AMD GPUs

2014-12-18 Thread Johnny Lu

How about the open cl port of gromacs?

http://streamcomputing.eu/blog/2014-11-01/ported-gromacs-cuda-opencl/

might have to check the list of bugs of 5.0 though.

On Thu, Dec 18, 2014 at 5:16 AM, Szilárd Páll pall.szil...@gmail.com
wrote:

 Hi,

 Please don't hijack other discussion threads!

 AMD GPUs will be supported in the next release, people did not use
 them before because they were not supported.

 Regarding performance, I only know the results of some early
 benchmarks in which the fastest card used was an R9 290 and ran about
 as fast as as GTX 780. Based on this expect that even the R9 290X will
 be a lot slower than a GTX 980, but it would be great if people on the
 list could try.

 Cheers,
 --
 Szilárd


 On Thu, Dec 18, 2014 at 9:26 AM, Albert mailmd2...@gmail.com wrote:
 
  Hi Szilard:
 
  If I understand correctly, Gromacs also support AMD GPU? How fast is it?
 I
  never see people use it beforer
 
  THX
 
  Albert
 
 
  On 12/17/2014 10:09 PM, Szilárd Páll wrote:
 
  Hi Jason,
 
  Good point, separate PME ranks may very well be able to help in this
  case. I typically use half of the ranks for PME with AMD CPU-based
  machines (from  3-4 sockets and above).
 
 
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[gmx-users] compiling for xeon phi

2014-12-17 Thread Johnny Lu

Hi. How to compile double precision gromacs for xeon phi? (is that
possible?)

Do I need to use intel compiler, or gnu c/c++ is fine?

Is the xeon phi code of gromacs 5.0.4 very different from the xeon phi code
of gromacs 4.6.7?

In the cmake command, do i have to change
-DCMAKE_TOOLCHAIN_FILE=Platform/XeonPhi
according to the platform that I am using?

Thanks again.

===
Below is my attempt at building gromacs 4.6.7 for xeon phi.

export CC=icc
export CXX=icpc

cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/XeonPhi

give following error

CMake Error at /mcms/x86_64/core/cmake/
2.8.12.2/share/cmake-2.8/Modules/CMakeDetermineSystem.cmake:99 (message):
  Could not find toolchain file: Platform/XeonPhi
Call Stack (most recent call first):
  CMakeLists.txt:47 (project)

CMake Error: Error required internal CMake variable not set, cmake may be
not be built correctly.
Missing variable is:
CMAKE_C_COMPILER_ENV_VAR
CMake Error: Error required internal CMake variable not set, cmake may be
not be built correctly.
Missing variable is:
CMAKE_C_COMPILER
CMake Error: Could not find cmake module file:
gromacs-4.6.7/build_phi/CMakeFiles/2.8.12.2/CMakeCCompiler.cmake
CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
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Re: [gmx-users] CG MD Simulation of DNA and PAMAM dendrimers

2014-12-17 Thread Johnny Lu

Hi. This mail list can not take attachment. So it might be better to just
past the mdp file in the message.

At which time step did the segmentation fault happen?



On Wed, Dec 17, 2014 at 1:43 PM, Doa Hawamdeh hawamdeh@gmail.com
wrote:

 Dear GROMACS users:

 I want to study the complexation between PAMAM dendrimer and DNA using
 coarse-graining molecular dynamics simualtions (MARTINI force field)
 utilizing GROMACS version 5.0.3.

 MD integrator is used with time step of 20 fs, but I could not run the
 simulation with this time step, I got *segmentation fault.  *Sure before
 running long simulation I minimized the system. I attached the .mdp file
 that I use. Could you please help me?

 Waiting your response.

 Thank you.
 Doa

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Re: [gmx-users] Ions drifting

2014-12-17 Thread Johnny Lu

Hi.

I guess the pbc option only make a previously non-periodic box become
periodic.

Do you want to:

1. Make the Na or Cl- ion always stay with the protein.

Or

2. Make the protein looks like it stays at the center of the box. (but it
can still rotate)
I think the protein would look like it stays one piece as well.

Or

3. Make the protein looks like it doesn't rotate.


May be this post can help:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-December/094369.html




On Wed, Dec 17, 2014 at 10:57 PM, jani vinod genomej...@gmail.com wrote:

 Dear Justin and Tsjerk,
 Thanks for suggestion . It seems to be visualization problem . Since when I
 observed gro file generated at the end of   simulation appear to be normal
 .
 I tried various option with pbc (whole followed by nojump) , pbc(mol -ur
 compact), pbc (whole , clust , nojump) but none of this seems to be working
 in my case.
 I followed the gromacs page  where they mentioned how to deal pbc problem
 but that also didn't help.
 So is their any protocol for such system where we want to see interaction
 of solvent with solute.

 Thanks and regards
 Vinod



 On Wed, Dec 17, 2014 at 6:29 PM, Justin Lemkul jalem...@vt.edu wrote:
 
 
 
  On 12/16/14 11:41 PM, jani vinod wrote:
 
  Thanks
  following was the mdp file
 
  title   = Protein in ions
  ; Run parameters
  integrator  = md;
  nsteps  = 5000  ;
  dt  = 0.002 ;
  ; Output control
  nstxout = 5000  ;
  nstvout = 5000  ;
  nstenergy   = 5000  ;
  nstlog  = 5000  ;
  nstxtcout   = 5000
   ;
  ; Bond parameters
  continuation= yes   ;
  constraint_algorithm= lincs ;
  constraints = all-bonds ;
  lincs_iter  = 1 ;
  lincs_order = 4 ;
  ; Neighborsearching
  ns_type = grid  ;
  nstlist = 10   ;
  rcoulomb= 1.0   ;
  rlist   = 1.0   ;
  rvdw= 1.0   ;
  ; Electrostatics
  coulombtype = PME   ;
  pme_order   = 4 ;
  fourierspacing  = 0.16  ;
  ; Temperature coupling is on
  tcoupl  = Nose-Hoover
  tc-grps = Protein Non_Protein
  tau_t   = 0.5 0.5   ;
  ref_t   = 300 300   ;
  ; Pressure coupling is on
  pcoupl  = Parrinello-Rahman ;
  pcoupltype  = isotropic ;
  tau_p   = 2.0   ;
  ref_p   = 1.0   ;
  compressibility = 4.5e-5;
  ; Periodic boundary conditions
  pbc = xyz   ;
  ; Dispersion correction
  DispCorr= EnerPres  ;
  ; Velocity generation
  gen_vel = no;
  nstcomm = 1
  comm-mode   = Linear
  comm-grps   = Protein Non_Protein
 
 
  It does not make sense to separate COM motion removal like this for a
  simple protein in water.  As to whether or not this is related to the
  problem at hand, I can't necessarily say, but it is artificial.
 
   . So I processed the trajectory with trjconv whole option  followed by
  nojump.
  After that the protein appear on one side and ions on other
 
 
  So this is all likely a visualization issue.  Use trjconv to center the
  protein in the unit cell in conjunction with -pbc mol.
 
  -Justin
 
  --
  ==
 
  Justin A. Lemkul, Ph.D.
  Ruth L. Kirschstein NRSA Postdoctoral Fellow
 
  Department of Pharmaceutical Sciences
  School of Pharmacy
  Health Sciences Facility II, Room 629
  University of Maryland, Baltimore
  20 Penn St.
  Baltimore, MD 21201
 
  jalem...@outerbanks.umaryland.edu | (410) 706-7441
  http://mackerell.umaryland.edu/~jalemkul
 
  ==
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Re: [gmx-users] 5.0.4 Compilation - SelectionUnitTests Failed

2014-12-16 Thread Johnny Lu

Hmm. Did you try gcc?
From the mail list, I heard that if the gnu c/c++ compiler is new enough,
it builds faster gromacs than intel c/c++ compiler and mkl.
I'm not sure about 5.0.4 though, and I am using 4.6.7 right now.

On Tue, Dec 16, 2014 at 10:09 AM, Mike Hanby mha...@uab.edu wrote:

 Howdy,

 I'm attempting to build Gromacs 5.0.4 using Intel compilers 13.1.1 for one
 of the users of our HPC fabric and it errors when running test 13 during
 the make check

 [--] Global test environment tear-down
 [==] 139 tests from 8 test cases ran. (462 ms total)
 [  PASSED  ] 138 tests.
 [  FAILED  ] 1 test, listed below:
 [  FAILED  ] SelectionCollectionDataTest.HandlesCharge

  1 FAILED TEST
 

 Total Test time (real) = 148.29 sec

 The following tests FAILED:
  13 - SelectionUnitTests (Failed)
 Errors while running CTest
 make[3]: *** [CMakeFiles/run-ctest] Error 8
 make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2
 make[1]: *** [CMakeFiles/check.dir/rule] Error 2
 make: *** [check] Error 2

 I've attached the cmake, make and make check logs.

 Any suggestions on what I can do to debug / fix this issue, or is it
 benign and I can safely move on to installing?

 Thanks, Mike
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[gmx-users] 0 +- 0.5 bar ok?

2014-12-15 Thread Johnny Lu

Hi.

Are these pressures acceptable for reviewers? (I haven't submit anything to
journals before). What would be different from a simulation with a truly 1
bar average pressure?

System 1: NVT simulation gives an 0.0 +- 0.5 bar average pressure over
600ns with 2 fs timestep. When I averaged the 2nd half of the simulation,
it gives -0.3 +- 0.5 bar average pressure over 300 ns. The system has 9K
water molecules, 3 Cl- ions, and 173 amino acid residues (2598 atoms).

System 2: Another simulation that i did was an alanine dipeptide simulation
with a 5.4 +- 0.2 bar pressure over 250 ns. The last 150 ns gives an
average pressure of 5.6 +- 0.2 bar. The system has 8k water molecules and
32 peptide atoms.

Thank you again.
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Re: [gmx-users] trjconv during transfer of .trr

2014-12-14 Thread Johnny Lu

Alternatively, is there a way to quickly check how many ns or frames do a
.trr file contain?

On Sun, Dec 14, 2014 at 5:47 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Hi.

 Before the queue manager of the cluster finishes transferring the .trr
 file to my homedirectory, if I start trjconv,
 and trjconv finishes running (which takes about half an hour) after the
 .trr file (6 GB) completes transferring to my home directory,

 will the converted .trr contains as many ns as the original .trr?

 I used trjconv to only get rid of the water in the .trr file.


 Or... part of the .trr file will get chop off when i convert with trjconv?


 Thank you for your help.

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Re: [gmx-users] trjconv during transfer of .trr

2014-12-14 Thread Johnny Lu

seems to be fine for slurm resource manager... so far.

On Sun, Dec 14, 2014 at 5:50 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Alternatively, is there a way to quickly check how many ns or frames do a
 .trr file contain?

 On Sun, Dec 14, 2014 at 5:47 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Hi.

 Before the queue manager of the cluster finishes transferring the .trr
 file to my homedirectory, if I start trjconv,
 and trjconv finishes running (which takes about half an hour) after the
 .trr file (6 GB) completes transferring to my home directory,

 will the converted .trr contains as many ns as the original .trr?

 I used trjconv to only get rid of the water in the .trr file.


 Or... part of the .trr file will get chop off when i convert with trjconv?


 Thank you for your help.


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Re: [gmx-users] Stop protein diffusion in simulation box to make a movie

2014-12-13 Thread Johnny Lu

hi. can this help?

http://manual.gromacs.org/programs/gmx-trjconv.html

On Sat, Dec 13, 2014 at 6:04 AM, Hassan Aaryapour hassan.grom...@gmail.com
wrote:

 Dear Gromacs Users,
 I made a trajectory movie using VMD and smoothing increased for
 getting the residues motion slower, but the protein is translate and
 diffuse in box, and causes very hard of seeing and analyzing how
 ligand structure changes during simulation. How can I stop the protein
 translation and following ligand motion easier?

 Thank you in advance
 Hassan
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Re: [gmx-users] Need to Sort Out

2014-12-13 Thread Johnny Lu

Hi. I'm quite new to molecular dynamics too.

How did you make that itp? Does your system contain only one protein/DNA
molecule?

May be try this tutorial for a single protein?
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/

Check multiple journal papers when you decide how to simulate (even if you
are just simulating a single small protein).
Some systems might need different simulation steps. And, depending on the
things that you want to look at, you might have to stage a different
simulation.

On Sat, Dec 13, 2014 at 1:46 PM, Devender Arora devar...@hotmail.com
wrote:

 I am facing a problem in Gromacs while running grommp please do give the
 right direction I am new to Molecular dynamics.


 Fatal error:
 Syntax error - File topol_Protein_chain_A.itp, line 6966
 Last line read:
 '[ molecules ]'
 Invalid order for directive molecules
 For more information and tips for troubleshooting, please check the GROMACS
 website at http://www.gromacs.org/Documentation/Errors

 :


 Thanks  Regards


 Devender Arora


 Ph.D Scholar


 Department of Biotechnology


 GB Pant engineering College


 Pauri Garhwal, Uttarakhand


 Contact No. +919720045608, +91986896786


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[gmx-users] trjconv precision lost from double to single conversion

Hi. I'm using gromacs 4.6.7

If the trr trajectory file is from double precision calculation, and I use
single precision trjconv to make a single precision trr trajectory, how
much precision will I lose in position and in force?

1, 0.1, 0.01, or 0.001 angstrom and Newton?

Is the lost of precision acceptable?

I noticed that single precision trr seems to take about half the hard disk
space of double precision trr.

Thank you.
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Re: [gmx-users] trjconv precision lost from double to single conversion

When I test the disk space that I would save by getting rid the water in
the trajectory, I found that only make the trajectory 1/4 as large as the
original.
The trajectory has both position and force.

Yet, the proteins only have about 1/10 the number of atoms of the whole
system.

Group 0 ( System) has 29859 elements
Group 1 (Protein) has  2598 elements

Should the trajectory file size reduced to 1/4 instead of 1/10?

The command that I used was:
echo -e 1\n1\n | $GMXHOME/trjconv_d -f $In_Traj -o $Out_Traj -s $In_ptr
-pbc mol -ur compact -center -force

Thanks again.

On Fri, Dec 12, 2014 at 10:31 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Hi. I'm using gromacs 4.6.7

 If the trr trajectory file is from double precision calculation, and I use
 single precision trjconv to make a single precision trr trajectory, how
 much precision will I lose in position and in force?

 1, 0.1, 0.01, or 0.001 angstrom and Newton?

 Is the lost of precision acceptable?

 I noticed that single precision trr seems to take about half the hard disk
 space of double precision trr.

 Thank you.

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Re: [gmx-users] trjconv precision lost from double to single conversion

nevermind the 2nd question. it does reduce to about 1/10 size.

On Fri, Dec 12, 2014 at 10:41 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 When I test the disk space that I would save by getting rid the water in
 the trajectory, I found that only make the trajectory 1/4 as large as the
 original.
 The trajectory has both position and force.

 Yet, the proteins only have about 1/10 the number of atoms of the whole
 system.

 Group 0 ( System) has 29859 elements
 Group 1 (Protein) has  2598 elements

 Should the trajectory file size reduced to 1/4 instead of 1/10?

 The command that I used was:
 echo -e 1\n1\n | $GMXHOME/trjconv_d -f $In_Traj -o $Out_Traj -s $In_ptr
 -pbc mol -ur compact -center -force

 Thanks again.

 On Fri, Dec 12, 2014 at 10:31 AM, Johnny Lu johnny.lu...@gmail.com
 wrote:

 Hi. I'm using gromacs 4.6.7

 If the trr trajectory file is from double precision calculation, and I
 use single precision trjconv to make a single precision trr trajectory, how
 much precision will I lose in position and in force?

 1, 0.1, 0.01, or 0.001 angstrom and Newton?

 Is the lost of precision acceptable?

 I noticed that single precision trr seems to take about half the hard
 disk space of double precision trr.

 Thank you.


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[gmx-users] pmetune and restarting

Hi.

I notice that after I stop a simulation by specifying the number of hours
that it runs with -maxh,
and then restarting the simulation, at the beginning of each restart, the
pme is tuned again.

Will that cause any error if I periodically restart the simulation? How big
is the error?

Is it possible to save and reuse pme tune result by a mdrun option?

Thank you.
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Re: [gmx-users] with 5.0: file INSTALL cannot find gmx

I'm not sure what happened, but so far when i install, i use full path
instead of $(pwd) and it was fine for gromacs 4.6 and 5.0, 5.0.2.
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[gmx-users] xeon-phi and double precision

2014-12-11 Thread Johnny Lu

Hi. Does xeon-phi make double precision gromacs faster?
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Re: [gmx-users] Question on installation

2014-12-09 Thread Johnny Lu

May be just let gromacs build its own fftw3 library, by
using -DGMX_BUILD_OWN_FFTW=ON in the cmake command,
is a better idea?

On Mon, Dec 8, 2014 at 2:23 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 12/8/14 12:38 PM, Igor Shchechkin wrote:

 Dear Gromacs users,

 I have obtained the error Cannot find fftw3f library installing
 4.5.3 version of Gromacs.

 fftw 3.3.4 version has been preliminary installed,
 names of include and lib directories present in CPPFLAGS and LDFLAGS
 configuring Gromacs,
 both FFTW and Gromacs are configured in single precision.
 Mailing list is sought and the information found is irrelevant to my case.

 Could you, please, help me?


 You need to provide the actual command(s) you issued.  If FFTW is
 installed, whatever you specified as a path during Gromacs installation was
 probably just wrong.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441
 http://mackerell.umaryland.edu/~jalemkul

 ==

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Re: [gmx-users] Dihedral angle calculation in Gromacs

2014-12-09 Thread Johnny Lu

what do you mean by tensor?

On Fri, Nov 28, 2014 at 4:22 AM, Ankit Agrawal aka...@gmail.com wrote:

 Hi

 I have pdb file which has crystal structure of Cadherin-23 (2WHV) with 2
 domains EC1  EC2. So I want to calculate angle between two domains
 (tensor) along with the principal axes.

 regards
 Ankit
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[gmx-users] Precision of xtc-precision

2014-12-06 Thread Johnny Lu

Hi.

What is the exact precision of xtc-precision = 1000 ?

Does that mean the positions are accurate to 0.001 nm, or to 0.1% ?

I searched gromacs 4.6.7 manual and gromacs.org for xtc-precision, but
didn't find answer.

Thank you again.
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[gmx-users] Different box volumes from gmxdump and g_energy

Hi.

I get two different volumes with g_energy and gmxdump.

Which one is true?

For now, I'm trying to get a NVT simulation with correct pressure, after a
300 ns NPT equilibration.
The 400 ns NPT equilibration has the following statistics, according to
g_energy of gromacs 4.6.7, and the equilibration seems to be sufficient.

  Last energy frame read 21438168 time 428763.375

  Statistics over 214381681 steps [ 0. through 428763.3600 ps ], 5
data sets
  All statistics are over 17108015 points

  Energy  Average   Err.Est.   RMSD  Tot-Drift

---
  Total Energy-3073506.1nan   -15.4944
(kJ/mol)
  Temperature 299.851 0.0018nan
-0.00756116  (K)
  Pressure1.011275.7e-05nan
0.000126851  (bar)
  Volume  298.385 0.0043nan 0.00672558
(nm^3)
  Density 1015.42  0.015nan -0.0229017
(kg/m^3)

  gcq#328: I used to be blond and stupid, but now I dyed it black
(Miss Li)

  The nan in RMSD is caused by that I did one restart of the simulation.

Getting the correct volume is very important for me because the isothermal
compressibility of water is 4.5e-5, and a small change in volume can lead
to a relatively large change in pressure.

gromacs5.0.1. g_energy_d
  time(ps) box-x   box-y   box-z volume
  -  --
  125142.107.5006117.5006115.303739  298.383881

gromacs4.6.7. g_energy

  time(ps)   volume
  -  --
  125142.10  298.383881

gromacs4.6.7. gmxdump
  box (3x3):
 box[0]={ 7.50577e+00,  0.0e+00,  0.0e+00}
 box[1]={ 0.0e+00,  7.50577e+00,  0.0e+00}
 box[2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}

  from the box vectors, volume is |z dot (x cross y)|
 7.50577 * 7.50577 * 5.30739 = 299.000218803

gromacs5.0.1. gmxdump_d
  box (3x3):
 box[0]={ 7.50577e+00,  0.0e+00,  0.0e+00}
 box[1]={ 0.0e+00,  7.50577e+00,  0.0e+00}
 box[2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}

example command for running gmx_dump:
  gmxdump_d -s ../npt13c.tpr -f ../npt13c_step62571050.cpt 
gmxdump5.0.1d_step62571050

example command for running g_energy:
  g_energy_d -f ../npt13c.edr npt13c_volume_gromacs5.0.1_d.xvg

since the timestep is 0.002 ps, the time(ps) corresponding to
  the check point file is:

  62571050 * 0.002 = 125142.1 ps

All the files (tpr, cpt, edr) are generated by mdrun of gromacs4.6.7 (mixed
precision). It seems that it is ok to use the g_energy and gmxdump of
gromacs 5.0.1 on these files.

Size of the .edr file is 5 gb.

Thank you again.
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Re: [gmx-users] Different box volumes from gmxdump and g_energy

g_energy seems more correct than gmxdump in box size.


  [= npt13c_step169777880. gmxdump =]
  box (3x3):
 box[0]={ 7.50577e+00,  0.0e+00,  0.0e+00}
 box[1]={ 0.0e+00,  7.50577e+00,  0.0e+00}
 box[2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}

  volume from box vector:
7.50577 * 7.50577 * 5.30739 = 299.000218803

  [= npt13c. g_energy =]
  time(ps)   volume
  -  --
  339555.76  298.385254

  [= commands for starting a NVT simulation, from the npt frame. =]
  ../../sofware/gromacs-4.6.7/bin/grompp -f nvt14d.mdp -c npt13c.tpr -t
npt13c_step169777880.cpt -o nvt14d.tpr

  [= gmxdump_nvt14d_step62571050. gmxdump =]
  box (3x3):
 box[0]={ 7.50062e+00,  0.0e+00,  0.0e+00}
 box[1]={ 0.0e+00,  7.50062e+00,  0.0e+00}
 box[2]={ 3.75032e+00,  3.75032e+00,  5.30375e+00}

  volume from box vector:
7.50062 * 7.50062 * 5.30375 = 298.385264414 (the same value in
g_energy of npt13c)

  [= gmxdump_nvt14d_step6247910. gmxdump =]
  box (3x3):
 box[0]={ 7.50062e+00,  0.0e+00,  0.0e+00}
 box[1]={ 0.0e+00,  7.50062e+00,  0.0e+00}
 box[2]={ 3.75032e+00,  3.75032e+00,  5.30375e+00}

  volume from box vector:
7.50062 * 7.50062 * 5.30375 = 298.385264414

On Wed, Dec 3, 2014 at 11:34 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Hi.

 I get two different volumes with g_energy and gmxdump.

 Which one is true?

 For now, I'm trying to get a NVT simulation with correct pressure, after a
 300 ns NPT equilibration.
 The 400 ns NPT equilibration has the following statistics, according to
 g_energy of gromacs 4.6.7, and the equilibration seems to be sufficient.

   Last energy frame read 21438168 time 428763.375

   Statistics over 214381681 steps [ 0. through 428763.3600 ps ],
 5 data sets
   All statistics are over 17108015 points

   Energy  Average   Err.Est.   RMSD  Tot-Drift

 ---
   Total Energy-3073506.1nan
 -15.4944  (kJ/mol)
   Temperature 299.851 0.0018nan
 -0.00756116  (K)
   Pressure1.011275.7e-05nan
 0.000126851  (bar)
   Volume  298.385 0.0043nan
 0.00672558  (nm^3)
   Density 1015.42  0.015nan
 -0.0229017  (kg/m^3)

   gcq#328: I used to be blond and stupid, but now I dyed it black
 (Miss Li)

   The nan in RMSD is caused by that I did one restart of the
 simulation.

 Getting the correct volume is very important for me because the isothermal
 compressibility of water is 4.5e-5, and a small change in volume can lead
 to a relatively large change in pressure.

 gromacs5.0.1. g_energy_d
   time(ps) box-x   box-y   box-z volume
   -  --
   125142.107.5006117.5006115.303739  298.383881

 gromacs4.6.7. g_energy

   time(ps)   volume
   -  --
   125142.10  298.383881

 gromacs4.6.7. gmxdump
   box (3x3):
  box[0]={ 7.50577e+00,  0.0e+00,  0.0e+00}
  box[1]={ 0.0e+00,  7.50577e+00,  0.0e+00}
  box[2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}

   from the box vectors, volume is |z dot (x cross y)|
  7.50577 * 7.50577 * 5.30739 = 299.000218803

 gromacs5.0.1. gmxdump_d
   box (3x3):
  box[0]={ 7.50577e+00,  0.0e+00,  0.0e+00}
  box[1]={ 0.0e+00,  7.50577e+00,  0.0e+00}
  box[2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}

 example command for running gmx_dump:
   gmxdump_d -s ../npt13c.tpr -f ../npt13c_step62571050.cpt 
 gmxdump5.0.1d_step62571050

 example command for running g_energy:
   g_energy_d -f ../npt13c.edr npt13c_volume_gromacs5.0.1_d.xvg

 since the timestep is 0.002 ps, the time(ps) corresponding to
   the check point file is:

   62571050 * 0.002 = 125142.1 ps

 All the files (tpr, cpt, edr) are generated by mdrun of gromacs4.6.7
 (mixed precision). It seems that it is ok to use the g_energy and gmxdump
 of gromacs 5.0.1 on these files.

 Size of the .edr file is 5 gb.

 Thank you again.

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Re: [gmx-users] Different box volumes from gmxdump and g_energy

yes.

I get an xvg file from the edr file with g_energy. Then from the xvg file,
i selected the observable (volume) corresponding to the timestep at which
the .cpt file is written.
Then I compared this value of volume, with the value of volume calculated
from the box vectors in the .cpt file.

On Wed, Dec 3, 2014 at 1:04 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 A .cpt file has one frame in it. An .edr file has values and statistics
 from many frames. Are you comparing things that are comparable?

 Mark

 On Wed, Dec 3, 2014 at 6:56 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  g_energy seems more correct than gmxdump in box size.
 
 
[= npt13c_step169777880. gmxdump =]
box (3x3):
   box[0]={ 7.50577e+00,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  7.50577e+00,  0.0e+00}
   box[2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}
 
volume from box vector:
  7.50577 * 7.50577 * 5.30739 = 299.000218803
 
[= npt13c. g_energy =]
time(ps)   volume
-  --
339555.76  298.385254
 
[= commands for starting a NVT simulation, from the npt frame. =]
../../sofware/gromacs-4.6.7/bin/grompp -f nvt14d.mdp -c npt13c.tpr
 -t
  npt13c_step169777880.cpt -o nvt14d.tpr
 
[= gmxdump_nvt14d_step62571050. gmxdump =]
box (3x3):
   box[0]={ 7.50062e+00,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  7.50062e+00,  0.0e+00}
   box[2]={ 3.75032e+00,  3.75032e+00,  5.30375e+00}
 
volume from box vector:
  7.50062 * 7.50062 * 5.30375 = 298.385264414 (the same value
 in
  g_energy of npt13c)
 
[= gmxdump_nvt14d_step6247910. gmxdump =]
box (3x3):
   box[0]={ 7.50062e+00,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  7.50062e+00,  0.0e+00}
   box[2]={ 3.75032e+00,  3.75032e+00,  5.30375e+00}
 
volume from box vector:
  7.50062 * 7.50062 * 5.30375 = 298.385264414
 
  On Wed, Dec 3, 2014 at 11:34 AM, Johnny Lu johnny.lu...@gmail.com
 wrote:
 
   Hi.
  
   I get two different volumes with g_energy and gmxdump.
  
   Which one is true?
  
   For now, I'm trying to get a NVT simulation with correct pressure,
 after
  a
   300 ns NPT equilibration.
   The 400 ns NPT equilibration has the following statistics, according to
   g_energy of gromacs 4.6.7, and the equilibration seems to be
 sufficient.
  
 Last energy frame read 21438168 time 428763.375
  
 Statistics over 214381681 steps [ 0. through 428763.3600 ps
 ],
   5 data sets
 All statistics are over 17108015 points
  
 Energy  Average   Err.Est.   RMSD
  Tot-Drift
  
  
 
 ---
 Total Energy-3073506.1nan
   -15.4944  (kJ/mol)
 Temperature 299.851 0.0018nan
   -0.00756116  (K)
 Pressure1.011275.7e-05nan
   0.000126851  (bar)
 Volume  298.385 0.0043nan
   0.00672558  (nm^3)
 Density 1015.42  0.015nan
   -0.0229017  (kg/m^3)
  
 gcq#328: I used to be blond and stupid, but now I dyed it black
   (Miss Li)
  
 The nan in RMSD is caused by that I did one restart of the
   simulation.
  
   Getting the correct volume is very important for me because the
  isothermal
   compressibility of water is 4.5e-5, and a small change in volume can
 lead
   to a relatively large change in pressure.
  
   gromacs5.0.1. g_energy_d
 time(ps) box-x   box-y   box-z volume
 -  --
 125142.107.5006117.5006115.303739  298.383881
  
   gromacs4.6.7. g_energy
  
 time(ps)   volume
 -  --
 125142.10  298.383881
  
   gromacs4.6.7. gmxdump
 box (3x3):
box[0]={ 7.50577e+00,  0.0e+00,  0.0e+00}
box[1]={ 0.0e+00,  7.50577e+00,  0.0e+00}
box[2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}
  
 from the box vectors, volume is |z dot (x cross y)|
7.50577 * 7.50577 * 5.30739 = 299.000218803
  
   gromacs5.0.1. gmxdump_d
 box (3x3):
box[0]={ 7.50577e+00,  0.0e+00,  0.0e+00}
box[1]={ 0.0e+00,  7.50577e+00,  0.0e+00}
box[2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}
  
   example command for running gmx_dump:
 gmxdump_d -s ../npt13c.tpr -f ../npt13c_step62571050.cpt 
   gmxdump5.0.1d_step62571050
  
   example command for running g_energy:
 g_energy_d -f ../npt13c.edr npt13c_volume_gromacs5.0.1_d.xvg
  
   since the timestep

Re: [gmx-users] Different box volumes from gmxdump and g_energy

The error in pressure of the nvt simulation (about -1.4 bar) is not
explained by the error in pressure of the npt simulation.
I wonder if the error in pressure of the NVT simulation is caused by that
in the NPT simulation I used a berendsen barostat with a very low coupling
time of 0.2 ps?

I guess the worse case is that I get the NPT frames with volumes around
(but not equal to) the average volume I get from g_energy, and then run NVT
simulations starting from each of these NPT frames. And hopefully I get a
NVT simulation with the correct pressure... I don't know what went wrong. I
did convert the cpt file to pdb file, and then look at them in vmd to check
for vacuum bubbles (and i don't see such bubbles in the water molecules).

Below is my estimation of the errors:

Somehow, the pressure of the nvt14d simulation is about -1.4 bar, instead
of 1 bar. This error in pressure is not explained by the err in volume from
the g_energy of npt13c, and the isothermal compressibility of water.


  [= g_energy of npt13c =]
  Statistics over 214381681 steps [ 0. through 428763.3600 ps ], 5
data sets
  All statistics are over 17108015 points

  Energy  Average   Err.Est.   RMSD  Tot-Drift

---
  Total Energy-3073506.1nan   -15.4944
(kJ/mol)
  Temperature 299.851 0.0018nan
-0.00756116  (K)
  Pressure1.011275.7e-05nan
0.000126851  (bar)
  Volume  298.385 0.0043nan 0.00672558
(nm^3)
  Density 1015.42  0.015nan -0.0229017
(kg/m^3)


  [= g_energy of nvt14d =]
  Last energy frame read 4715311 time 94306.219

  Statistics over 22153111 steps [ 5. through 94306.2200 ps ],
1 data sets
  All statistics are over 2215312 points

  Energy  Average   Err.Est.   RMSD  Tot-Drift

---
  Pressure   -1.40405   0.39146.2623.11836
(bar)

  gcq#98: Jesus Can't Save You, Though It's Nice to Think He Tried
(Black Crowes)


  [= Approximate Maximal Error in Pressure (95% confidence, or two
standard deviation) =]
  Assume the error estimation in averaged volume of npt13c is correct.
  4.5e-5 = - (dV/dP)_T / V
  (Delta P)= - (Delta V)/ V / 4.5e-5
  (Delta P)= - (0.0043*2)/ (298.385 - 0.0043*2) / 4.5e-5 = -0.6 bar

  Thus, there is 5% chance that the NPT simulation has a pressure as
low as 1.0 - 0.6 = 0.4 bar.
  Yet, the actual pressure of the NVT simulation is -1.40405 +- 0.39,
and 0.4 bar is not within two standard deviations of this value.




On Wed, Dec 3, 2014 at 1:08 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 yes.

 I get an xvg file from the edr file with g_energy. Then from the xvg file,
 i selected the observable (volume) corresponding to the timestep at which
 the .cpt file is written.
 Then I compared this value of volume, with the value of volume calculated
 from the box vectors in the .cpt file.

 On Wed, Dec 3, 2014 at 1:04 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

 A .cpt file has one frame in it. An .edr file has values and statistics
 from many frames. Are you comparing things that are comparable?

 Mark

 On Wed, Dec 3, 2014 at 6:56 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  g_energy seems more correct than gmxdump in box size.
 
 
[= npt13c_step169777880. gmxdump =]
box (3x3):
   box[0]={ 7.50577e+00,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  7.50577e+00,  0.0e+00}
   box[2]={ 3.75289e+00,  3.75289e+00,  5.30739e+00}
 
volume from box vector:
  7.50577 * 7.50577 * 5.30739 = 299.000218803
 
[= npt13c. g_energy =]
time(ps)   volume
-  --
339555.76  298.385254
 
[= commands for starting a NVT simulation, from the npt frame. =]
../../sofware/gromacs-4.6.7/bin/grompp -f nvt14d.mdp -c
 npt13c.tpr -t
  npt13c_step169777880.cpt -o nvt14d.tpr
 
[= gmxdump_nvt14d_step62571050. gmxdump =]
box (3x3):
   box[0]={ 7.50062e+00,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  7.50062e+00,  0.0e+00}
   box[2]={ 3.75032e+00,  3.75032e+00,  5.30375e+00}
 
volume from box vector:
  7.50062 * 7.50062 * 5.30375 = 298.385264414 (the same value
 in
  g_energy of npt13c)
 
[= gmxdump_nvt14d_step6247910. gmxdump =]
box (3x3):
   box[0]={ 7.50062e+00,  0.0e+00,  0.0e+00}
   box[1]={ 0.0e+00,  7.50062e+00,  0.0e+00}
   box[2]={ 3.75032e+00,  3.75032e+00,  5.30375e+00}
 
volume from box vector:
  7.50062 * 7.50062 * 5.30375

[gmx-users] dump current rlist in cpt

2014-11-20 Thread Johnny Lu

Hi.

is it possible to check current rlist, and vdw cut-off in a cpt file.

I want to know if the big energy jump upon extending/continuing/restarting
simulation with gromacs 4.6.7 is caused by the load balancing bug (
http://redmine.gromacs.org/issues/1603)

Thank you.
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Re: [gmx-users] changing ewald_rtol

2014-11-18 Thread Johnny Lu

Thank you very much for the answer.

On Tue, Nov 18, 2014 at 2:03 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 On Tue, Nov 18, 2014 at 7:38 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  Hi.
 
  from online manual:
 
  *ewald-rtol (1e-5)* The relative strength of the Ewald-shifted direct
  potential at *rcoulomb* is given by *ewald-rtol*. Decreasing this will
 give
  a more accurate direct sum, but then you need more wave vectors for the
  reciprocal sum.
 
  Is it ok to use ewald-rtol=1e-9 for Amber99SB-ILDN forcefield?
 

 That's not a question that has a useful single answer.
 1) It wasn't parameterized with any Ewald method, so any subsquent use of
 that method is valid only upon empirical evidence.
 2) Different observables in different systems have different dependencies
 on the quality of the electrostatics model, and this one parameter is only
 part of any story.
 3) A tiny magnitude of forces at the cutoff matters little if they're being
 added to other forces at shorter distances - and if there's more than about
 5 orders of magnitude difference, then the small ones get lost in the
 accumulation in floating-point representation
 4) Making one part of the electrostatics approximation super accurate while
 ignoring the other doesn't do any good when you add them together, because
 the largest error dominates.
 5) Some other error might be more dominant still (e.g. incomplete sampling,
 interior residues have the same charges as exterior residues, no
 polarizability)

 Will the sum in reciprocal space become very inaccurate?
 

 Yes, like the docs say, because ewald-rtol and rcoulomb are used to compute
 the Ewald splitting parameter beta, which is then used in reciprocal space
 also.

 Or this will just make the simulation run slower?
 

 By itself, it's just multiplication by a different scaling factor. Fixing
 the issues in reciprocal space (increasing number of grid points and/or
 spline interpolation order) will be expensive.

 Mark


  Thanks again.
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Re: [gmx-users] Equilibration from Non-shifted to Shifted Potential

2014-11-14 Thread Johnny Lu

I guess I get the idea now. F = -dV(x)/dx. So no time derivative is
involved. So shifting the potential would not cause a suddenly impulse on
the system.

By the way, is Potential-shift the default vdw and coulomb-modifier (so
that is used even if i didn't specify a modifier) for gromacs 4.6.7?
I didn't see the default value when I searched for vdw-modifier (p.214) of
gromacs manual 4.6.7, or when I look at the online manual.

   coulomb-modifier = Potential-shift
   rcoulomb-switch  = 0
   rcoulomb = 1
   vdwtype  = Cut-off
   vdw-modifier = Potential-shift


On Fri, Nov 14, 2014 at 9:31 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Hi,

 Try it and see ;-)

 mdrun -nsteps 10 -reprod -deffnm shifted
 mdrun -nsteps 10 -reprod -deffnm not-shifted
 gmx check -f shifted -f2 not-shifted
 gmx check -e shifted -e2 not-shifted

 Alternatively, given that the forces are not computed from the energies
 (e.g. by central difference or some such), what role does the potential
 energy play in the integration scheme? :-)

 Mark


 On Fri, Nov 14, 2014 at 3:19 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  Hi.
 
  If I change my potential from non-shifted to shift, will the sudden
 change
  of energy from non-shifted to shifted potential at step 0 completely mess
  up the equilibration?
 
  Thanks again.
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Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

2014-11-12 Thread Johnny Lu

This seems to have nothing to do with shifted potentials or gpu.

I run a tripeptide double precisiion NVE simulation on a machine with xeon
cpu and without gpu. kill it, then continue it with the cpt file generated.
That energy jump still exists.

On Tue, Nov 11, 2014 at 1:39 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Going from non-shift to shifted potential changes the energy. So I was not
 surprised by the sudden jump of energy between step 0 and step 10 for the
 previous simulation (npt14).

 But the jump near step 0 for the current simulation (npt15) is not right.

 This is an equilibration run.

 I have just uploaded the files at http://redmine.gromacs.org/issues/1640


 On Tue, Nov 11, 2014 at 10:54 AM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

 On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu johnny.lu...@gmail.com
 wrote:

  Hi.
 
  I ran 30ns NPT with Potential-shift-Verlet on both potentials,
 continuing
  from a NPT without Potential-shift-Verlet. The energy dropped from -3e5
 to
  -4e5, which is fine.
 
  After that, I continue the 30ns NPT with the same mdp file, except with
 a
  longer run time (300ns).
 
  The total energy was -4e5 at step 0, and then -3e5 at step 5000, and
 now at
  about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed
 after
  step 0?
 

 IIRC, the restart ought to compute the same energy on the initial
 coordinates as it did at the end of the previous run, and even if there's
 no re-computation on the same coordinates, obviously it should not  jump
 by
 1e5 in a few steps (or one? can't tell from the resolution). I would think
 that might be a bug in filling a data structure for the output, but
 probably not one in the simulation itself. Please file an issue at
 http://redmine.gromacs.org, tarballing all the relevant files, and I'll
 try
 to look at it.

 The long-time behaviour of both simulations is pretty suspect though.
 Since
 you're prepared to be ultra-conservative with your non-bonded and SETTLE
 settings, I would explore using a 0.5fs time step (in normal and
 ultra-conservative mode). Berendsen is not a good barostat algorithm for
 production work, too... but I would not expect such a problem from its
 use.
 Perhaps more importantly, why are you turning off the long-range
 dispersion
 correction?

 Mark

 I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
  grompp for both simulations.
 
  The plot of total energies for the two simulations:
  http://oi60.tinypic.com/ddmejd.jpg
  The two mdp files: http://oi58.tinypic.com/11980si.jpg
 
  The commands that I used for continuing the simulations:
 
  The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp
 -f
  npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr
 
  The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp
 -f
  npt15.mdp -c npt14.tpr -t npt14_step3000.cpt -o npt15.tpr
 
  Thanks.
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Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

2014-11-11 Thread Johnny Lu

by the way, the machine has 4 Tesla K40m gpu, 32 xeon cpu with avx, and i
ran: nohup ../../mdrun -deffnm npt15 -cpt 1 -cpnum 

On Tue, Nov 11, 2014 at 9:38 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Hi.

 I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
 from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to
 -4e5, which is fine.

 After that, I continue the 30ns NPT with the same mdp file, except with a
 longer run time (300ns).

 The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now
 at about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed
 after step 0?

 I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
 grompp for both simulations.

 The plot of total energies for the two simulations:
 http://oi60.tinypic.com/ddmejd.jpg
 The two mdp files: http://oi58.tinypic.com/11980si.jpg

 The commands that I used for continuing the simulations:

 The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp -f
 npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr

 The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f
 npt15.mdp -c npt14.tpr -t npt14_step3000.cpt -o npt15.tpr

 Thanks.


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Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

2014-11-11 Thread Johnny Lu

The system has 30k water and a protein with ~170 amino acid.
Here are the PME tuning:

npt14:
DD  step 4 load imb.: force 58.1%

step   10: timed with pme grid 80 80 80, coulomb cutoff 1.000: 37.1 M-cycles
step   20: timed with pme grid 64 64 64, coulomb cutoff 1.173: 32.6 M-cycles
step   30: timed with pme grid 56 56 56, coulomb cutoff 1.341: 34.5 M-cycles
step   40: timed with pme grid 48 48 48, coulomb cutoff 1.564: 40.7 M-cycles
step   50: timed with pme grid 72 72 72, coulomb cutoff 1.043: 33.9 M-cycles
step   60: timed with pme grid 64 64 64, coulomb cutoff 1.173: 32.2 M-cycles
step   70: timed with pme grid 60 60 60, coulomb cutoff 1.251: 32.8 M-cycles
step   80: timed with pme grid 56 56 56, coulomb cutoff 1.341: 32.2 M-cycles
step   90: timed with pme grid 52 52 52, coulomb cutoff 1.444: 32.2 M-cycles
step  100: timed with pme grid 72 72 72, coulomb cutoff 1.043: 33.8 M-cycles
step  110: timed with pme grid 64 64 64, coulomb cutoff 1.173: 40.3 M-cycles
step  120: timed with pme grid 60 60 60, coulomb cutoff 1.251: 32.4 M-cycles
step  130: timed with pme grid 56 56 56, coulomb cutoff 1.341: 33.0 M-cycles
step  140: timed with pme grid 52 52 52, coulomb cutoff 1.444: 32.1 M-cycles
  optimal pme grid 52 52 52, coulomb cutoff 1.444
DD  step 4999 load imb.: force 55.3%

npt15:

DD  step 4 load imb.: force 41.2%

step   10: timed with pme grid 80 80 80, coulomb cutoff 1.000: 36.6 M-cycles
step   20: timed with pme grid 64 64 64, coulomb cutoff 1.181: 32.9 M-cycles
step   30: timed with pme grid 56 56 56, coulomb cutoff 1.350: 33.6 M-cycles
step   40: timed with pme grid 48 48 48, coulomb cutoff 1.575: 33.2 M-cycles
step   50: timed with pme grid 44 44 44, coulomb cutoff 1.718: 35.8 M-cycles
step   60: timed with pme grid 40 40 40, coulomb cutoff 1.890: 40.8 M-cycles
step   70: timed with pme grid 80 80 80, coulomb cutoff 1.000: 36.5 M-cycles
step   80: timed with pme grid 72 72 72, coulomb cutoff 1.050: 33.8 M-cycles
step   90: timed with pme grid 64 64 64, coulomb cutoff 1.181: 32.0 M-cycles
step  100: timed with pme grid 60 60 60, coulomb cutoff 1.260: 32.3 M-cycles
step  110: timed with pme grid 56 56 56, coulomb cutoff 1.350: 31.6 M-cycles
step  120: timed with pme grid 52 52 52, coulomb cutoff 1.454: 32.1 M-cycles
step  130: timed with pme grid 48 48 48, coulomb cutoff 1.575: 32.3 M-cycles
step  140: timed with pme grid 44 44 44, coulomb cutoff 1.718: 35.3 M-cycles
step  150: timed with pme grid 42 42 42, coulomb cutoff 1.800: 37.7 M-cycles
step  160: timed with pme grid 72 72 72, coulomb cutoff 1.050: 33.5 M-cycles
step  170: timed with pme grid 64 64 64, coulomb cutoff 1.181: 32.0 M-cycles
step  180: timed with pme grid 60 60 60, coulomb cutoff 1.260: 31.9 M-cycles
step  190: timed with pme grid 56 56 56, coulomb cutoff 1.350: 31.4 M-cycles
step  200: timed with pme grid 52 52 52, coulomb cutoff 1.454: 31.6 M-cycles
step  210: timed with pme grid 48 48 48, coulomb cutoff 1.575: 32.0 M-cycles
  optimal pme grid 56 56 56, coulomb cutoff 1.350
DD  step 4999 load imb.: force 41.0%





On Tue, Nov 11, 2014 at 9:44 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 by the way, the machine has 4 Tesla K40m gpu, 32 xeon cpu with avx, and i
 ran: nohup ../../mdrun -deffnm npt15 -cpt 1 -cpnum 

 On Tue, Nov 11, 2014 at 9:38 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Hi.

 I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
 from a NPT without Potential-shift-Verlet. The energy dropped from -3e5 to
 -4e5, which is fine.

 After that, I continue the 30ns NPT with the same mdp file, except with a
 longer run time (300ns).

 The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now
 at about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed
 after step 0?

 I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
 grompp for both simulations.

 The plot of total energies for the two simulations:
 http://oi60.tinypic.com/ddmejd.jpg
 The two mdp files: http://oi58.tinypic.com/11980si.jpg

 The commands that I used for continuing the simulations:

 The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp
 -f npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr

 The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f
 npt15.mdp -c npt14.tpr -t npt14_step3000.cpt -o npt15.tpr

 Thanks.



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Re: [gmx-users] restarting of shifted potential, 4.6.7 bug?

2014-11-11 Thread Johnny Lu

Going from non-shift to shifted potential changes the energy. So I was not
surprised by the sudden jump of energy between step 0 and step 10 for the
previous simulation (npt14).

But the jump near step 0 for the current simulation (npt15) is not right.

This is an equilibration run.

I have just uploaded the files at http://redmine.gromacs.org/issues/1640


On Tue, Nov 11, 2014 at 10:54 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 On Tue, Nov 11, 2014 at 3:38 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  Hi.
 
  I ran 30ns NPT with Potential-shift-Verlet on both potentials, continuing
  from a NPT without Potential-shift-Verlet. The energy dropped from -3e5
 to
  -4e5, which is fine.
 
  After that, I continue the 30ns NPT with the same mdp file, except with a
  longer run time (300ns).
 
  The total energy was -4e5 at step 0, and then -3e5 at step 5000, and now
 at
  about 25 ns, it goes back to -3.5e5. Why the energy suddenly changed
 after
  step 0?
 

 IIRC, the restart ought to compute the same energy on the initial
 coordinates as it did at the end of the previous run, and even if there's
 no re-computation on the same coordinates, obviously it should not  jump by
 1e5 in a few steps (or one? can't tell from the resolution). I would think
 that might be a bug in filling a data structure for the output, but
 probably not one in the simulation itself. Please file an issue at
 http://redmine.gromacs.org, tarballing all the relevant files, and I'll
 try
 to look at it.

 The long-time behaviour of both simulations is pretty suspect though. Since
 you're prepared to be ultra-conservative with your non-bonded and SETTLE
 settings, I would explore using a 0.5fs time step (in normal and
 ultra-conservative mode). Berendsen is not a good barostat algorithm for
 production work, too... but I would not expect such a problem from its use.
 Perhaps more importantly, why are you turning off the long-range dispersion
 correction?

 Mark

 I used the same machine and same mixed precision gromacs 4.6.7 mdrun and
  grompp for both simulations.
 
  The plot of total energies for the two simulations:
  http://oi60.tinypic.com/ddmejd.jpg
  The two mdp files: http://oi58.tinypic.com/11980si.jpg
 
  The commands that I used for continuing the simulations:
 
  The previous simulation (npt14): ../../sofware/gromacs-4.6.7/bin/grompp
 -f
  npt14.mdp -c npt13.tpr -t npt13_step22620750.cpt -o npt14.tpr
 
  The current simulation (npt15): ../../sofware/gromacs-4.6.7/bin/grompp -f
  npt15.mdp -c npt14.tpr -t npt14_step3000.cpt -o npt15.tpr
 
  Thanks.
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[gmx-users] Avg. Volume in NPT by Small Coupling Time

Hi.

How to get an accurate average volume for a system, such that the pressure
will be at 1 bar in a subsequent NVT run using this average volume?

Is it ok to use Berendsen barostat with a very small time constant (0.2 ps)
?
(At first I picked 0.1ps, gromacs 4.6.7 told me to use at least 0.2 ps).

I was hoping that a smaller time constant would allow the simulation to
sample the volume more frequently and Berendsen barostat would help the
system to converge to the correct average volume faster.

What are the possible draw backs?

So far (2 ns), I see that the pressure fluctuation is smaller than a PR
barostat.

It seems to be fine to use Berendsen barostat for this purpose ( [
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-February/058453.html]
)

Thank you again.
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Re: [gmx-users] Pressure Question

I see. I'm using the V-rescaling thermostat in all simulations that I ran.
I don't think I will use NPT for production run.

I'm trying to get NVE production run in the end.
If I use NVT production run, I will try to account for the effect of the
thermostat (I'm not sure I can do that very well).


On Thu, Nov 6, 2014 at 10:47 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Hi,

 Note that using the Berendsen thermostat in Gromacs adds defects for no
 gain, compared with the Bussi v-rescale thermostat. The latter *is*
 Berendsen, plus a stochastic term that produces the right energy and
 velocity distributions (unlike Berendsen). I'd give serious consideration
 to rejecting a paper that used Gromacs and the Berendsen thermostat,
 particularly if they did not discuss why the known defects of Berendsen
 were acceptable for their work.

 Mark

 On Thu, Nov 6, 2014 at 4:18 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  That post in the amber mailing list was quite interesting. May be using a
  weak berendsen thermostat in NVT is fine for them. Thanks for sharing
 that.
 
  On Thu, Nov 6, 2014 at 6:39 AM, Johnny Lu johnny.lu...@gmail.com
 wrote:
 
   I was not offended by the suggestion. With a sufficiently large number
 of
   water molecules, the protein would behave in the same way, under all
  three
   ensembles.
   Barostat and thermostat are artificial in some way. At least, even the
   diffusion coefficient is different in a force field paper that used
 both
   NVE and NVT. Langevin thermostat destroys some momentum transfer.
  
   This is my first paper, and I don't know if the reviewer will be fine
 if
  I
   report that my simulation has an average pressure of 11 bar with error
  0.5
   bar.
  
  
   On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane 
   stephane.teletc...@univ-nantes.fr wrote:
  
   Le 06/11/2014 06:16, Antonio Baptista a écrit :
  
  
   In particular, the virial-based instantaneous pressure (call it P')
   computed in simulations has its ensemble average equal to the
  thermodynamic
   pressure P (check any good book on molecular simulation). But, as
  others
   already pointed out, this P' is well-known to show extremelly large
   fluctuations, meaning that its average computed from the simulation
 has
   usually a very large statistical spread. In other words, although the
   ensemble average of P' is strictly equal to P, its simulation average
  is a
   random variable that often shows large deviations from P (especially
  for
   short simulations). To get an idea of what is an acceptable error for
  the
   average of P', you may look at its distribution histogram in the NPT
   simulation.
  
  
   Dear Antonio,
  
   Sorry if my message sound aggressive when I talked about totally
   irrevelevant, I will clarify my thoughts.
  
   From a theoretical point of view, you are right, each ensemble is
   accessible.
  
   From a biological point of view, though, the concept of fixing the
  volume
   is less reasonable:
   we live at constant pressure and temperature, and also at tighly
   controlled pH, and salt concentrations.
  
   The volume varies though, as you feel it when the weather is getting
 hot
   or cold.
  
   My point was exactly what your are telling in a more formal way than
 me:
   this P' is well-known to show extremely large fluctuations
  
   Well, digging a bit more on my feeling, I also found opposite
  arguments
   on the AMBER mailing list,
   like here: http://archive.ambermd.org/201103/0431.html
  
   So I'll got back again on my research and adjust my mind on the
 actual
   bleeding edge simulations
   taking into account all the recent code and force fields progresses.
  
   Best,
  
   Stéphane
  
   --
   Team Protein Design In Silico
   UFIP, UMR 6286 CNRS,
   UFR Sciences et Techniques,
   2, rue de la Houssinière, Bât. 25,
   44322 Nantes cedex 03, France
   Tél : +33 251 125 636
   Fax : +33 251 125 632
   http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
  
   --
   Gromacs Users mailing list
  
   * Please search the archive at http://www.gromacs.org/
   Support/Mailing_Lists/GMX-Users_List before posting!
  
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 * For (un

Re: [gmx-users] Avg. Volume in NPT by Small Coupling Time

Assume sampling is sufficient in all stages of simulations.

Will the berendsen barostat with this coupling constant give both the
correct average volume and correct average pressure? (despite the
distribution is not canonical)
Will that average pressure change when I switch to NVT ensemble?

Can I switch to NVT directly (without doing a NPT with PR barostat) for a
while, and then finally go to NVE production run?
(a nature communication paper did that, but didn't report the barostat
coupling constant they used in the NPT simulation.)


On Thu, Nov 6, 2014 at 10:51 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Hi,

 I think that's fine for rapidly forcing the volume to be close to the right
 equilibrium value, with low fluctuations. Then switch to gentler NPT (or
 constant-volume) for making a proper observation of the pressure.

 Mark

 On Thu, Nov 6, 2014 at 4:44 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  Hi.
 
  How to get an accurate average volume for a system, such that the
 pressure
  will be at 1 bar in a subsequent NVT run using this average volume?
 
  Is it ok to use Berendsen barostat with a very small time constant (0.2
 ps)
  ?
  (At first I picked 0.1ps, gromacs 4.6.7 told me to use at least 0.2 ps).
 
  I was hoping that a smaller time constant would allow the simulation to
  sample the volume more frequently and Berendsen barostat would help the
  system to converge to the correct average volume faster.
 
  What are the possible draw backs?
 
  So far (2 ns), I see that the pressure fluctuation is smaller than a PR
  barostat.
 
  It seems to be fine to use Berendsen barostat for this purpose ( [
 
 
 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2011-February/058453.html
  ]
  )
 
  Thank you again.
  --
  Gromacs Users mailing list
 
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  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
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Re: [gmx-users] Pressure Question

If the problem of using a 11 bar simulation is as big as the problem of
drawing conclusion from a single simulation, I guess I have to get a
pressure closer to 1 bar. Thanks.

On Thu, Nov 6, 2014 at 10:55 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 I see. I'm using the V-rescaling thermostat in all simulations that I ran.
 I don't think I will use NPT for production run.

 I'm trying to get NVE production run in the end.
 If I use NVT production run, I will try to account for the effect of the
 thermostat (I'm not sure I can do that very well).


 On Thu, Nov 6, 2014 at 10:47 AM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

 Hi,

 Note that using the Berendsen thermostat in Gromacs adds defects for no
 gain, compared with the Bussi v-rescale thermostat. The latter *is*
 Berendsen, plus a stochastic term that produces the right energy and
 velocity distributions (unlike Berendsen). I'd give serious consideration
 to rejecting a paper that used Gromacs and the Berendsen thermostat,
 particularly if they did not discuss why the known defects of Berendsen
 were acceptable for their work.

 Mark

 On Thu, Nov 6, 2014 at 4:18 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  That post in the amber mailing list was quite interesting. May be using
 a
  weak berendsen thermostat in NVT is fine for them. Thanks for sharing
 that.
 
  On Thu, Nov 6, 2014 at 6:39 AM, Johnny Lu johnny.lu...@gmail.com
 wrote:
 
   I was not offended by the suggestion. With a sufficiently large
 number of
   water molecules, the protein would behave in the same way, under all
  three
   ensembles.
   Barostat and thermostat are artificial in some way. At least, even the
   diffusion coefficient is different in a force field paper that used
 both
   NVE and NVT. Langevin thermostat destroys some momentum transfer.
  
   This is my first paper, and I don't know if the reviewer will be fine
 if
  I
   report that my simulation has an average pressure of 11 bar with error
  0.5
   bar.
  
  
   On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane 
   stephane.teletc...@univ-nantes.fr wrote:
  
   Le 06/11/2014 06:16, Antonio Baptista a écrit :
  
  
   In particular, the virial-based instantaneous pressure (call it
 P')
   computed in simulations has its ensemble average equal to the
  thermodynamic
   pressure P (check any good book on molecular simulation). But, as
  others
   already pointed out, this P' is well-known to show extremelly large
   fluctuations, meaning that its average computed from the simulation
 has
   usually a very large statistical spread. In other words, although
 the
   ensemble average of P' is strictly equal to P, its simulation
 average
  is a
   random variable that often shows large deviations from P (especially
  for
   short simulations). To get an idea of what is an acceptable error
 for
  the
   average of P', you may look at its distribution histogram in the NPT
   simulation.
  
  
   Dear Antonio,
  
   Sorry if my message sound aggressive when I talked about totally
   irrevelevant, I will clarify my thoughts.
  
   From a theoretical point of view, you are right, each ensemble is
   accessible.
  
   From a biological point of view, though, the concept of fixing the
  volume
   is less reasonable:
   we live at constant pressure and temperature, and also at tighly
   controlled pH, and salt concentrations.
  
   The volume varies though, as you feel it when the weather is getting
 hot
   or cold.
  
   My point was exactly what your are telling in a more formal way than
 me:
   this P' is well-known to show extremely large fluctuations
  
   Well, digging a bit more on my feeling, I also found opposite
  arguments
   on the AMBER mailing list,
   like here: http://archive.ambermd.org/201103/0431.html
  
   So I'll got back again on my research and adjust my mind on the
 actual
   bleeding edge simulations
   taking into account all the recent code and force fields progresses.
  
   Best,
  
   Stéphane
  
   --
   Team Protein Design In Silico
   UFIP, UMR 6286 CNRS,
   UFR Sciences et Techniques,
   2, rue de la Houssinière, Bât. 25,
   44322 Nantes cedex 03, France
   Tél : +33 251 125 636
   Fax : +33 251 125 632
   http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
  
   --
   Gromacs Users mailing list
  
   * Please search the archive at http://www.gromacs.org/
   Support/Mailing_Lists/GMX-Users_List before posting!
  
   * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  
   * For (un)subscribe requests visit
   https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
 or
   send a mail to gmx-users-requ...@gromacs.org.
  
  
  
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  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
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  send a mail

Re: [gmx-users] Version problem

can look for all files with name mdrun by

$ find / -name mdrun *  mdrun_search
and then
$ cat mdrun_search


On Thu, Nov 6, 2014 at 7:25 AM, Erik Marklund erik.markl...@chem.ox.ac.uk
wrote:

 Hi,

 'which mdrun' only tells you the location of the mdrun you're currently
 using and is no good here. How did you install 5.0.2? The CMake files
 should tell you where installation directory is.

 Kind regards,
 Erik

 On 6 Nov 2014, at 11:43, sa...@physics.iisc.ernet.in wrote:

 
  tried which mdrun
  showing the path /usr/bin/mdrun, which v4.6.5, however I have downloaded
  v5.0.2.tar.gz and used for installation.
 
 
  try to find mdrun program by typing this command on terminal:
  which mdrun
  will show path of mdrun program where it located.
  On Nov 6, 2014 4:01 PM, sa...@physics.iisc.ernet.in wrote:
 
  Dear Dr. Carsten Kutzner,
   I am unable to find the gmx5/bin/GMXRC in my machine,
  used 'locate' and 'find' to search the location.
  However I have source the following:
  source /usr/share/gromacs/shell-specific/GMXRC.bashrc
  Without this also mdrun is running. I am definitely missing something.
  Kindly help.
 
  With best regards,
 
  Satya
 
  On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote:
 
  Dear all,
  I am new to GROMACS, just finish installation of v5.0.2, started
  reading
  online manual, as instructed executed the command: mdrun -version and
  the
  printout pasted below.
 
  It is printing GROMACS version 4.6.5, however I have installed
  version
  5.0.2. What is the problem?
  Find the directory to where you have installed your GROMACS 5.0
  executables
  and then do
 
  source /path/to/gmx5/bin/GMXRC
 
  which mdrun
 
  should now give you the 5.0 mdrun
 
  Carsten
 
 
  Regards,
  Satyabrata Das
 
 
 ==
  Program: mdrun
  Gromacs version:VERSION 4.6.5
  Precision:  single
  Memory model:   64 bit
  MPI library:thread_mpi
  OpenMP support: enabled
  GPU support:disabled
  invsqrt routine:gmx_software_invsqrt(x)
  CPU acceleration:   SSE4.1
  FFT library:fftw-3.3.3-sse2-avx
  Large file support: enabled
  RDTSCP usage:   enabled
  Built on:   Sun Dec 15 04:01:11 UTC 2013
  Built by:   buildd@panlong [CMAKE]
  Build OS/arch:  Linux 3.2.0-37-generic x86_64
  Build CPU vendor:   GenuineIntel
  Build CPU brand:Intel(R) Xeon(R) CPU   E5620  @ 2.40GHz
  Build CPU family:   6   Model: 44   Stepping: 2
  Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr
  nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3
  sse4.1
  sse4.2 ssse3
  C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real
  (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2
  C compiler flags:   -msse4.1-Wextra
  -Wno-missing-field-initializers
  -Wno-sign-compare -Wall -Wno-unused -Wunused-value
  -Wno-unused-parameter
  -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
  -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
  -DNDEBUG
  satyabrata@satyabrata-desktop:~$
 
 
 
  --
  This message has been scanned for viruses and
  dangerous content by MailScanner, and is
  believed to be clean.
 
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe requests visit
  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
 or
  send a mail to gmx-users-requ...@gromacs.org.
 
 
  --
  Dr. Carsten Kutzner
  Max Planck Institute for Biophysical Chemistry
  Theoretical and Computational Biophysics
  Am Fassberg 11, 37077 Goettingen, Germany
  Tel. +49-551-2012313, Fax: +49-551-2012302
  http://www.mpibpc.mpg.de/grubmueller/kutzner
  http://www.mpibpc.mpg.de/grubmueller/sppexa
 
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe requests visit
  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
  send
  a mail to gmx-users-requ...@gromacs.org.
 
  --
  This message has been scanned for viruses and
  dangerous content by MailScanner, and is
  believed to be clean.
 
 
 
 
 
  --
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  dangerous content by MailScanner, and is
  believed to be clean.
 
  --
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  * Please search the archive at
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  posting!
 
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  send a mail to gmx-users-requ...@gromacs.org.
 
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  *

Re: [gmx-users] Version problem

I typed an extra space that shouldn't be there.

$ find / -name mdrun*  mdrun_search

On Thu, Nov 6, 2014 at 5:03 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 can look for all files with name mdrun by

 $ find / -name mdrun *  mdrun_search
 and then
 $ cat mdrun_search


 On Thu, Nov 6, 2014 at 7:25 AM, Erik Marklund erik.markl...@chem.ox.ac.uk
  wrote:

 Hi,

 'which mdrun' only tells you the location of the mdrun you're currently
 using and is no good here. How did you install 5.0.2? The CMake files
 should tell you where installation directory is.

 Kind regards,
 Erik

 On 6 Nov 2014, at 11:43, sa...@physics.iisc.ernet.in wrote:

 
  tried which mdrun
  showing the path /usr/bin/mdrun, which v4.6.5, however I have downloaded
  v5.0.2.tar.gz and used for installation.
 
 
  try to find mdrun program by typing this command on terminal:
  which mdrun
  will show path of mdrun program where it located.
  On Nov 6, 2014 4:01 PM, sa...@physics.iisc.ernet.in wrote:
 
  Dear Dr. Carsten Kutzner,
   I am unable to find the gmx5/bin/GMXRC in my machine,
  used 'locate' and 'find' to search the location.
  However I have source the following:
  source /usr/share/gromacs/shell-specific/GMXRC.bashrc
  Without this also mdrun is running. I am definitely missing something.
  Kindly help.
 
  With best regards,
 
  Satya
 
  On 06 Nov 2014, at 07:15, sa...@physics.iisc.ernet.in wrote:
 
  Dear all,
  I am new to GROMACS, just finish installation of v5.0.2, started
  reading
  online manual, as instructed executed the command: mdrun -version
 and
  the
  printout pasted below.
 
  It is printing GROMACS version 4.6.5, however I have installed
  version
  5.0.2. What is the problem?
  Find the directory to where you have installed your GROMACS 5.0
  executables
  and then do
 
  source /path/to/gmx5/bin/GMXRC
 
  which mdrun
 
  should now give you the 5.0 mdrun
 
  Carsten
 
 
  Regards,
  Satyabrata Das
 
 
 ==
  Program: mdrun
  Gromacs version:VERSION 4.6.5
  Precision:  single
  Memory model:   64 bit
  MPI library:thread_mpi
  OpenMP support: enabled
  GPU support:disabled
  invsqrt routine:gmx_software_invsqrt(x)
  CPU acceleration:   SSE4.1
  FFT library:fftw-3.3.3-sse2-avx
  Large file support: enabled
  RDTSCP usage:   enabled
  Built on:   Sun Dec 15 04:01:11 UTC 2013
  Built by:   buildd@panlong [CMAKE]
  Build OS/arch:  Linux 3.2.0-37-generic x86_64
  Build CPU vendor:   GenuineIntel
  Build CPU brand:Intel(R) Xeon(R) CPU   E5620  @ 2.40GHz
  Build CPU family:   6   Model: 44   Stepping: 2
  Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr
  nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3
  sse4.1
  sse4.2 ssse3
  C compiler: /usr/bin/x86_64-linux-gnu-gcc GNU gcc-4.8.real
  (Ubuntu/Linaro 4.8.2-10ubuntu1) 4.8.2
  C compiler flags:   -msse4.1-Wextra
  -Wno-missing-field-initializers
  -Wno-sign-compare -Wall -Wno-unused -Wunused-value
  -Wno-unused-parameter
  -Wno-array-bounds -Wno-maybe-uninitialized -Wno-strict-overflow
  -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
  -DNDEBUG
  satyabrata@satyabrata-desktop:~$
 
 
 
  --
  This message has been scanned for viruses and
  dangerous content by MailScanner, and is
  believed to be clean.
 
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe requests visit
  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
 or
  send a mail to gmx-users-requ...@gromacs.org.
 
 
  --
  Dr. Carsten Kutzner
  Max Planck Institute for Biophysical Chemistry
  Theoretical and Computational Biophysics
  Am Fassberg 11, 37077 Goettingen, Germany
  Tel. +49-551-2012313, Fax: +49-551-2012302
  http://www.mpibpc.mpg.de/grubmueller/kutzner
  http://www.mpibpc.mpg.de/grubmueller/sppexa
 
  --
  Gromacs Users mailing list
 
  * Please search the archive at
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  posting!
 
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 or
  send
  a mail to gmx-users-requ...@gromacs.org.
 
  --
  This message has been scanned for viruses and
  dangerous content by MailScanner, and is
  believed to be clean.
 
 
 
 
 
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[gmx-users] speed of 5.0.2 v.s 4.6

Hi.

Do the two version of gromacs with mixed precision have similar speed?

Thanks again.
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Re: [gmx-users] speed of 5.0.2 v.s 4.6

Thanks. I guess I will keep version 4.6.7 for now.

On Wed, Nov 5, 2014 at 11:40 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Yes, in general.

 Mark

 On Wed, Nov 5, 2014 at 5:11 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  Hi.
 
  Do the two version of gromacs with mixed precision have similar speed?
 
  Thanks again.
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Re: [gmx-users] Pressure Question

The statistics was calculated for 80 ns of NVT simulation, after a 80 ns
NPT simulation.

In papers, I saw people talked about using the average volume of a previous
NPT simulation to choose the frame with the correct volume. And then, run
NVT starting from the NPT frame.
But they don't talk about the pressure that they get in the NVT simulation
(even in a force field paper).

I just want to know if the reviewer will be ok with my paper, if I mention
the pressure that I get in the NVT simulation.


On Wed, Nov 5, 2014 at 12:16 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Hi,

 That's hard to say. You'd need to do multiple converged simulations at each
 set of conditions to know. First, make sure you've made a significant
 observation of the pressure.

 Mark


 On Tue, Nov 4, 2014 at 6:00 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  Hi.
 
  If my NVT simulation of a protein in 30k molecules of water has a
 pressure
  of 11 bar (error 0.5 bar from g_energy), will the dynamics (not
  distribution of conformations) change enough that the mechanism inferred
  from this simulation be significantly more unreliable than the mechanism
  inferred from a 1 bar simulation? (Will the reviewers cut my paper into
  ribbons?)
 
  Thanks again.
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Re: [gmx-users] Pressure Question

the protein has about 170 amino acid.

On Wed, Nov 5, 2014 at 1:13 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 The statistics was calculated for 80 ns of NVT simulation, after a 80 ns
 NPT simulation.

 In papers, I saw people talked about using the average volume of a
 previous NPT simulation to choose the frame with the correct volume. And
 then, run NVT starting from the NPT frame.
 But they don't talk about the pressure that they get in the NVT simulation
 (even in a force field paper).

 I just want to know if the reviewer will be ok with my paper, if I mention
 the pressure that I get in the NVT simulation.


 On Wed, Nov 5, 2014 at 12:16 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

 Hi,

 That's hard to say. You'd need to do multiple converged simulations at
 each
 set of conditions to know. First, make sure you've made a significant
 observation of the pressure.

 Mark


 On Tue, Nov 4, 2014 at 6:00 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  Hi.
 
  If my NVT simulation of a protein in 30k molecules of water has a
 pressure
  of 11 bar (error 0.5 bar from g_energy), will the dynamics (not
  distribution of conformations) change enough that the mechanism inferred
  from this simulation be significantly more unreliable than the mechanism
  inferred from a 1 bar simulation? (Will the reviewers cut my paper into
  ribbons?)
 
  Thanks again.
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Re: [gmx-users] Pressure Question

Well... I finally have to accept that I really need NVE. Some forum posts
suggested to run NPT, then NVT, and finally NVE.

For ideal gas law, if we fix the number of molecules and the temperature,
then fixing the volume at different value means changing the pressure.
So, I guess pressure is still meaningful, if I have to decide the correct
volume to run the NVT simulation.

For a large number of ideal gas molecules, averages of all thermodynamic
variables should be defined, regardless of which three of them is fixed or
which ensemble do I choose to represent the state.
For a small number of molecules, the distribution of the thermodynamic
variables should still have a definition (so, the average and the
distribution of pressure is still meaningful).

For a protein simulation, it still has a partition function, and equation
of state.

I mainly want to know how much error in pressure (deviation from 1 bar) is
acceptable.

On Wed, Nov 5, 2014 at 2:35 PM, Téletchéa Stéphane 
stephane.teletc...@univ-nantes.fr wrote:

 Le 04/11/2014 18:00, Johnny Lu a écrit :

  Hi.

 If my NVT simulation of a protein in 30k molecules of water has a pressure
 of 11 bar (error 0.5 bar from g_energy), will the dynamics (not
 distribution of conformations) change enough that the mechanism inferred
 from this simulation be significantly more unreliable than the mechanism
 inferred from a 1 bar simulation? (Will the reviewers cut my paper into
 ribbons?)

 Thanks again.


 Hi,

 Considering only your NVT parameters for your simulation,
 I would consider it totally irrelevant to talk about pressure where your
 constrain the volume.
 This value or any other one has not really a meaning in this situation,
 and I seen
 many variations in the pressure value in this microcanonical ensemble
 without paying too much
 attention on it.

 In an NPT simulation, then you should be able to find back a normal 1
 bar simulation I think.

 Do you have any reason to do first an NPT simulation, and then an NVT
 one?
 I would personally let the system equilibrate in NVT, then swith to the
 more natural NPT,
 provided actual code and force fields are now good enough in this ensemble.

 Best,

 Stéphane

 --
 Team Protein Design In Silico
 UFIP, UMR 6286 CNRS,
 UFR Sciences et Techniques,
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 44322 Nantes cedex 03, France
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Re: [gmx-users] pseudo-random algorithm

2014-11-04 Thread Johnny Lu

Thanks for answering my question.

On Wed, Oct 29, 2014 at 6:36 PM, Roland Schulz rol...@utk.edu wrote:

 Hi,

 Gromacs  5.0 uses a Mersenne twister. See gmx_random.h. Starting with 5.0
 it uses Random123 threefry2x64. Why do you think your results are affected
 by the PRNG?

 Roland

 On Wed, Oct 29, 2014 at 6:23 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  Hi.
 
  Before I start to feel optimistic about my alanine tripeptide simulation,
  can I know
 
  which pseudo-random number algorithm does my installation of gromacs
 4.6.6
  use?
 
  It was installed on linux centos 5 with kernel 2.6.32-220.7.1.el6.x86_64,
  and the machine has 12 intel cpu and no gpu.
 
  I was using the V-rescale thermostat.
 
  Thanks again.
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[gmx-users] Pressure Question

2014-11-04 Thread Johnny Lu

Hi.

If my NVT simulation of a protein in 30k molecules of water has a pressure
of 11 bar (error 0.5 bar from g_energy), will the dynamics (not
distribution of conformations) change enough that the mechanism inferred
from this simulation be significantly more unreliable than the mechanism
inferred from a 1 bar simulation? (Will the reviewers cut my paper into
ribbons?)

Thanks again.
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Re: [gmx-users] problems with testing a new gromacs installation (myfirst) for correctness

2014-11-04 Thread Johnny Lu

Hi. did you try to download the regression tests manually? I don't know if
the problem that I encountered was the same one:

http://comments.gmane.org/gmane.science.biology.gromacs.user/71882

I had to turn regression test download off in addition to setting path to
regression test.



On Sat, Nov 1, 2014 at 12:45 PM, infoseca i...@seca-tech.de wrote:

 hello

 my name is hans, i am a master student in biophysics at the lmu munich.

 first thanks a lot to all spending time to engage with my problem.

 my machine is configured as follows.
 processor intel i5 2450M 2,5 Ghz
 OS windows 7 64 bit
 linux emulation with cygwin x86_64 version 1.7.32
 gromacs version is 5.0.2
 i installed cygwin with the following packages beside the defaults. devel
 (gdn, gdb, make, cmake, gcc 4.9.0.1), shels(tcsh), editors (vi),
 lib(libxml2-devel 2.9.2.1, libboost,libgcc1 4.9.0.1)
 i have uninstalled the default fftw3 package from cygwin as recommended in
 the gromacs instruction.
 i unpacked gromacs in my default cygwin user folder = /home/gl/
 the configuration and compiling shell script i used was

 cd gromacs-5.0.2
 mkdir build
 cd build
 cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_EXTERNAL_BLAS=OFF
 -DGMX_EXTERNAL_LAPACK=OFF -DGMX_SIMD=SSE2 -DREGRESSIONTEST_DOWNLOAD=ON
 make
 make check

 i tried it several times with different cmake options with and without
 DGMX_EXTERNAL_BLAS=OFF -DGMX_EXTERNAL_LAPACK=OFF,
 with and without -DGMX_BUILD_OWN_FFTW=ON (if i did without this option i
 install the newest fftw3 version (3.0.2) before.
 but the result was always the same
 the configuration and the compilation works without any warning.
 but the testing provides a lot of errors and always the same result
 as shown in the test logs.  i attached them to this email.
 i hope someone can help me.

 thanks and best regards

 hans

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Re: [gmx-users] pressure dependence on volume.

2014-10-20 Thread Johnny Lu

One less thing to worry about then. I will try to fix this in another way.
Thanks.
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Re: [gmx-users] pressure dependence on volume.

2014-10-19 Thread Johnny Lu

The averaged volume of the 1bar pressure NPT simulation over 150ns was very
clearly 298.5 nm^3.
But now, when I set the volume of the NVT simulation to 298.7 nm^3 by
starting from a NPT frame that has the volume, the average was 1.2 bar with
error estimate 0.53, over 52 ns.

The same tactic also didn't work for a 300 ns NPT simulation and
subsequently 300 ns NVT simulation. This NVT simulation pressure was
averaged to be around 4 bar.

Why starting a NVT simulation from a NPT frame with the averaged NPT volume
didn't give the target pressure of 1 bar?



On Sun, Oct 19, 2014 at 2:20 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:

 Hi Johnny,

 The density is M/V. The only parameter changing with pressure coupling is
 V, so the density and volume are fully correlated. No surprise there.

 Cheers,

 Tsjerk
 On Oct 19, 2014 2:27 AM, Johnny Lu johnny.lu...@gmail.com wrote:

  The frames with density closest to the average density also have volumes
  closest to the averaged volume.
 
  On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu johnny.lu...@gmail.com
 wrote:
 
   I searched the energy file made by g_energy, and found that NPT frames
   with very similar densities have very similar volume.
  
   So, I guess using density is same as using volume in this case.
  
   On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu johnny.lu...@gmail.com
  wrote:
  
   Would manually setting the box size make vacuum bubbles?
  
   On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu johnny.lu...@gmail.com
   wrote:
  
   my bad. that formula for density is wrong. But I till don't see why
   using the same averaged density (instead of volume) for the NVT and
 NPT
   simulations would give a different result.
  
   On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu johnny.lu...@gmail.com
   wrote:
  
   Was the density calculated by # particles /  volume ?
  
   If so, using volume (as I did), and using density would give the
 same
   wrong pressure, upon transitioning from NPT to NVT.
  
  
  
  
  
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Re: [gmx-users] pressure dependence on volume.

2014-10-19 Thread Johnny Lu

I saved .cpt file every minute. And using the xvg file generated by
g_energy, I picked the .cpt file with the volume that I want, and then run
a NVT simulation, continuing from thee NPT .cpt file.

The volume of the .cpt file of the NPT simulation should be same as the
volume of the NVT file. Is it so? Or manually setting the volume makes some
magical differences?

On Sun, Oct 19, 2014 at 10:24 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Thanks for answering my questions too.

 On Sun, Oct 19, 2014 at 10:18 AM, Johnny Lu johnny.lu...@gmail.com
 wrote:

 The averaged volume of the 1bar pressure NPT simulation over 150ns was
 very clearly 298.5 nm^3.
 But now, when I set the volume of the NVT simulation to 298.7 nm^3 by
 starting from a NPT frame that has the volume, the average was 1.2 bar with
 error estimate 0.53, over 52 ns.

 The same tactic also didn't work for a 300 ns NPT simulation and
 subsequently 300 ns NVT simulation. This NVT simulation pressure was
 averaged to be around 4 bar.

 Why starting a NVT simulation from a NPT frame with the averaged NPT
 volume didn't give the target pressure of 1 bar?



 On Sun, Oct 19, 2014 at 2:20 AM, Tsjerk Wassenaar tsje...@gmail.com
 wrote:

 Hi Johnny,

 The density is M/V. The only parameter changing with pressure coupling is
 V, so the density and volume are fully correlated. No surprise there.

 Cheers,

 Tsjerk
 On Oct 19, 2014 2:27 AM, Johnny Lu johnny.lu...@gmail.com wrote:

  The frames with density closest to the average density also have
 volumes
  closest to the averaged volume.
 
  On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu johnny.lu...@gmail.com
 wrote:
 
   I searched the energy file made by g_energy, and found that NPT
 frames
   with very similar densities have very similar volume.
  
   So, I guess using density is same as using volume in this case.
  
   On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu johnny.lu...@gmail.com
  wrote:
  
   Would manually setting the box size make vacuum bubbles?
  
   On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu johnny.lu...@gmail.com
   wrote:
  
   my bad. that formula for density is wrong. But I till don't see why
   using the same averaged density (instead of volume) for the NVT
 and NPT
   simulations would give a different result.
  
   On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu johnny.lu...@gmail.com
 
   wrote:
  
   Was the density calculated by # particles /  volume ?
  
   If so, using volume (as I did), and using density would give the
 same
   wrong pressure, upon transitioning from NPT to NVT.
  
  
  
  
  
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Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

2014-10-19 Thread Johnny Lu

how long were those simulations?
Were there enough time for the new ensemble to equilibrate, if you changed
ensemble from NVE to NVT?

On Sun, Oct 19, 2014 at 11:34 AM, Wade wad...@foxmail.com wrote:

 Dear Mark and Lu,
   Thank you very much for your responses.
 Based on your suggestions, I performed some tests:
 1) I considered the influence of the time-step (with LINCS constraint),
 thermostat, and simulation precision in NVT simulation
 (tip4p water box, 300K, after 2ns NVE simulation).
 Below are results:
 ---
 Time-step (fs)  thermostat (V or N)  precision (S or D)
  drift/ns = delt E/av E*100%
 0.1 V   D   0.3
 1   V   D   2
 2   V   D   5.8


 0.1 V   S   80
 1   V   S   1.5
 2   V   S   6.4


 0.1 N   D   0.3
 1   N   D   2.5
 2   N   D   20


 0.1 N   S   76
 1   N   S   1.7
 2   N   S   11.5
 --
 Above results shown that no matter the v-rescale or nose-hoover
 thermostat, the conserved Energy has nearly no drift (~0.3%/ns)
  when an very small time-step (0.1 fs) has been employed. But, even with
 0.1fs step length, the integration can only be conserved in
 the double precision simulations.
 For a commonly used time-step, such as 2 fs (with LINCS constraint), the
 drifts of the conserved energy are about 6-7% per ns.
 Such a drift might be not very significant in a short simulation. But, its
 accumulation in a long-time (e.g. several ns) simulation should be huge.


 2) I checked the time-dependency of auxiliary dynamics purely, and found
 that it was the origination of the constant-rate drift of conserved energy.
 I also noticed that the exact solution of Eq.7 in bussi’s paper (Eq. A7)
 has been realized in gromacs to get the rescaling factor.
 But, I don’t know what the origination of the integration error is, and
 How can we deal with it.
 As Lu said, does it comes from the summation of dK? If yes, how can we
 deal with the drift when we use an affordable time-step in a long-time
 simulation?


 With best wishes,


 Wade
 ‍
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Re: [gmx-users] pressure dependence on volume.

Was the density calculated by # particles /  volume ?

If so, using volume (as I did), and using density would give the same wrong
pressure, upon transitioning from NPT to NVT.
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Re: [gmx-users] pressure dependence on volume.

my bad. that formula for density is wrong. But I till don't see why using
the same averaged density (instead of volume) for the NVT and NPT
simulations would give a different result.

On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Was the density calculated by # particles /  volume ?

 If so, using volume (as I did), and using density would give the same
 wrong pressure, upon transitioning from NPT to NVT.

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Re: [gmx-users] pressure dependence on volume.

Would manually setting the box size make vacuum bubbles?

On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 my bad. that formula for density is wrong. But I till don't see why using
 the same averaged density (instead of volume) for the NVT and NPT
 simulations would give a different result.

 On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Was the density calculated by # particles /  volume ?

 If so, using volume (as I did), and using density would give the same
 wrong pressure, upon transitioning from NPT to NVT.



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[gmx-users] Check for Vacuum Bubbles Density

Hi.

The NPT simulation has 9K TIP3P water with 173 amino acid residues and uses
Amber99SB-ILDN force field, and use Berendsen barostat and V-rescale
thermostat. I plan to run NVT with the same pressure an temperature after
this.

The average density is 1015 kg/m^3 over 35ns. The density was near 1015
over more than 300 ns, in previous NPT simulations.

Statistics over 34744941 steps [ 0. through 34744.9400 ps ], 5 data
sets
All statistics are over 6948989 points

Energy  Average   Err.Est.   RMSD  Tot-Drift

---
Total Energy-307197210 880.41   -1408.29
(kJ/mol)
Temperature 299.993 0.00371.70813  0.0273197
(K)
Pressure1.00317  0.009138.426 -0.0381886
(bar)
Volume  298.567  0.049   0.371817  -0.314958
(nm^3)
Density  1014.8   0.171.263771.07078
(kg/m^3)

This is higher than the 982.3 value in the mail-list [
https://www.mail-archive.com/gmx-users@gromacs.org/msg29327.html]. Why the
density is different?

I used a 1.0 nm cut off, following the force-field paper: Improved
side-chain torsion potentials for the Amber ff99SB protein force field [
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/], but I also added
dispersion correction. Should I not use dispersion correction?

I look at the trajectory in VMD with periodic images turn on. But there
were many water that overlap each other, and I can not see any vacuum
bubble clearly  (if there is a vacuum bubble) [
http://archive.ambermd.org/201103/0431.html]. Is there a better way to
check for vacuum bubbles?

I didn't know a long NVT equilibration at 300 K, right after minimization,
can make vacuum bubbles. The NVT equilibration was 300 ps.

I also didn't know that I should run berendsen barostat before
Parrinello-Rahman, so those 300+ ns NPT simulations before this one all
uses
Parrinello-Rahman barostat.

If there is no vacuum bubbles, I think I was just lucky.

Below is the mdp file I used for the NPT simulation:
title   = NPT production
; Run parameters
integrator  = md-vv ; leap-frog integrator
nsteps  = 3600  ; 1 ns
dt  = 0.001 ; 1 fs

; Output control
nstenergy   = 10   ; save energies every 1.0 ps

nstlog  = 5000  ; update log file every 0.2 ps
; Bond parameters
continuation= yes   ; Restarting after NVT
constraint_algorithm = lincs; holonomic constraints
constraints = H-bonds   ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 2 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in
nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in
nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in
nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.1   ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = system; single thermostat
tau_t   = 1.0   ; time constant, in ps
ref_t   = 300   ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl  = berendsen ; 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
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; Velocity generation is off
cutoff-scheme = Verlet

Thank you again.
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Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

For V-rescale thermostat, the bussi paper seems to say the tilde H is the
integral of the auxiliary dynamics. Not sure if this is same as the
conserved energy in gromacs, which is also the integral of the auxiliary
dynamics.

I guess numerical error causes the system to lose/gain total energy in a
linear way. Rise/drop of tilde H may reflect the extra energy that the
thermostat has to put in to compensate for this numerical error. [just my
guess]

If the energy of the system is conserved without the thermostat, tilde H
should be constant... I guess.

The Bussi paper at [
marge.uochb.cas.cz/~roesel/teach/Clanky/paper5_Bussi_v_rescale.pdf] says
tilde H is the conserved quantity.
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Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

Oh, integrating with rectangles under the curve causes error. I guess
larger time-steps can cause error in tilde H by this method of integration
alone.

On Sat, Oct 18, 2014 at 11:25 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 For V-rescale thermostat, the bussi paper seems to say the tilde H is the
 integral of the auxiliary dynamics. Not sure if this is same as the
 conserved energy in gromacs, which is also the integral of the auxiliary
 dynamics.

 I guess numerical error causes the system to lose/gain total energy in a
 linear way. Rise/drop of tilde H may reflect the extra energy that the
 thermostat has to put in to compensate for this numerical error. [just my
 guess]

 If the energy of the system is conserved without the thermostat, tilde H
 should be constant... I guess.

 The Bussi paper at [
 marge.uochb.cas.cz/~roesel/teach/Clanky/paper5_Bussi_v_rescale.pdf] says
 tilde H is the conserved quantity.



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Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

Does double precision cause a less drop/rise in tilde H over time, when
compared to a mixed precision run under same condition ?

On Sat, Oct 18, 2014 at 11:28 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Oh, integrating with rectangles under the curve causes error. I guess
 larger time-steps can cause error in tilde H by this method of integration
 alone.

 On Sat, Oct 18, 2014 at 11:25 AM, Johnny Lu johnny.lu...@gmail.com
 wrote:

 For V-rescale thermostat, the bussi paper seems to say the tilde H is the
 integral of the auxiliary dynamics. Not sure if this is same as the
 conserved energy in gromacs, which is also the integral of the auxiliary
 dynamics.

 I guess numerical error causes the system to lose/gain total energy in a
 linear way. Rise/drop of tilde H may reflect the extra energy that the
 thermostat has to put in to compensate for this numerical error. [just my
 guess]

 If the energy of the system is conserved without the thermostat, tilde H
 should be constant... I guess.

 The Bussi paper at [
 marge.uochb.cas.cz/~roesel/teach/Clanky/paper5_Bussi_v_rescale.pdf] says
 tilde H is the conserved quantity.




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Re: [gmx-users] Use NVT to mimic NVE

The conserved energy from g_energy, which I saw someone say is tilde H,
drop more crazily if I use 1s coupling constant.

On Mon, Oct 13, 2014 at 5:52 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Hi,

 What is your target observable? What got worse?

 Mark

 On Mon, Oct 13, 2014 at 11:17 PM, Johnny Lu johnny.lu...@gmail.com
 wrote:

  The simulation get worse in a new way.
 
  I see that thermostat scales velocity and may not fix numerical error in
  potential energy.
 
  On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu johnny.lu...@gmail.com
 wrote:
 
   I just want something that will patch up the energy lost due to
 numerical
   error of NVE simulation of the system ran by mixed precision gromacs,
   instead of a thermostat.
  
   I hope the velocity rescaling is sufficiently uncorrelated with the
  motion
   of the protein.
  
   So far, the simulations ran 2.5 ns, and the fluctuation of total energy
   seems to be within 1% of total energy, with a 100ps or 1ns coupling
   constant.
  
   May be I should try a 10 ns coupling constant, just to see if the
   simulation would go belly up.
  
   On Mon, Oct 13, 2014 at 11:02 AM, Michael Shirts mrshi...@gmail.com
   wrote:
  
I guess, if I pick a coupling constant that is just small enough to
   keep the
   energy conserved, I would get a NVT simulation that is as close as a
 NVE
   simulation as possible.
  
Is this correct?
  
   Yes, but then at that point the thermostat isn't actually
  thermostatting.
   The Bussi comment is merely to show that his thermostat correctly
  reduces
   to Newton's law in the limit, not that it would be useful to run it in
   that
   limit.
  
   On Mon, Oct 13, 2014 at 10:28 AM, Johnny Lu johnny.lu...@gmail.com
   wrote:
  
On page 014101-3, the Bussi paper (
  http://dx.doi.org/10.1063/1.2408420)
mentioned: On the other hand, for coupling constant approaching
infinity,the Hamiltonian dynamics is recovered.
Does that means that for a large enough coupling constant, the
   velocities
are nearly not rescaled, and the dynamics (like rate of motion)
 would
  be
same as that of NVE?
   
A larger coupling constant, means a smaller diffusion coefficient in
  the
axillary dynamics by equation 6.
   
While the effects of the velocity rescaling at each step will
   accumulate, a
larger coupling constant means the thermostat perturb less of the
   dynamics,
and the resulting dynamics is closer to a NVE simulation.
There is no worry that the thermostat would suddenly rescale the
   dynamics
every x step, because in the procedure of the thermostat, the
  velocities
are rescaled every step, regardless of the coupling constant.
   
I guess, if I pick a coupling constant that is just small enough to
  keep
the energy conserved, I would get a NVT simulation that is as close
  as a
NVE simulation as possible.
   
Is this correct?
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Re: [gmx-users] Use NVT to mimic NVE

I mean here seems to say conserved energy is tilde H [
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html
]

On Sat, Oct 18, 2014 at 6:44 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 The conserved energy from g_energy, which I saw someone say is tilde H,
 drop more crazily if I use 1s coupling constant.

 On Mon, Oct 13, 2014 at 5:52 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

 Hi,

 What is your target observable? What got worse?

 Mark

 On Mon, Oct 13, 2014 at 11:17 PM, Johnny Lu johnny.lu...@gmail.com
 wrote:

  The simulation get worse in a new way.
 
  I see that thermostat scales velocity and may not fix numerical error in
  potential energy.
 
  On Mon, Oct 13, 2014 at 2:07 PM, Johnny Lu johnny.lu...@gmail.com
 wrote:
 
   I just want something that will patch up the energy lost due to
 numerical
   error of NVE simulation of the system ran by mixed precision gromacs,
   instead of a thermostat.
  
   I hope the velocity rescaling is sufficiently uncorrelated with the
  motion
   of the protein.
  
   So far, the simulations ran 2.5 ns, and the fluctuation of total
 energy
   seems to be within 1% of total energy, with a 100ps or 1ns coupling
   constant.
  
   May be I should try a 10 ns coupling constant, just to see if the
   simulation would go belly up.
  
   On Mon, Oct 13, 2014 at 11:02 AM, Michael Shirts mrshi...@gmail.com
   wrote:
  
I guess, if I pick a coupling constant that is just small enough to
   keep the
   energy conserved, I would get a NVT simulation that is as close as a
 NVE
   simulation as possible.
  
Is this correct?
  
   Yes, but then at that point the thermostat isn't actually
  thermostatting.
   The Bussi comment is merely to show that his thermostat correctly
  reduces
   to Newton's law in the limit, not that it would be useful to run it
 in
   that
   limit.
  
   On Mon, Oct 13, 2014 at 10:28 AM, Johnny Lu johnny.lu...@gmail.com
   wrote:
  
On page 014101-3, the Bussi paper (
  http://dx.doi.org/10.1063/1.2408420)
mentioned: On the other hand, for coupling constant approaching
infinity,the Hamiltonian dynamics is recovered.
Does that means that for a large enough coupling constant, the
   velocities
are nearly not rescaled, and the dynamics (like rate of motion)
 would
  be
same as that of NVE?
   
A larger coupling constant, means a smaller diffusion coefficient
 in
  the
axillary dynamics by equation 6.
   
While the effects of the velocity rescaling at each step will
   accumulate, a
larger coupling constant means the thermostat perturb less of the
   dynamics,
and the resulting dynamics is closer to a NVE simulation.
There is no worry that the thermostat would suddenly rescale the
   dynamics
every x step, because in the procedure of the thermostat, the
  velocities
are rescaled every step, regardless of the coupling constant.
   
I guess, if I pick a coupling constant that is just small enough to
  keep
the energy conserved, I would get a NVT simulation that is as close
  as a
NVE simulation as possible.
   
Is this correct?
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Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

Does this old maillist post say tilde H is conserved energy? [
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html
]

On Sat, Oct 18, 2014 at 12:46 PM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 On Sat, Oct 18, 2014 at 4:32 PM, Wade wad...@foxmail.com wrote:

  Dear Mark,
  Thank your very much for your reply. However, I still confused
 because
  results showed that the conserved En. was time dependent (with small
  fluctuation); but, the total energy in the ener file has small drift with
  high fluctuations.
 

 Both these things vary doesn't mean anything. Numbers, or it didn't
 happen ;-)


  Further, I rechecked the code  (gmx-4.5.5) ?in these days, and I noticed
 a
  part of code might be useful (enerd-term[F_ECONSERVED] =
  enerd-term[F_ETOT] +
 compute_conserved_from_auxiliary(ir,state,MassQ);).
  It will be actived when the leap-frog integrator is employed.
  To assure the the conserved En. is either H or H-tilde, I changed the
 code
  as this: enerd-term[F_ECONSERVED] = enerd-term[F_ETOT];. Result shown
  that the total energy and conserved En. are same now in the output of
  ener file?.
 

 Great. A = A...


  Dose it means that the conserved En. in ener file is H-tilde?
 

 ...which doesn't say what B is... The question is whether there's an
 intrinsic time dependence on the value returned by
 compute_conserved_from_auxiliary. You can only do that by removing the
 *other* term.


 
  ?
 
  If yes, why does the conserved En. drifted with a constant rate in a 10
 ns
  ?simulation for a pure water box (216 tip4p water)?
 
 
 Because it's characteristic of the drift of your setup or of the
 implementation of what is reported as the conserved quantity. I suggested a
 diagnostic procedure. Did you try it? If not, why not?

 Mark

 With best wishes,
 
 
  Wade
 
 
  (part of the code please see below, I hope I have got the key point).
  ?
 
 
 ~
  /* #  BEGIN PREPARING EDR OUTPUT  ###  */
  /* sum up the foreign energy and dhdl terms */
  sum_dhdl(enerd,state-lambda,ir); /* use the directly determined
  last velocity, not actually the averaged half steps */if
 (bTrotter
   ir-eI==eiVV) {enerd-term[F_EKIN] = last_ekin;
}enerd-term[F_ETOT] = enerd-term[F_EPOT] +
  enerd-term[F_EKIN];if (bVV){
  enerd-term[F_ECONSERVED] = enerd-term[F_ETOT] +
  saved_conserved_quantity;}else {
  enerd-term[F_ECONSERVED] = enerd-term[F_ETOT] +
  compute_conserved_from_auxiliary(ir,state,MassQ);?
 
 
 ~~
 
 
 
 
 
 
 
 
 
 
  That could well be true. I did look carefully at the code earlier this
  year, and decided it was correct and wrote output of sensible things.
  However I don't remember whether the conserved quantity reported is H or
  H-tilde, and don't have time now to go back. But IIRC because one of
 them
  has a time dependence, you can run double-precision GROMACS in a
  conservative NVE setup and observe no drift, then add this thermostat,
 and
  from that run you will know which of H and H-tilde is reported as the
  conserved quantity.
 
  Mark
 
   Is that right? I really need your help.
   Any suggestion is valuable.
  
   Wade?
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Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

Figure 2 of the Bussi paper has a diagram with constant tilde H for NVT
simulation with 2fs time step, and another one with rising tilde H for NVT
simulation with 40fs timestep, and say: for tilde H in the NVT
calculation. We notice that, while in the NVE calculation the system
explodes at some point, the NVT calculation is always stable, thanks to the
thermostat. However, in spite of the stability, the drift in tilde H
indicates that thesampling is inaccurate under these conditions.

So, tilde H should be constant even in a NVT simulation, and I don't
exactly agree with the old mail-list post at [
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html
]

On Sat, Oct 18, 2014 at 6:51 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Does this old maillist post say tilde H is conserved energy? [
 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html
 ]

 On Sat, Oct 18, 2014 at 12:46 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

 On Sat, Oct 18, 2014 at 4:32 PM, Wade wad...@foxmail.com wrote:

  Dear Mark,
  Thank your very much for your reply. However, I still confused
 because
  results showed that the conserved En. was time dependent (with small
  fluctuation); but, the total energy in the ener file has small drift
 with
  high fluctuations.
 

 Both these things vary doesn't mean anything. Numbers, or it didn't
 happen ;-)


  Further, I rechecked the code  (gmx-4.5.5) ?in these days, and I
 noticed a
  part of code might be useful (enerd-term[F_ECONSERVED] =
  enerd-term[F_ETOT] +
 compute_conserved_from_auxiliary(ir,state,MassQ);).
  It will be actived when the leap-frog integrator is employed.
  To assure the the conserved En. is either H or H-tilde, I changed the
 code
  as this: enerd-term[F_ECONSERVED] = enerd-term[F_ETOT];. Result
 shown
  that the total energy and conserved En. are same now in the output
 of
  ener file?.
 

 Great. A = A...


  Dose it means that the conserved En. in ener file is H-tilde?
 

 ...which doesn't say what B is... The question is whether there's an
 intrinsic time dependence on the value returned by
 compute_conserved_from_auxiliary. You can only do that by removing the
 *other* term.


 
  ?
 
  If yes, why does the conserved En. drifted with a constant rate in a 10
 ns
  ?simulation for a pure water box (216 tip4p water)?
 
 
 Because it's characteristic of the drift of your setup or of the
 implementation of what is reported as the conserved quantity. I suggested
 a
 diagnostic procedure. Did you try it? If not, why not?

 Mark

 With best wishes,
 
 
  Wade
 
 
  (part of the code please see below, I hope I have got the key point).
  ?
 
 
 ~
  /* #  BEGIN PREPARING EDR OUTPUT  ###  */
  /* sum up the foreign energy and dhdl terms */
  sum_dhdl(enerd,state-lambda,ir); /* use the directly determined
  last velocity, not actually the averaged half steps */if
 (bTrotter
   ir-eI==eiVV) {enerd-term[F_EKIN] = last_ekin;
}enerd-term[F_ETOT] = enerd-term[F_EPOT] +
  enerd-term[F_EKIN];if (bVV){
  enerd-term[F_ECONSERVED] = enerd-term[F_ETOT] +
  saved_conserved_quantity;}else {
  enerd-term[F_ECONSERVED] = enerd-term[F_ETOT] +
  compute_conserved_from_auxiliary(ir,state,MassQ);?
 
 
 ~~
 
 
 
 
 
 
 
 
 
 
  That could well be true. I did look carefully at the code earlier this
  year, and decided it was correct and wrote output of sensible things.
  However I don't remember whether the conserved quantity reported is H
 or
  H-tilde, and don't have time now to go back. But IIRC because one of
 them
  has a time dependence, you can run double-precision GROMACS in a
  conservative NVE setup and observe no drift, then add this thermostat,
 and
  from that run you will know which of H and H-tilde is reported as the
  conserved quantity.
 
  Mark
 
   Is that right? I really need your help.
   Any suggestion is valuable.
  
   Wade?
   --‍
  --
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  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
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Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

The bussi paper is at [
marge.uochb.cas.cz/~roesel/teach/Clanky/paper5_Bussi_v_rescale.pdf
http://marge.uochb.cas.cz/%7Eroesel/teach/Clanky/paper5_Bussi_v_rescale.pdf
].

I seem to vaguely remember someone wrote if tilde H drop linearly, it means
the energy is conserved. But I'm not sure now.

On Sat, Oct 18, 2014 at 6:58 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Figure 2 of the Bussi paper has a diagram with constant tilde H for NVT
 simulation with 2fs time step, and another one with rising tilde H for NVT
 simulation with 40fs timestep, and say: for tilde H in the NVT
 calculation. We notice that, while in the NVE calculation the system
 explodes at some point, the NVT calculation is always stable, thanks to the
 thermostat. However, in spite of the stability, the drift in tilde H
 indicates that thesampling is inaccurate under these conditions.

 So, tilde H should be constant even in a NVT simulation, and I don't
 exactly agree with the old mail-list post at [
 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html
 ]

 On Sat, Oct 18, 2014 at 6:51 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Does this old maillist post say tilde H is conserved energy? [
 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html
 ]

 On Sat, Oct 18, 2014 at 12:46 PM, Mark Abraham mark.j.abra...@gmail.com
 wrote:

 On Sat, Oct 18, 2014 at 4:32 PM, Wade wad...@foxmail.com wrote:

  Dear Mark,
  Thank your very much for your reply. However, I still confused
 because
  results showed that the conserved En. was time dependent (with small
  fluctuation); but, the total energy in the ener file has small drift
 with
  high fluctuations.
 

 Both these things vary doesn't mean anything. Numbers, or it didn't
 happen ;-)


  Further, I rechecked the code  (gmx-4.5.5) ?in these days, and I
 noticed a
  part of code might be useful (enerd-term[F_ECONSERVED] =
  enerd-term[F_ETOT] +
 compute_conserved_from_auxiliary(ir,state,MassQ);).
  It will be actived when the leap-frog integrator is employed.
  To assure the the conserved En. is either H or H-tilde, I changed the
 code
  as this: enerd-term[F_ECONSERVED] = enerd-term[F_ETOT];. Result
 shown
  that the total energy and conserved En. are same now in the output
 of
  ener file?.
 

 Great. A = A...


  Dose it means that the conserved En. in ener file is H-tilde?
 

 ...which doesn't say what B is... The question is whether there's an
 intrinsic time dependence on the value returned by
 compute_conserved_from_auxiliary. You can only do that by removing the
 *other* term.


 
  ?
 
  If yes, why does the conserved En. drifted with a constant rate in a
 10 ns
  ?simulation for a pure water box (216 tip4p water)?
 
 
 Because it's characteristic of the drift of your setup or of the
 implementation of what is reported as the conserved quantity. I
 suggested a
 diagnostic procedure. Did you try it? If not, why not?

 Mark

 With best wishes,
 
 
  Wade
 
 
  (part of the code please see below, I hope I have got the key point).
  ?
 
 
 ~
  /* #  BEGIN PREPARING EDR OUTPUT  ###  */
  /* sum up the foreign energy and dhdl terms */
  sum_dhdl(enerd,state-lambda,ir); /* use the directly
 determined
  last velocity, not actually the averaged half steps */if
 (bTrotter
   ir-eI==eiVV) {enerd-term[F_EKIN] = last_ekin;
}enerd-term[F_ETOT] = enerd-term[F_EPOT] +
  enerd-term[F_EKIN];if (bVV){
  enerd-term[F_ECONSERVED] = enerd-term[F_ETOT] +
  saved_conserved_quantity;}else {
  enerd-term[F_ECONSERVED] = enerd-term[F_ETOT] +
  compute_conserved_from_auxiliary(ir,state,MassQ);?
 
 
 ~~
 
 
 
 
 
 
 
 
 
 
  That could well be true. I did look carefully at the code earlier this
  year, and decided it was correct and wrote output of sensible things.
  However I don't remember whether the conserved quantity reported is H
 or
  H-tilde, and don't have time now to go back. But IIRC because one of
 them
  has a time dependence, you can run double-precision GROMACS in a
  conservative NVE setup and observe no drift, then add this
 thermostat, and
  from that run you will know which of H and H-tilde is reported as the
  conserved quantity.
 
  Mark
 
   Is that right? I really need your help.
   Any suggestion is valuable.
  
   Wade?
   --‍
  --
  Gromacs Users mailing list
 
  * Please search the archive at
  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
  posting!
 
  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 
  * For (un)subscribe requests visit
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 --
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 * Please

Re: [gmx-users] Conserved energy (Conserved En.) in NVT simulation (Wade)

From Bussi paper: If we use this analysis and go to the limit of an
infinitesimal time step, we find [Equation 15] where the last two terms
come from the integration of Eq. 7 along the trajectory. Note that a
similar integration along the path is present in H_{Nosé}. However, in our
scheme a stochastic integration is also necessary. In the continuum limit
the changes in energy induced by the rescaling compensate exactly the
fluctuations in H. For a finite time step this compensation is only
approximate and the conservation of tilde{H} provides a measure on the
accuracy of the integration. This accuracy has to be interpreted in the
sense of the ability of generating configurations representative of the
ensemble. The physical meaning of Eq. 15 is that the fluxes of energy
between the system and the thermostat are exactly balanced.

Does that mean even with a finite timestep, if the conformations in the
trajectory are all correctly sampled from the intended ensemble without any
biases, tilde H should still be constant?

It is a bit unfortunate that they didn't say how the drift rate of tilde H
related to deviation of distribution of conformations from the intended
ensemble.

On Sat, Oct 18, 2014 at 7:02 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 The bussi paper is at [
 marge.uochb.cas.cz/~roesel/teach/Clanky/paper5_Bussi_v_rescale.pdf
 http://marge.uochb.cas.cz/%7Eroesel/teach/Clanky/paper5_Bussi_v_rescale.pdf
 ].

 I seem to vaguely remember someone wrote if tilde H drop linearly, it
 means the energy is conserved. But I'm not sure now.

 On Sat, Oct 18, 2014 at 6:58 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 Figure 2 of the Bussi paper has a diagram with constant tilde H for NVT
 simulation with 2fs time step, and another one with rising tilde H for NVT
 simulation with 40fs timestep, and say: for tilde H in the NVT
 calculation. We notice that, while in the NVE calculation the system
 explodes at some point, the NVT calculation is always stable, thanks to the
 thermostat. However, in spite of the stability, the drift in tilde H
 indicates that thesampling is inaccurate under these conditions.

 So, tilde H should be constant even in a NVT simulation, and I don't
 exactly agree with the old mail-list post at [
 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html
 ]

 On Sat, Oct 18, 2014 at 6:51 PM, Johnny Lu johnny.lu...@gmail.com
 wrote:

 Does this old maillist post say tilde H is conserved energy? [
 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-August/083330.html
 ]

 On Sat, Oct 18, 2014 at 12:46 PM, Mark Abraham mark.j.abra...@gmail.com
  wrote:

 On Sat, Oct 18, 2014 at 4:32 PM, Wade wad...@foxmail.com wrote:

  Dear Mark,
  Thank your very much for your reply. However, I still confused
 because
  results showed that the conserved En. was time dependent (with small
  fluctuation); but, the total energy in the ener file has small drift
 with
  high fluctuations.
 

 Both these things vary doesn't mean anything. Numbers, or it didn't
 happen ;-)


  Further, I rechecked the code  (gmx-4.5.5) ?in these days, and I
 noticed a
  part of code might be useful (enerd-term[F_ECONSERVED] =
  enerd-term[F_ETOT] +
 compute_conserved_from_auxiliary(ir,state,MassQ);).
  It will be actived when the leap-frog integrator is employed.
  To assure the the conserved En. is either H or H-tilde, I changed the
 code
  as this: enerd-term[F_ECONSERVED] = enerd-term[F_ETOT];. Result
 shown
  that the total energy and conserved En. are same now in the
 output of
  ener file?.
 

 Great. A = A...


  Dose it means that the conserved En. in ener file is H-tilde?
 

 ...which doesn't say what B is... The question is whether there's an
 intrinsic time dependence on the value returned by
 compute_conserved_from_auxiliary. You can only do that by removing the
 *other* term.


 
  ?
 
  If yes, why does the conserved En. drifted with a constant rate in a
 10 ns
  ?simulation for a pure water box (216 tip4p water)?
 
 
 Because it's characteristic of the drift of your setup or of the
 implementation of what is reported as the conserved quantity. I
 suggested a
 diagnostic procedure. Did you try it? If not, why not?

 Mark

 With best wishes,
 
 
  Wade
 
 
  (part of the code please see below, I hope I have got the key point).
  ?
 
 
 ~
  /* #  BEGIN PREPARING EDR OUTPUT  ###  */
  /* sum up the foreign energy and dhdl terms */
  sum_dhdl(enerd,state-lambda,ir); /* use the directly
 determined
  last velocity, not actually the averaged half steps */if
 (bTrotter
   ir-eI==eiVV) {enerd-term[F_EKIN] = last_ekin;
}enerd-term[F_ETOT] = enerd-term[F_EPOT] +
  enerd-term[F_EKIN];if (bVV){
  enerd-term[F_ECONSERVED] = enerd-term[F_ETOT] +
  saved_conserved_quantity;}else

Re: [gmx-users] pressure dependence on volume.

I searched the energy file made by g_energy, and found that NPT frames with
very similar densities have very similar volume.

So, I guess using density is same as using volume in this case.

On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Would manually setting the box size make vacuum bubbles?

 On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 my bad. that formula for density is wrong. But I till don't see why using
 the same averaged density (instead of volume) for the NVT and NPT
 simulations would give a different result.

 On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu johnny.lu...@gmail.com
 wrote:

 Was the density calculated by # particles /  volume ?

 If so, using volume (as I did), and using density would give the same
 wrong pressure, upon transitioning from NPT to NVT.




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Re: [gmx-users] pressure dependence on volume.

The frames with density closest to the average density also have volumes
closest to the averaged volume.

On Sat, Oct 18, 2014 at 8:18 PM, Johnny Lu johnny.lu...@gmail.com wrote:

 I searched the energy file made by g_energy, and found that NPT frames
 with very similar densities have very similar volume.

 So, I guess using density is same as using volume in this case.

 On Sat, Oct 18, 2014 at 9:09 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Would manually setting the box size make vacuum bubbles?

 On Sat, Oct 18, 2014 at 9:08 AM, Johnny Lu johnny.lu...@gmail.com
 wrote:

 my bad. that formula for density is wrong. But I till don't see why
 using the same averaged density (instead of volume) for the NVT and NPT
 simulations would give a different result.

 On Sat, Oct 18, 2014 at 8:52 AM, Johnny Lu johnny.lu...@gmail.com
 wrote:

 Was the density calculated by # particles /  volume ?

 If so, using volume (as I did), and using density would give the same
 wrong pressure, upon transitioning from NPT to NVT.





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Re: [gmx-users] Not achieving any speedup using Open MPI

i heard that mixing mpi and open mp together is bad idea (run more slow),
unless the simulation has large number of atoms, and use many cpu.

May be comparing gromacs running on a single computer, with and without
openmp will show a difference in speed.

On Fri, Oct 17, 2014 at 10:05 AM, Da-Wei Li lida...@gmail.com wrote:

 For a system with only ~20K atoms and you are using normal LAN, I feel your
 result is not unexpected.

 dawei

 On Fri, Oct 17, 2014 at 9:20 AM, Rytis Slatkevičius ryti...@gmail.com
 wrote:

  Hello,
 
  first of all: I am not a scientist, but rather an IT person trying to set
  up Gromacs for fellow scientists. My goal is to set up Gromacs on several
  local computers (connected with 1gbps LAN) and achieve some speedup of
 our
  runs using MPI.
 
  I have installed Gromacs 5.0.2 from Debian repository (package
  gromacs-openmpi). I can run Gromacs over multiple computers, I see
  processes being spooled up, so MPI itself is working. However, I am not
  seeing any speedup at all - in fact, I get a significant slowdown.
 
  When running on a rather old dualcore laptop, I can finish a d.lzm run
 from
  http://www.gromacs.org/About_Gromacs/Benchmarks within 109s or so. If I
  add
  a quadcore machine into the mix, I would expect the computation to be
 much
  faster - but instead I finish everything within 139 seconds! The quadcore
  can finish the job in 45 seconds when running on its own without Open
 MPI.
 
  I can't wrap my head around what I am doing wrong. My command line is:
 
  mpirun --display-map --hostfile hosts mdrun_mpi -v -deffnm d.lzm -dlb yes
 
  Any help would be appreciated.
 
  --
  Pagarbiai / Sincerely
  Rytis Slatkevičius
  +370 670 7
  --
  Gromacs Users mailing list
 
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[gmx-users] pressure dependence on volume.

Hi.

Mainly TIP3P water, 300K. The pressure is near 1 bar.

A less than 1% error in volume would cause how much error in average
pressure?

From three npt simulations of 72 ns with Berendsen barostat, I get the
average volume is 298.5 nm^3.

Continuing from a frame with volume very close to 298.5 nm^3 (~0.01
deviation from this volume), I run NVT simulation that at first gives a
system that doesn't seem to be at equilibrium.

Thanks again.
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Re: [gmx-users] pressure dependence on volume.

At least for real water, a 0.2% error in volume can mean the pressure is
~30 bar when the target pressure is 1 bar.
http://docs.engineeringtoolbox.com/documents/309/water-density-temperature-pressure_2.png

On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu johnny.lu...@gmail.com wrote:

 Hi.

 Mainly TIP3P water, 300K. The pressure is near 1 bar.

 A less than 1% error in volume would cause how much error in average
 pressure?

 From three npt simulations of 72 ns with Berendsen barostat, I get the
 average volume is 298.5 nm^3.

 Continuing from a frame with volume very close to 298.5 nm^3 (~0.01
 deviation from this volume), I run NVT simulation that at first gives a
 system that doesn't seem to be at equilibrium.

 Thanks again.

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* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] pressure dependence on volume.

I am trying to transit from NPT to NVT.
Using the averaged volume of NPT for NVT somehow didn't give me the 1 bar
pressure in NVT.
I don't know why that happened.

Was it the difference between constant pressure and constant volume heat
capacity? But then, the thermostat should take care of that quite quickly.
After that, N, V, and T would be same for NPT simulation and the NVT
simulation... which means the pressure should be the same.

Both the NVT and NPT uses the V-rescale thermostat, and the NPT uses
Berendsen barostat.

Right now I'm selecting NPT frames with different volumes, and see if the
NVT simulations continuing from those frames would give me the 1 bar
pressure.

On Fri, Oct 17, 2014 at 3:53 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 10/17/14 11:49 AM, Johnny Lu wrote:

 At least for real water, a 0.2% error in volume can mean the pressure is
 ~30 bar when the target pressure is 1 bar.
 http://docs.engineeringtoolbox.com/documents/309/water-density-
 temperature-pressure_2.png

 On Fri, Oct 17, 2014 at 10:49 AM, Johnny Lu johnny.lu...@gmail.com
 wrote:

  Hi.

 Mainly TIP3P water, 300K. The pressure is near 1 bar.

 A less than 1% error in volume would cause how much error in average
 pressure?

  From three npt simulations of 72 ns with Berendsen barostat, I get the
 average volume is 298.5 nm^3.

 Continuing from a frame with volume very close to 298.5 nm^3 (~0.01
 deviation from this volume), I run NVT simulation that at first gives a
 system that doesn't seem to be at equilibrium.


 Does that time point correspond to the desired pressure?  The pressure
 tensor is calculated from the virial and the kinetic energy, so those are
 the quantities you should be looking at for instantaneous pressures.

 -Justin

 --
 ==

 Justin A. Lemkul, Ph.D.
 Ruth L. Kirschstein NRSA Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 629
 University of Maryland, Baltimore
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Re: [gmx-users] Understanding comments in pdb2gmx output