[gmx-users] pressure coupling without pbc

[MURAT OZTURK]

Hello,

I have read somewhere in the list that I cannot do pressure coupling
without pbc.

What I essentially need is a box with impermeable walls, that get smaller
as the simulation proceeds.

I do anisotropic pressure coupling with two impermeable walls (in xy axis)
for another simulation, and it works.

I basically need 4 more walls and isotropic pressure coupling, is this
entirely impossible in GROMACS?

Thanks,

Murat
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Re: [gmx-users] Pressure coupling

[Mark Abraham]

Probably. See manual 7.3.15. Semiisotropic with some zero compressibilities
is probably what you want.

Mark


On Sun, Jun 2, 2013 at 9:33 PM, Marcelo Vanean  wrote:

> Hello everyone. I want to know if can be applied pressure coupling only in
> the z direction, allowing the edges x and y simulation box with fixed size.
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[gmx-users] Pressure coupling

[Marcelo Vanean]

Hello everyone. I want to know if can be applied pressure coupling only in
the z direction, allowing the edges x and y simulation box with fixed size.
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[gmx-users] Pressure coupling and Isothermal compressibility for a biphasic system

[bipin singh]

Hello All,

I have some doubts regarding the use of pressure coupling and
isothermal compressibility for a biphasic system (octane+water boxes
built over each other). I have two questions regarding that:

(1) Which pressure coupling (pcoupl) type would be suitable for this
type of system ?

(2) As water and octane have different compressibility, is it possible
to mention the compressibility of water and octane separately?

Please provide your suggestions.



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Thanks and Regards,
Bipin Singh
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Re: [gmx-users] Pressure coupling doubt

[Mark Abraham]

On 29/03/2012 5:38 PM, bipin singh wrote:

Hello,

I have two doubts regarding pressure coupling in Gromacs:

1) When I use pcoupl=no

the mdp.out shows the following

; Pressure coupling
pcoupl   = no
Pcoupltype   = Isotropic
nstpcouple   = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p= 1
compressibility  =
ref-p=

I have not used the pcoupl(=no) then why it is showing Pcoupltype=Isotropic.


... because that was either the value you input, or the default value. 
Neither matters, because you said not to use pressure coupling.





(2) This is a silly question: What will happen if we use following
option in mdp of NVT simulation:

  pcoupl=no
  compressibility= 4.5e-5

does it will affect the NVT criteria ? or It will ignore the
compressibility input?


It will ignore it.

Mark
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[gmx-users] Pressure coupling doubt

[bipin singh]

Hello,

I have two doubts regarding pressure coupling in Gromacs:

1) When I use pcoupl=no

the mdp.out shows the following

; Pressure coupling
pcoupl   = no
Pcoupltype   = Isotropic
nstpcouple   = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p= 1
compressibility  =
ref-p=

I have not used the pcoupl(=no) then why it is showing Pcoupltype=Isotropic.


(2) This is a silly question: What will happen if we use following
option in mdp of NVT simulation:

 pcoupl=no
 compressibility= 4.5e-5

does it will affect the NVT criteria ? or It will ignore the
compressibility input?
-- 
---
Regards,
Bipin Singh
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Re: [gmx-users] Pressure coupling and membrane-type simulations

[Peter C. Lai]

On 2012-02-21 03:41:07PM -0500, Justin A. Lemkul wrote:
> 
> 
> Andrew DeYoung wrote:
> > Hi,
> > 
> > I am interested in doing a membrane-type simulation, in which I have
> > all-atom membrane "walls" parallel to xy plane, at z = -z_0 and z = +z_0
> > (where z_0 is a constant).  I would like to run an NPT simulation at 1 atm.
> > 
> > 
> > What type of pressure coupling should I use?  Isotropic pressure coupling
> > requires only one input value (either compressibility or reference pressure
> > ref_p), whereas I think that semiisotropic, anisotropic, and surface-tension
> > pressure coupling require specification of both the compressibility and
> > ref_p (tensors).
> > 
> > Clearly, I should not use isotropic pressure coupling, because clearly my
> > system is not isotropic.  However, what if I do not know and cannot find in
> > the literature the compressibility of the liquid system that I am placing
> > between the membrane "walls"?  If I do not know the compressibility very
> > accurately or at all, then it seems that I cannot use semiisotropic,
> > anisotropic, or surface-tension pressure coupling.  
> > 
> > If you have time, I would like to ask an additional question.  Now suppose I
> > know the compressibility of the liquid between the membrane.  Now what
> > pressure coupling type should I use; should I use semiisotropic,
> > anisotropic, or surface-tension pressure coupling?  Both semiisotropic and
> > surface-tension look reasonable.  In the manual
> > (http://manual.gromacs.org/current/online/mdp_opt.html#pc), semiisotropic
> > pressure coupling is useful for systems that are isotropic in x and y, but
> > different in z (which is the situation I have here).  Surface-tension also
> > looks like it describes a similar situation, but it requires the
> > specification of the surface tension of the liquid, which I do not know.  
> > 
> > I am sorry that my questions are quite vague.  If you have time, do you have
> > any general thoughts?  Or can you please recommend any papers that would
> > help me understand and choose between the pressure coupling types?
> > 
> 
> I doubt I can really answer much of this, but isn't the most pressing 
> consideration the walls themselves?  If they're reasonably rigid, the 
> compressibility of the fluid layer is largely irrelevant, isn't it?  Then 
> again, 
> if the walls are not rigid, then they become a liability under pressure 
> coupling 
> as they may buckle.  Seems to me this should be the principal concern.
> 
> -Justin
> 

Another consideration is that the documentation states when using built-in
implicit walls at z=0 and z=zbox to use anistropic pressure coupling with the 
x/y compressibility set to 0 "otherwise the surface area will change".
Maybe start with that and go from there?

-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] Pressure coupling and membrane-type simulations

[Justin A. Lemkul]

Andrew DeYoung wrote:

Hi,

I am interested in doing a membrane-type simulation, in which I have
all-atom membrane "walls" parallel to xy plane, at z = -z_0 and z = +z_0
(where z_0 is a constant).  I would like to run an NPT simulation at 1 atm.


What type of pressure coupling should I use?  Isotropic pressure coupling
requires only one input value (either compressibility or reference pressure
ref_p), whereas I think that semiisotropic, anisotropic, and surface-tension
pressure coupling require specification of both the compressibility and
ref_p (tensors).

Clearly, I should not use isotropic pressure coupling, because clearly my
system is not isotropic.  However, what if I do not know and cannot find in
the literature the compressibility of the liquid system that I am placing
between the membrane "walls"?  If I do not know the compressibility very
accurately or at all, then it seems that I cannot use semiisotropic,
anisotropic, or surface-tension pressure coupling.  


If you have time, I would like to ask an additional question.  Now suppose I
know the compressibility of the liquid between the membrane.  Now what
pressure coupling type should I use; should I use semiisotropic,
anisotropic, or surface-tension pressure coupling?  Both semiisotropic and
surface-tension look reasonable.  In the manual
(http://manual.gromacs.org/current/online/mdp_opt.html#pc), semiisotropic
pressure coupling is useful for systems that are isotropic in x and y, but
different in z (which is the situation I have here).  Surface-tension also
looks like it describes a similar situation, but it requires the
specification of the surface tension of the liquid, which I do not know.  


I am sorry that my questions are quite vague.  If you have time, do you have
any general thoughts?  Or can you please recommend any papers that would
help me understand and choose between the pressure coupling types?



I doubt I can really answer much of this, but isn't the most pressing 
consideration the walls themselves?  If they're reasonably rigid, the 
compressibility of the fluid layer is largely irrelevant, isn't it?  Then again, 
if the walls are not rigid, then they become a liability under pressure coupling 
as they may buckle.  Seems to me this should be the principal concern.


-Justin

--


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


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[gmx-users] Pressure coupling and membrane-type simulations

[Andrew DeYoung]

Hi,

I am interested in doing a membrane-type simulation, in which I have
all-atom membrane "walls" parallel to xy plane, at z = -z_0 and z = +z_0
(where z_0 is a constant).  I would like to run an NPT simulation at 1 atm.


What type of pressure coupling should I use?  Isotropic pressure coupling
requires only one input value (either compressibility or reference pressure
ref_p), whereas I think that semiisotropic, anisotropic, and surface-tension
pressure coupling require specification of both the compressibility and
ref_p (tensors).

Clearly, I should not use isotropic pressure coupling, because clearly my
system is not isotropic.  However, what if I do not know and cannot find in
the literature the compressibility of the liquid system that I am placing
between the membrane "walls"?  If I do not know the compressibility very
accurately or at all, then it seems that I cannot use semiisotropic,
anisotropic, or surface-tension pressure coupling.  

If you have time, I would like to ask an additional question.  Now suppose I
know the compressibility of the liquid between the membrane.  Now what
pressure coupling type should I use; should I use semiisotropic,
anisotropic, or surface-tension pressure coupling?  Both semiisotropic and
surface-tension look reasonable.  In the manual
(http://manual.gromacs.org/current/online/mdp_opt.html#pc), semiisotropic
pressure coupling is useful for systems that are isotropic in x and y, but
different in z (which is the situation I have here).  Surface-tension also
looks like it describes a similar situation, but it requires the
specification of the surface tension of the liquid, which I do not know.  

I am sorry that my questions are quite vague.  If you have time, do you have
any general thoughts?  Or can you please recommend any papers that would
help me understand and choose between the pressure coupling types?

Thank you very much for your time!

Andrew DeYoung
Carnegie Mellon University

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Re: [gmx-users] pressure coupling

[mohammad agha]

Thank you very much.

Yes, I checked NPT run and I saw the size and volume of box had been increased. 
So I increased size of box to 12.
My system consists of: 151 lipids+151 ions+16200 water and antifreezawater 
molecules

May I know your idea about this, please?

Best Regards
Sara




 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Saturday, December 17, 2011 10:22 AM
Subject: Re: [gmx-users] pressure coupling
 

On 17/12/2011 5:40 PM, mohammad agha wrote: 
Thank you very much.
>Excuse me, I did another thing, may I know is it right, Please?
>
>I did editconf before equilibration (pr.mdp) and increased my box vector from 
>11.2 to 12:
>editconf -f em3.gro -o out.gro -c -d 1.0 -bt cubic -box 12 12 12 -center 6 6 6
>and I minimized my system (out.gro) and then did equilibration
  (pr.mdp). My system gave me warning for box sizes 11.4, 11.6
  and 11.8, consequently I select 12 and pr.mdp is run without
  warning.
>Is it right?
We don't know. You've been changing your box volume but haven't said
anything about the contents. You need to look at how the box changes
over the NPT run, like I said last time. If your generated solvent
density was wrong such that you needed to add about 20% more volume,
then expect to need to equilibrate for quite a while.

Mark



>
>Best Regards
>Sara
>
>
>
>
>
>
>
>
>
>
>
>
>
> From: Mark Abraham 
>To: Discussion list for GROMACS users  
>Sent: Saturday, December 17, 2011 9:31 AM
>Subject: Re: [gmx-users] pressure coupling
> 
>
>On 17/12/2011 4:58 PM, mohammad agha wrote: 
>Dear GROMACS Users
>>
>>
>>I have a warning after doing pr.mdp as followed, I read errors in GROMACS 
>>site and checked mailing list, but my warning is only step1 and after that 
>>equilibration is run normally till end.  
>>
>>
>>
>>
>>
>>500 steps, 15.0 ps.
>>step 0
>>Step 1  Warning: pressure scaling more than 1%,
  mu: 1.04679 1.04679 1.04679
>>
>>Step 1  Warning: pressure scaling more than 1%,
  mu: 1.04679 1.04679 1.04679
>>
>>
>>
>>my pr.mdp about pressure coupling is:
>>
>>
>>pcoupl        = berendsen
>>pcoupltype    = isotropic    ; uniform scaling of
  box vectors
>>tau_p        = 4 ; time constant, in ps
>>ref_p        = 1.0     ; reference pressure, in
  bar
>>compressibility = 4.5e-5  ;isothermal
  compressibility of water, bar^-1
>>
>>
>>
>>
>>I work in Martini Coarse-Grained and my time step is 0.03 ps. I increased 
>>tau_p but my warning increased to step 1 and step 11, I think this warning 
>>since it is only in initial steps isn't important, is my idea right?
>>
>That kind of thing is normal in the very early stages of
NPT equilibration when the volume is not quite right.
mdrun is just warning you that there are some changes
going on. Use g_energy to see those. If it bothers you,
then you will want to adjust your density (i.e. number
of water molecules) before starting.
>
>Mark
>
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>
>
>
>

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Re: [gmx-users] pressure coupling

[Mark Abraham]

On 17/12/2011 5:40 PM, mohammad agha wrote:

Thank you very much.
Excuse me, I did another thing, may I know is it right, Please?
I did editconf before equilibration (pr.mdp) and increased my box 
vector from 11.2 to 12:
editconf -f em3.gro -o out.gro -c -d 1.0 -bt cubic -box 12 12 12 
-center 6 6 6
and I minimized my system (out.gro) and then did equilibration 
(pr.mdp). My system gave me warning for box sizes 11.4, 11.6 and 11.8, 
consequently I select 12 and pr.mdp is run without warning.

Is it right?


We don't know. You've been changing your box volume but haven't said 
anything about the contents. You need to look at how the box changes 
over the NPT run, like I said last time. If your generated solvent 
density was wrong such that you needed to add about 20% more volume, 
then expect to need to equilibrate for quite a while.


Mark



Best Regards
Sara






*From:* Mark Abraham 
*To:* Discussion list for GROMACS users 
*Sent:* Saturday, December 17, 2011 9:31 AM
*Subject:* Re: [gmx-users] pressure coupling

On 17/12/2011 4:58 PM, mohammad agha wrote:

Dear GROMACS Users

I have a warning after doing pr.mdp as followed, I read errors in 
GROMACS site and checked mailing list, but my warning is only step1 
and after that equilibration is run normally till end.



500 steps, 15.0 ps.
step 0
Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 
1.04679


Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 
1.04679


my pr.mdp about pressure coupling is:

pcoupl= berendsen
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 4 ; time constant, in ps
ref_p= 1.0 ; reference pressure, in bar
compressibility = 4.5e-5  ;isothermal compressibility of water, bar^-1


I work in Martini Coarse-Grained and my time step is 0.03 ps. I 
increased tau_p but my warning increased to step 1 and step 11, I 
think this warning since it is only in initial steps isn't important, 
is my idea right?




That kind of thing is normal in the very early stages of NPT 
equilibration when the volume is not quite right. mdrun is just 
warning you that there are some changes going on. Use g_energy to see 
those. If it bothers you, then you will want to adjust your density 
(i.e. number of water molecules) before starting.


Mark

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Re: [gmx-users] pressure coupling

[mohammad agha]

Thank you very much.
Excuse me, I did another thing, may I know is it right, Please?

I did editconf before equilibration (pr.mdp) and increased my box vector from 
11.2 to 12:
editconf -f em3.gro -o out.gro -c -d 1.0 -bt cubic -box 12 12 12 -center 6 6 6
and I minimized my system (out.gro) and then did equilibration (pr.mdp). My 
system gave me warning for box sizes 11.4, 11.6 and 11.8, consequently I select 
12 and pr.mdp is run without warning.
Is it right?

Best Regards
Sara








 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Saturday, December 17, 2011 9:31 AM
Subject: Re: [gmx-users] pressure coupling
 

On 17/12/2011 4:58 PM, mohammad agha wrote: 
Dear GROMACS Users
>
>
>I have a warning after doing pr.mdp as followed, I read errors in GROMACS site 
>and checked mailing list, but my warning is only step1 and after that 
>equilibration is run normally till end.  
>
>
>
>
>
>500 steps, 15.0 ps.
>step 0
>Step 1  Warning: pressure scaling more than 1%, mu: 1.04679
  1.04679 1.04679
>
>Step 1  Warning: pressure scaling more than 1%, mu: 1.04679
  1.04679 1.04679
>
>
>
>my pr.mdp about pressure coupling is:
>
>
>pcoupl        = berendsen
>pcoupltype    = isotropic    ; uniform scaling of box vectors
>tau_p        = 4 ; time constant, in ps
>ref_p        = 1.0     ; reference pressure, in bar
>compressibility = 4.5e-5  ;isothermal compressibility of
  water, bar^-1
>
>
>
>
>I work in Martini Coarse-Grained and my time step is 0.03 ps. I increased 
>tau_p but my warning increased to step 1 and step 11, I think this warning 
>since it is only in initial steps isn't important, is my idea right?
>
That kind of thing is normal in the very early stages of NPT
equilibration when the volume is not quite right. mdrun is just
warning you that there are some changes going on. Use g_energy to
see those. If it bothers you, then you will want to adjust your
density (i.e. number of water molecules) before starting.

Mark

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Re: [gmx-users] pressure coupling

[Mark Abraham]

On 17/12/2011 4:58 PM, mohammad agha wrote:

Dear GROMACS Users

I have a warning after doing pr.mdp as followed, I read errors in 
GROMACS site and checked mailing list, but my warning is only step1 
and after that equilibration is run normally till end.



500 steps, 15.0 ps.
step 0
Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 
1.04679


Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 
1.04679


my pr.mdp about pressure coupling is:

pcoupl= berendsen
pcoupltype= isotropic; uniform scaling of box vectors
tau_p= 4 ; time constant, in ps
ref_p= 1.0 ; reference pressure, in bar
compressibility = 4.5e-5  ;isothermal compressibility of water, bar^-1


I work in Martini Coarse-Grained and my time step is 0.03 ps. I 
increased tau_p but my warning increased to step 1 and step 11, I 
think this warning since it is only in initial steps isn't important, 
is my idea right?




That kind of thing is normal in the very early stages of NPT 
equilibration when the volume is not quite right. mdrun is just warning 
you that there are some changes going on. Use g_energy to see those. If 
it bothers you, then you will want to adjust your density (i.e. number 
of water molecules) before starting.


Mark
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[gmx-users] pressure coupling

[mohammad agha]

Dear GROMACS Users

I have a warning after doing pr.mdp as followed, I read errors in GROMACS site 
and checked mailing list, but my warning is only step1 and after that 
equilibration is run normally till end.  



500 steps, 15.0 ps.
step 0
Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 1.04679

Step 1  Warning: pressure scaling more than 1%, mu: 1.04679 1.04679 1.04679


my pr.mdp about pressure coupling is:

pcoupl        = berendsen
pcoupltype    = isotropic    ; uniform scaling of box vectors
tau_p        = 4 ; time constant, in ps
ref_p        = 1.0     ; reference pressure, in bar
compressibility = 4.5e-5  ;isothermal compressibility of water, bar^-1


I work in Martini Coarse-Grained and my time step is 0.03 ps. I increased tau_p 
but my warning increased to step 1 and step 11, I think this warning since it 
is only in initial steps isn't important, is my idea right?

Best Regards
Sara
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[gmx-users] Pressure coupling problem

[Fabian Casteblanco]

Thank you Justin and Peter for your responses.  I tried extending the time
on the npt equilibration.  It helped but not much.  My final pressure after
the MD run was about 1.15 bar compared to ref_p which was set to 1 bar.
Peter, I will try to analyze the potential error using RMSD and Drift.

Thanks.

On Mon, Apr 11, 2011 at 4:55 PM, Fabian Casteblanco <
fabian.castebla...@gmail.com> wrote:

> Hi,
>
> I'm still in my first few months of using Gromacs.  I started by creating
> an *.itp and *.top file for *Ethanol* using CHARMM force field
> parameters.  I made the molecule and it looked fine, put 1000 molecules in a
> box, energy minimized it to a negative potential energy, viewed it on VMD,
> again looks fine.  When I started running the NVT script, I set it equal to
> a ref_T of 298 K.  It equilibrated at the temperature.  Then I tried using
> an NPT script to equilibrate it to a ref_p of 1 bar.  This is where I get
> the problem.  The output shows the density is close to the actual
> experimental value of 0.789 g/cm^3.  But for some reason, my pressure never
> gets an average of 1 bar.  It keeps oscillating, which I understand is
> normal, but the average is always 1.3 or 1.4 bar (it seems the longer I let
> it run, the larger the average pressure; 1.38 for 50,000 steps,dt=0.002 and
> 1.45 for 75,000 steps,dt=0.002).  I don't understand why the ref_p of 1 bar
> is not working when I run this NPT.mdp script file.  My simple goal is to
> have 1000 molecules of ethanol using CHARMM ff parameters at 25degC and 1
> bar and somewhere near the experimental density.
>
> I would really appreciate anybody's help!  I'm new to this but I'm eager to
> keep getting better.
>
> Thanks.
>
> *NVT SCRIPT  (this works fine and takes me to 298 K)*
> File Edit Options Buffers Tools Help
> title   =CHARMM ETHANOL  NVT equilibration
> ;define =-DPOSRES   ;position restrain the protein
> ;Run parameters
> integrator  =md ;leap-frog algorithm
> nsteps  =5  ;2 * 5 = 100 ps
> dt  =0.002  ;2fs
> ;Output control
> nstxout =100;save coordinates every 0.2 ps
> nstvout =100;save velocities every 0.2 ps
> nstenergy   =100;save energies every 0.2 ps
> nstlog  =100;update log file every 0.2 ps
> ;Bond parameters
> continuation=no ;first dynamics run
> constraint_algorithm=lincs  ;holonomic constraints
> constraints =all-bonds  ;all bonds (even heavy atom-H
> bonds)constraind
> lincs_iter  =1  ;accuracy of LINCS
> lincs_order =4  ;also related to accuracy
> ;Neighborhood searching
> ns_type =grid   ;search neighboring grid cells
> nstlist =5  ;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
> electrostat\
> ;ics
> pme_order   =4  ;cubic interpolation
> fourierspacing  =0.16   ;grid spacing for FFT
> ;Temperature coupling is on
> tcoupl  =V-rescale  ;modified Berendsen thermostat
> tc_grps =SYSTEM   ;two coupling groups - more accurate
> tau_t   =0.1;0.1  ;time constant, in ps
> ref_t   =298;25   ;reference temperature, one for
> each \
> ;group, in K
> ;Pressure coupling is off
> pcoupl  =no ;no pressure coupling in NVT
> ;Periodic boundary conditions
> pbc =xyz; 3-D PBC
> ;Dispersion correction
> DispCorr=EnerPres   ;account for cut-off vdW scheme
> ;Velocity generation
> gen_vel =yes;assign velocities from Maxwell
> distribution
> gen_temp=25 ;temperature for Maxwell distribution
> gen_seed=-1 ;generate a random seed
> ;END
>
> *NPT SCRIPT*
> File Edit Options Buffers Tools Help
> title   =Ethanol npt equilibration
> ;define =-DPOSRES   ;position restrain the protein
> ;Run parameters
> integrator  =md ;leap-frog algorithm
> nsteps  =5  ;2 * 5 = 100 ps
> dt  =0.002  ;2fs
> ;Output control
> nstxout =100;save coordinates every 0.2 ps
> nstvout =100;save velocities every 0.2 ps
> nstenergy   =100;save energies every 0.2 ps
> nstlog  =100;update log file every 0.2 ps
> ;Bond parameters
> continuation=yes;Restarting after NVT
> constraint_algorithm=lincs  ;holonomic constraints
> constraints =all-bonds  ;all bonds (even heavy atom-H
> bonds)constraind
> lincs_iter  =1  ;accuracy of LINCS
> lincs_order =4  ;als

Re: [gmx-users] Pressure coupling problem

[Peter C. Lai]

So your density graph looks stabilized? I also tend to look for changes in 
box x, y, z as well since the scale of their changes is easier to track.
Sometimes it helps to look at the error vs. rmsd vs total drift statistics as 
well for such parameters that are easier to track - again if density shows
stability for 0-150ps then check your boxes, it might be shrinking or 
growing due to the pressure perturbation, and you can use the average rate 
of change of those to find your equilibration point instead of trying to 
do something with a -300 to 300 bar pressure smear or whatnot.

On 2011-04-11 04:17:59PM -0500, Justin A. Lemkul wrote:
> 
> 
> Fabian Casteblanco wrote:
> > Hi,
> >  
> > I'm still in my first few months of using Gromacs.  I started by 
> > creating an *.itp and *.top file for /Ethanol/ using CHARMM force field 
> > parameters.  I made the molecule and it looked fine, put 1000 molecules 
> > in a box, energy minimized it to a negative potential energy, viewed it 
> > on VMD, again looks fine.  When I started running the NVT script, I set 
> > it equal to a ref_T of 298 K.  It equilibrated at the temperature.  Then 
> > I tried using an NPT script to equilibrate it to a ref_p of 1 bar.  This 
> > is where I get the problem.  The output shows the density is close to 
> > the actual experimental value of 0.789 g/cm^3.  But for some reason, my 
> > pressure never gets an average of 1 bar.  It keeps oscillating, which I 
> > understand is normal, but the average is always 1.3 or 1.4 bar (it seems 
> > the longer I let it run, the larger the average pressure; 1.38 for 
> > 50,000 steps,dt=0.002 and 1.45 for 75,000 steps,dt=0.002).  I don't 
> > understand why the ref_p of 1 bar is not working when I run this NPT.mdp 
> > script file.  My simple goal is to have 1000 molecules of ethanol using 
> > CHARMM ff parameters at 25degC and 1 bar and somewhere near the 
> > experimental density.
> >  
> 
> Your equilibration period (100-150 ps) is rather short, and the systematic 
> increase suggests that you're simply not equilibrated yet.
> 
> Also bear in mind that a quantity that is prone to pressure fluctuations in 
> the 
> hundreds to thousands can only be so accurate.  There was a very thorough 
> discussion about the statistical significance of pressure values that are not 
> equal to ref_p just some time ago.  You may want to look through the archives 
> to 
> find this discussion.
> 
> -Justin
> 
> > I would really appreciate anybody's help!  I'm new to this but I'm eager 
> > to keep getting better.
> >  
> > Thanks.
> >  
> > _NVT SCRIPT  (this works fine and takes me to 298 K)_
> > File Edit Options Buffers Tools Help
> > title   =CHARMM ETHANOL  NVT equilibration
> > ;define =-DPOSRES   ;position restrain the protein
> > ;Run parameters
> > integrator  =md ;leap-frog algorithm
> > nsteps  =5  ;2 * 5 = 100 ps
> > dt  =0.002  ;2fs
> > ;Output control
> > nstxout =100;save coordinates every 0.2 ps
> > nstvout =100;save velocities every 0.2 ps
> > nstenergy   =100;save energies every 0.2 ps
> > nstlog  =100;update log file every 0.2 ps
> > ;Bond parameters
> > continuation=no ;first dynamics run
> > constraint_algorithm=lincs  ;holonomic constraints
> > constraints =all-bonds  ;all bonds (even heavy atom-H 
> > bonds)constraind
> > lincs_iter  =1  ;accuracy of LINCS
> > lincs_order =4  ;also related to accuracy
> > ;Neighborhood searching
> > ns_type =grid   ;search neighboring grid cells
> > nstlist =5  ;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 
> > electrostat\
> > ;ics
> > pme_order   =4  ;cubic interpolation
> > fourierspacing  =0.16   ;grid spacing for FFT
> > ;Temperature coupling is on
> > tcoupl  =V-rescale  ;modified Berendsen thermostat
> > tc_grps =SYSTEM   ;two coupling groups - more accurate
> > tau_t   =0.1;0.1  ;time constant, in ps
> > ref_t   =298;25   ;reference temperature, one 
> > for each \
> > ;group, in K
> > ;Pressure coupling is off
> > pcoupl  =no ;no pressure coupling in NVT
> > ;Periodic boundary conditions
> > pbc =xyz; 3-D PBC
> > ;Dispersion correction
> > DispCorr=EnerPres   ;account for cut-off vdW scheme
> > ;Velocity generation
> > gen_vel =yes;assign velocities from Maxwell distribution
> > gen_temp=25 ;temperature for Maxwell distribution
> > 

[gmx-users] Pressure coupling problem

[Fabian Casteblanco]

Hi,

I'm still in my first few months of using Gromacs.  I started by
creating an *.itp and *.top file for Ethanol using CHARMM force field
parameters.  I made the molecule and it looked fine, put 1000
molecules in a box, energy minimized it to a negative potential
energy, viewed it on VMD, again looks fine.  When I started running
the NVT script, I set it equal to a ref_T of 298 K.  It equilibrated
at the temperature.  Then I tried using an NPT script to equilibrate
it to a ref_p of 1 bar.  This is where I get the problem.  The output
shows the density is close to the actual experimental value of 0.789
g/cm^3.  But for some reason, my pressure never gets an average of 1
bar.  It keeps oscillating, which I understand is normal, but the
average is always 1.3 or 1.4 bar (it seems the longer I let it run,
the larger the average pressure; 1.38 for 50,000 steps,dt=0.002 and
1.45 for 75,000 steps,dt=0.002).  I don't understand why the ref_p of
1 bar is not working when I run this NPT.mdp script file.  My simple
goal is to have 1000 molecules of ethanol using CHARMM ff parameters
at 25degC and 1 bar and somewhere near the experimental density.

I would really appreciate anybody's help!  I'm new to this but I'm
eager to keep getting better.

Thanks.

NVT SCRIPT  (this works fine and takes me to 298 K)
File Edit Options Buffers Tools Help
title   =CHARMM ETHANOL  NVT equilibration
;define =-DPOSRES   ;position restrain the protein
;Run parameters
integrator  =md ;leap-frog algorithm
nsteps  =5  ;2 * 5 = 100 ps
dt  =0.002  ;2fs
;Output control
nstxout =100    ;save coordinates every 0.2 ps
nstvout =100    ;save velocities every 0.2 ps
nstenergy   =100    ;save energies every 0.2 ps
nstlog  =100    ;update log file every 0.2 ps
;Bond parameters
continuation    =no ;first dynamics run
constraint_algorithm=lincs  ;holonomic constraints
constraints =all-bonds  ;all bonds (even heavy atom-H bonds)constraind
lincs_iter  =1  ;accuracy of LINCS
lincs_order =4  ;also related to accuracy
;Neighborhood searching
ns_type =grid   ;search neighboring grid cells
nstlist =5  ;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 electrostat\
;ics
pme_order   =4  ;cubic interpolation
fourierspacing  =0.16   ;grid spacing for FFT
;Temperature coupling is on
tcoupl  =V-rescale  ;modified Berendsen thermostat
tc_grps =SYSTEM   ;two coupling groups - more accurate
tau_t   =0.1    ;0.1  ;time constant, in ps
ref_t   =298    ;25   ;reference temperature, one for each \
;group, in K
;Pressure coupling is off
pcoupl  =no ;no pressure coupling in NVT
;Periodic boundary conditions
pbc =xyz    ; 3-D PBC
;Dispersion correction
DispCorr    =EnerPres   ;account for cut-off vdW scheme
;Velocity generation
gen_vel =yes    ;assign velocities from Maxwell distribution
gen_temp    =25 ;temperature for Maxwell distribution
gen_seed    =-1 ;generate a random seed
;END

NPT SCRIPT
File Edit Options Buffers Tools Help
title   =Ethanol npt equilibration
;define =-DPOSRES   ;position restrain the protein
;Run parameters
integrator  =md ;leap-frog algorithm
nsteps  =5  ;2 * 5 = 100 ps
dt  =0.002  ;2fs
;Output control
nstxout =100    ;save coordinates every 0.2 ps
nstvout =100    ;save velocities every 0.2 ps
nstenergy   =100    ;save energies every 0.2 ps
nstlog  =100    ;update log file every 0.2 ps
;Bond parameters
continuation    =yes    ;Restarting after NVT
constraint_algorithm=lincs  ;holonomic constraints
constraints =all-bonds  ;all bonds (even heavy atom-H bonds)constraind
lincs_iter  =1  ;accuracy of LINCS
lincs_order =4  ;also related to accuracy
;Neighborhood searching
ns_type =grid   ;search neighboring grid cells
nstlist =5  ;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 electrostat\
;ics
pme_order   =4  ;cubic interpolation
fourierspacing  =0.16   ;grid spacing for FFT
;Temperatur

Re: [gmx-users] Pressure coupling problem

[Justin A. Lemkul]

Fabian Casteblanco wrote:

Hi,
 
I'm still in my first few months of using Gromacs.  I started by 
creating an *.itp and *.top file for /Ethanol/ using CHARMM force field 
parameters.  I made the molecule and it looked fine, put 1000 molecules 
in a box, energy minimized it to a negative potential energy, viewed it 
on VMD, again looks fine.  When I started running the NVT script, I set 
it equal to a ref_T of 298 K.  It equilibrated at the temperature.  Then 
I tried using an NPT script to equilibrate it to a ref_p of 1 bar.  This 
is where I get the problem.  The output shows the density is close to 
the actual experimental value of 0.789 g/cm^3.  But for some reason, my 
pressure never gets an average of 1 bar.  It keeps oscillating, which I 
understand is normal, but the average is always 1.3 or 1.4 bar (it seems 
the longer I let it run, the larger the average pressure; 1.38 for 
50,000 steps,dt=0.002 and 1.45 for 75,000 steps,dt=0.002).  I don't 
understand why the ref_p of 1 bar is not working when I run this NPT.mdp 
script file.  My simple goal is to have 1000 molecules of ethanol using 
CHARMM ff parameters at 25degC and 1 bar and somewhere near the 
experimental density.
 


Your equilibration period (100-150 ps) is rather short, and the systematic 
increase suggests that you're simply not equilibrated yet.


Also bear in mind that a quantity that is prone to pressure fluctuations in the 
hundreds to thousands can only be so accurate.  There was a very thorough 
discussion about the statistical significance of pressure values that are not 
equal to ref_p just some time ago.  You may want to look through the archives to 
find this discussion.


-Justin

I would really appreciate anybody's help!  I'm new to this but I'm eager 
to keep getting better.
 
Thanks.
 
_NVT SCRIPT  (this works fine and takes me to 298 K)_

File Edit Options Buffers Tools Help
title   =CHARMM ETHANOL  NVT equilibration
;define =-DPOSRES   ;position restrain the protein
;Run parameters
integrator  =md ;leap-frog algorithm
nsteps  =5  ;2 * 5 = 100 ps
dt  =0.002  ;2fs
;Output control
nstxout =100;save coordinates every 0.2 ps
nstvout =100;save velocities every 0.2 ps
nstenergy   =100;save energies every 0.2 ps
nstlog  =100;update log file every 0.2 ps
;Bond parameters
continuation=no ;first dynamics run
constraint_algorithm=lincs  ;holonomic constraints
constraints =all-bonds  ;all bonds (even heavy atom-H 
bonds)constraind

lincs_iter  =1  ;accuracy of LINCS
lincs_order =4  ;also related to accuracy
;Neighborhood searching
ns_type =grid   ;search neighboring grid cells
nstlist =5  ;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 
electrostat\

;ics
pme_order   =4  ;cubic interpolation
fourierspacing  =0.16   ;grid spacing for FFT
;Temperature coupling is on
tcoupl  =V-rescale  ;modified Berendsen thermostat
tc_grps =SYSTEM   ;two coupling groups - more accurate
tau_t   =0.1;0.1  ;time constant, in ps
ref_t   =298;25   ;reference temperature, one 
for each \

;group, in K
;Pressure coupling is off
pcoupl  =no ;no pressure coupling in NVT
;Periodic boundary conditions
pbc =xyz; 3-D PBC
;Dispersion correction
DispCorr=EnerPres   ;account for cut-off vdW scheme
;Velocity generation
gen_vel =yes;assign velocities from Maxwell distribution
gen_temp=25 ;temperature for Maxwell distribution
gen_seed=-1 ;generate a random seed
;END
 
_NPT SCRIPT_

File Edit Options Buffers Tools Help
title   =Ethanol npt equilibration
;define =-DPOSRES   ;position restrain the protein
;Run parameters
integrator  =md ;leap-frog algorithm
nsteps  =5  ;2 * 5 = 100 ps
dt  =0.002  ;2fs
;Output control
nstxout =100;save coordinates every 0.2 ps
nstvout =100;save velocities every 0.2 ps
nstenergy   =100;save energies every 0.2 ps
nstlog  =100;update log file every 0.2 ps
;Bond parameters
continuation=yes;Restarting after NVT
constraint_algorithm=lincs  ;holonomic constraints
constraints =all-bonds  ;all bonds (even heavy atom-H 
bonds)constraind

lincs_iter  =1  ;accuracy of LINCS
lincs_order =4  ;also related to accuracy
;Neighborh

[gmx-users] Pressure coupling problem

[Fabian Casteblanco]

Hi,

I'm still in my first few months of using Gromacs.  I started by creating an
*.itp and *.top file for *Ethanol* using CHARMM force field parameters.  I
made the molecule and it looked fine, put 1000 molecules in a box, energy
minimized it to a negative potential energy, viewed it on VMD, again looks
fine.  When I started running the NVT script, I set it equal to a ref_T of
298 K.  It equilibrated at the temperature.  Then I tried using an NPT
script to equilibrate it to a ref_p of 1 bar.  This is where I get the
problem.  The output shows the density is close to the actual experimental
value of 0.789 g/cm^3.  But for some reason, my pressure never gets an
average of 1 bar.  It keeps oscillating, which I understand is normal, but
the average is always 1.3 or 1.4 bar (it seems the longer I let it run, the
larger the average pressure; 1.38 for 50,000 steps,dt=0.002 and 1.45 for
75,000 steps,dt=0.002).  I don't understand why the ref_p of 1 bar is not
working when I run this NPT.mdp script file.  My simple goal is to have 1000
molecules of ethanol using CHARMM ff parameters at 25degC and 1 bar and
somewhere near the experimental density.

I would really appreciate anybody's help!  I'm new to this but I'm eager to
keep getting better.

Thanks.

*NVT SCRIPT  (this works fine and takes me to 298 K)*
File Edit Options Buffers Tools Help
title   =CHARMM ETHANOL  NVT equilibration
;define =-DPOSRES   ;position restrain the protein
;Run parameters
integrator  =md ;leap-frog algorithm
nsteps  =5  ;2 * 5 = 100 ps
dt  =0.002  ;2fs
;Output control
nstxout =100;save coordinates every 0.2 ps
nstvout =100;save velocities every 0.2 ps
nstenergy   =100;save energies every 0.2 ps
nstlog  =100;update log file every 0.2 ps
;Bond parameters
continuation=no ;first dynamics run
constraint_algorithm=lincs  ;holonomic constraints
constraints =all-bonds  ;all bonds (even heavy atom-H
bonds)constraind
lincs_iter  =1  ;accuracy of LINCS
lincs_order =4  ;also related to accuracy
;Neighborhood searching
ns_type =grid   ;search neighboring grid cells
nstlist =5  ;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
electrostat\
;ics
pme_order   =4  ;cubic interpolation
fourierspacing  =0.16   ;grid spacing for FFT
;Temperature coupling is on
tcoupl  =V-rescale  ;modified Berendsen thermostat
tc_grps =SYSTEM   ;two coupling groups - more accurate
tau_t   =0.1;0.1  ;time constant, in ps
ref_t   =298;25   ;reference temperature, one for
each \
;group, in K
;Pressure coupling is off
pcoupl  =no ;no pressure coupling in NVT
;Periodic boundary conditions
pbc =xyz; 3-D PBC
;Dispersion correction
DispCorr=EnerPres   ;account for cut-off vdW scheme
;Velocity generation
gen_vel =yes;assign velocities from Maxwell distribution
gen_temp=25 ;temperature for Maxwell distribution
gen_seed=-1 ;generate a random seed
;END

*NPT SCRIPT*
File Edit Options Buffers Tools Help
title   =Ethanol npt equilibration
;define =-DPOSRES   ;position restrain the protein
;Run parameters
integrator  =md ;leap-frog algorithm
nsteps  =5  ;2 * 5 = 100 ps
dt  =0.002  ;2fs
;Output control
nstxout =100;save coordinates every 0.2 ps
nstvout =100;save velocities every 0.2 ps
nstenergy   =100;save energies every 0.2 ps
nstlog  =100;update log file every 0.2 ps
;Bond parameters
continuation=yes;Restarting after NVT
constraint_algorithm=lincs  ;holonomic constraints
constraints =all-bonds  ;all bonds (even heavy atom-H
bonds)constraind
lincs_iter  =1  ;accuracy of LINCS
lincs_order =4  ;also related to accuracy
;Neighborhood searching
ns_type =grid   ;search neighboring grid cells
nstlist =5  ;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
electrostat\
;ics
pme_order   =4  ;cubic interpolation
fourierspacing  =0.16   ;grid spacing for FFT
;Temp

Re: [gmx-users] pressure coupling not enough values (I need 2)

[Justin A. Lemkul]

afsaneh maleki wrote:

Hi,


grompp show the error as below:

ERROR: pressure coupling not enough values (I need 2)

 


I used ref_p   =1.  In  file.mdp

How to solve this problem?



Without seeing the rest of your pressure coupling settings, I can only assume 
that you're using semi-isotropic coupling, and thus, per the manual:


"Pressure coupling which is isotropic in the x and y direction, but different in 
the z direction. This can be useful for membrane simulations. 2 values are 
needed for x/y and z directions respectively."


-Justin



thanks in advance,
Afsaneh



--


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


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[gmx-users] pressure coupling not enough values (I need 2)

[afsaneh maleki]

Hi,


grompp show the error as below:

ERROR: pressure coupling not enough values (I need 2)



I used ref_p   =1.  In  file.mdp

How to solve this problem?

thanks in advance,
Afsaneh
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Re: [gmx-users] Pressure coupling

[David van der Spoel]

On 2010-07-15 16.01, Justin A. Lemkul wrote:



Sai Pooja wrote:

Hi,

I am aware there have been many threads on this topic and I have
looked at some of them. I would still like to make this query. I am
running an npt equilibration run for a solvated protein using
Charmm27-Tip3p (nocmap). I ran the simulation for 1ns. The average
values of pressure converge to 1.1 (ref=1.0), however, the
fluctuations are not only large but range from -10^2 --- +10^2. I am
pasting an excerpt from my log file here:



Seems perfectly normal to me.

http://www.gromacs.org/Documentation/Terminology/Pressure#Fluctuation





Moreover, in this particular version of gromacs (git version, 20th
June, 2010), RMS fluctuations are not reported in the log file.


mdrun -nocompact



This might be nice to restore, but you can still get all of that from
g_energy.

-Justin


Pooja




--
Quaerendo Invenietis-Seek and you shall discover.






--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Pressure coupling

[Justin A. Lemkul]

Sai Pooja wrote:

Hi,

I am aware there have been many threads on this topic and I have looked 
at some of them. I would still like to make this query. I am running an 
npt equilibration run for a solvated protein using Charmm27-Tip3p 
(nocmap). I ran the simulation for 1ns. The average values of pressure 
converge to 1.1 (ref=1.0), however, the fluctuations are not only large 
but range from -10^2 --- +10^2. I am pasting an excerpt from my log file 
here:




Seems perfectly normal to me.

http://www.gromacs.org/Documentation/Terminology/Pressure#Fluctuation





Moreover, in this particular version of gromacs (git version, 20th June, 
2010), RMS fluctuations are not reported in the log file.




This might be nice to restore, but you can still get all of that from g_energy.

-Justin


Pooja




--
Quaerendo Invenietis-Seek and you shall discover.



--


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


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[gmx-users] Pressure coupling

[Sai Pooja]

Hi,

I am aware there have been many threads on this topic and I have looked at
some of them. I would still like to make this query. I am running an npt
equilibration run for a solvated protein using Charmm27-Tip3p (nocmap). I
ran the simulation for 1ns. The average values of pressure converge to 1.1
(ref=1.0), however, the fluctuations are not only large but range from -10^2
--- +10^2. I am pasting an excerpt from my log file here:

   Step   Time Lambda
 90  900.00.0

   Energies (kJ/mol)
U-BProper Dih.  Improper Dih.  LJ-14 Coulomb-14
1.77111e+031.22478e+031.24096e+028.99612e+021.07960e+04
LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)   RF excl.
2.02487e+04   -7.73436e+02   -1.72259e+05   -1.50772e+03   -5.33117e+03
  PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
   -1.44807e+052.84204e+04   -1.16387e+053.01479e+022.42087e+02
   Constr. rmsd
7.88740e-06

Writing checkpoint, step 901680 at Thu Jul 15 08:59:29 2010

Writing checkpoint, step 931750 at Thu Jul 15 09:14:29 2010

Writing checkpoint, step 961715 at Thu Jul 15 09:29:29 2010

Writing checkpoint, step 991540 at Thu Jul 15 09:44:29 2010

   Step   Time Lambda
100 1000.00.0

Writing checkpoint, step 100 at Thu Jul 15 09:48:44 2010

   Energies (kJ/mol)
U-BProper Dih.  Improper Dih.  LJ-14 Coulomb-14
1.84487e+031.18241e+031.19723e+029.27247e+021.08372e+04
LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)   RF excl.
1.96480e+04   -7.72423e+02   -1.71261e+05   -1.59122e+03   -5.33098e+03
  PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
   -1.44396e+052.80310e+04   -1.16365e+052.97348e+02   -4.83396e+01
   Constr. rmsd
7.88949e-06

Statistics over 101 steps using 21 frames

   Energies (kJ/mol)
U-BProper Dih.  Improper Dih.  LJ-14 Coulomb-14
1.78254e+031.17488e+031.26460e+029.19148e+021.08095e+04
LJ (SR)LJ (LR)   Coulomb (SR)   Coulomb (LR)   RF excl.
1.96458e+04   -7.74885e+02   -1.71741e+05   -1.51523e+03   -5.33115e+03
  PotentialKinetic En.   Total EnergyTemperature Pressure (bar)
   -1.44904e+052.84063e+04   -1.16498e+053.01329e+021.10779e+00
   Constr. rmsd
0.0e+00

  Box-X  Box-Y  Box-Z
5.45508e+005.45508e+003.85733e+00

   Total Virial (kJ/mol)
9.47569e+032.10309e+007.87684e+00
1.74263e+009.46418e+03   -3.05302e+00
8.24251e+00   -2.41221e+009.45496e+03

   Pressure (bar)
2.11556e+00   -2.05272e+00   -2.29518e+00
   -1.94883e+002.43768e+005.18363e-01
   -2.40126e+003.33003e-01   -1.22987e+00


Moreover, in this particular version of gromacs (git version, 20th June,
2010), RMS fluctuations are not reported in the log file.

Pooja




-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
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Re: [gmx-users] pressure coupling

[Justin A. Lemkul]

Shuangxing Dai wrote:

Thanks for the response.
Yes, I know that large fluctuations will be expected. But why the 
average was not even correct? Also, how can I reach some state ( some 
pressre and temperature) and know/tell that the system is 
in equilibrium if the average is not correct with large fluctuation? I 
mean I do not know the criteria of Gromacs. Or maybe my procedure is wrong?




You've only run 100 ps total equilibration.  For an extremely high temperature, 
I might expect it to take quite a bit longer, especially since you're dealing 
with a system that will be subject to large fluctuations (due to its size).


-Justin


Message: 1
Date: Mon, 05 Jul 2010 10:39:30 -0400
From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] pressure coupling
To: Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>>

Message-ID: <4c31eea2.7070...@vt.edu <mailto:4c31eea2.7070...@vt.edu>>
Content-Type: text/plain; charset=UTF-8; format=flowed



Shuangxing Dai wrote:

 Hi, all,
  I am trying to do anisotropic coupling using Parrinello-Rahman. I
 want to reach the equilibrium state at 1000K, 0.1MPa( 1  bar). However,
 I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K,
 fluctuation is 626 bar for pressure and 11.21 K for temperature.)  I run
 energy minimization first, then Berenderson pressure coupling for 50 ps,
 finally Parrinello-Rahman pressure coupling for 50 ps. Anyone has
 experience on anisotropic coupling and know why?
   My system has just 4000 atoms. This is my .mdp file:



For a small system, large fluctations in the pressure are to be expected:

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

-Justin


 ;define   = -DPOSRES
 ; RUN CONTROL PARAMETERS =
 integrator   = sd
 ; start time and timestep in ps =
 tinit= 0
 dt   = 0.001
 nsteps   = 5
 ; number of steps for center of mass motion removal =
 nstcomm  = 100
 ; OUTPUT CONTROL OPTIONS =
 ; Output frequency for coords (x), velocities (v) and forces (f) =
 nstxout  = 0
 nstvout  = 0
 nstfout  = 0
 ; Output frequency for energies to log file and energy file =
 nstlog   = 10
 nstenergy= 10
 ; Output frequency and precision for xtc file =
 nstxtcout= 10
 xtc-precision= 1000
 ; NEIGHBORSEARCHING PARAMETERS =
 ; nblist update frequency =
 nstlist  = 20
 ; ns algorithm (simple or grid) =
 ns_type  = grid

 ;OPTIONS FOR PRESSURE COUPLING
 Pcoupl   = Parrinello-Rahman
 pcoupltype   = anisotropic
 tau_p= 5
 compressibility  = 2.1645e-07  2.1645e-07 2.7322e-07 0 0 0
 ref_p= 1 1 1 0 0 0
 ;OPTIONS FOR TEMPERATURE COUPLING
 tc_grps  = system
 tau_t= 1
 ref_t= 1000
 ; OPTIONS FOR BONDS =
 constraints  = hbonds
 ; Type of constraint algorithm =
 constraint-algorithm = Lincs
 ; Do not constrain the start configuration =
 unconstrained-start  = no
 ; Relative tolerance of shake =
 shake-tol= 0.0001
 ; Highest order in the expansion of the constraint coupling matrix =
 lincs-order  = 12
 ; Lincs will write a warning to the stderr if in one step a bond =
 ; rotates over more degrees than =
 lincs-warnangle  = 30
 ; Periodic boundary conditions: xyz, no, xy
 pbc  = xyz
 periodic_molecules   = no
 ; nblist cut-off
 rlist= 1

 ; OPTIONS FOR ELECTROSTATICS AND VDW
 ; Method for doing electrostatics
 coulombtype  = PME
 rcoulomb = 1
 ; Method for doing Van der Waals
 vdw-type = Cut-off
 ; cut-off lengths
 rvdw = 1

 ; Spacing for the PME/PPPM FFT grid
 fourierspacing   = 0.12
 ; FFT grid size, when a value is 0 fourierspacing will be used
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 ; EWALD/PME/PPPM parameters
 pme_order= 6
 ewald_rtol   = 1e-4
 ewald_geometry   = 3d
 epsilon_surface  = 0
 optimize_fft = no




 I used the same procedure to reach different state ( like 0.01 K, 100K,
 300K, 500K, 800K, 1000K). Only the 0.01 K got the correct average
 pressure and small fluctuation.
 T p(bar)  delta p T (K)   delta T
 0.01  1.03E+002.12E+009.95E-031.21E-04
 100   5.48359 71.5565 91.198  1.25218
 300   2.62807 162.926 290.324 3.36594
 500   16.6356 1048.76 492.616 5.45231
 800   59.3245 594.773 799.314 9.18876
 1000  80.2257 626.789 1007.23 11.2159

 Thanks in ad

Re: [gmx-users] pressure coupling

[Shuangxing Dai]

Thanks for the response.
Yes, I know that large fluctuations will be expected. But why the average
was not even correct? Also, how can I reach some state ( some pressre and
temperature) and know/tell that the system is in equilibrium if the average
is not correct with large fluctuation? I mean I do not know the criteria of
Gromacs. Or maybe my procedure is wrong?

Message: 1
Date: Mon, 05 Jul 2010 10:39:30 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] pressure coupling
To: Discussion list for GROMACS users 
Message-ID: <4c31eea2.7070...@vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed



Shuangxing Dai wrote:
> Hi, all,
>  I am trying to do anisotropic coupling using Parrinello-Rahman. I
> want to reach the equilibrium state at 1000K, 0.1MPa( 1  bar). However,
> I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K,
> fluctuation is 626 bar for pressure and 11.21 K for temperature.)  I run
> energy minimization first, then Berenderson pressure coupling for 50 ps,
> finally Parrinello-Rahman pressure coupling for 50 ps. Anyone has
> experience on anisotropic coupling and know why?
>   My system has just 4000 atoms. This is my .mdp file:
>

For a small system, large fluctations in the pressure are to be expected:

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

-Justin

> ;define   = -DPOSRES
> ; RUN CONTROL PARAMETERS =
> integrator   = sd
> ; start time and timestep in ps =
> tinit= 0
> dt   = 0.001
> nsteps   = 5
> ; number of steps for center of mass motion removal =
> nstcomm  = 100
> ; OUTPUT CONTROL OPTIONS =
> ; Output frequency for coords (x), velocities (v) and forces (f) =
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
> ; Output frequency for energies to log file and energy file =
> nstlog   = 10
> nstenergy= 10
> ; Output frequency and precision for xtc file =
> nstxtcout= 10
> xtc-precision= 1000
> ; NEIGHBORSEARCHING PARAMETERS =
> ; nblist update frequency =
> nstlist  = 20
> ; ns algorithm (simple or grid) =
> ns_type  = grid
>
> ;OPTIONS FOR PRESSURE COUPLING
> Pcoupl   = Parrinello-Rahman
> pcoupltype   = anisotropic
> tau_p= 5
> compressibility  = 2.1645e-07  2.1645e-07 2.7322e-07 0 0 0
> ref_p= 1 1 1 0 0 0
> ;OPTIONS FOR TEMPERATURE COUPLING
> tc_grps  = system
> tau_t= 1
> ref_t= 1000
> ; OPTIONS FOR BONDS =
> constraints  = hbonds
> ; Type of constraint algorithm =
> constraint-algorithm = Lincs
> ; Do not constrain the start configuration =
> unconstrained-start  = no
> ; Relative tolerance of shake =
> shake-tol= 0.0001
> ; Highest order in the expansion of the constraint coupling matrix =
> lincs-order  = 12
> ; Lincs will write a warning to the stderr if in one step a bond =
> ; rotates over more degrees than =
> lincs-warnangle  = 30
> ; Periodic boundary conditions: xyz, no, xy
> pbc  = xyz
> periodic_molecules   = no
> ; nblist cut-off
> rlist= 1
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = PME
> rcoulomb = 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw = 1
>
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 6
> ewald_rtol   = 1e-4
> ewald_geometry   = 3d
> epsilon_surface  = 0
> optimize_fft = no
>
>
>
>
> I used the same procedure to reach different state ( like 0.01 K, 100K,
> 300K, 500K, 800K, 1000K). Only the 0.01 K got the correct average
> pressure and small fluctuation.
> T p(bar)  delta p T (K)   delta T
> 0.01  1.03E+002.12E+009.95E-031.21E-04
> 100   5.48359 71.5565 91.198  1.25218
> 300   2.62807 162.926 290.324 3.36594
> 500   16.6356 1048.76 492.616 5.45231
> 800   59.3245 594.773 799.314 9.18876
> 1000  80.2257 626.789 1007.23 11.2159
>
> Thanks in advance,

Re: [gmx-users] pressure coupling

[Justin A. Lemkul]

Shuangxing Dai wrote:

Hi, all,
 I am trying to do anisotropic coupling using Parrinello-Rahman. I 
want to reach the equilibrium state at 1000K, 0.1MPa( 1  bar). However, 
I find that the fluctuation is so large ( p=80.22 bar, T=1007.23 K, 
fluctuation is 626 bar for pressure and 11.21 K for temperature.)  I run 
energy minimization first, then Berenderson pressure coupling for 50 ps, 
finally Parrinello-Rahman pressure coupling for 50 ps. Anyone has 
experience on anisotropic coupling and know why? 
  My system has just 4000 atoms. This is my .mdp file:




For a small system, large fluctations in the pressure are to be expected:

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

-Justin


;define   = -DPOSRES
; RUN CONTROL PARAMETERS =
integrator   = sd
; start time and timestep in ps =
tinit= 0
dt   = 0.001
nsteps   = 5
; number of steps for center of mass motion removal =
nstcomm  = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 0
nstvout  = 0
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 10
nstenergy= 10
; Output frequency and precision for xtc file =
nstxtcout= 10
xtc-precision= 1000
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 20
; ns algorithm (simple or grid) =
ns_type  = grid

;OPTIONS FOR PRESSURE COUPLING
Pcoupl   = Parrinello-Rahman
pcoupltype   = anisotropic
tau_p= 5
compressibility  = 2.1645e-07  2.1645e-07 2.7322e-07 0 0 0
ref_p= 1 1 1 0 0 0
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps  = system
tau_t= 1
ref_t= 1000
; OPTIONS FOR BONDS =
constraints  = hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start  = no
; Relative tolerance of shake =
shake-tol= 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order  = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle  = 30
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1


; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths   
rvdw = 1


; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-4
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no




I used the same procedure to reach different state ( like 0.01 K, 100K, 
300K, 500K, 800K, 1000K). Only the 0.01 K got the correct average 
pressure and small fluctuation.

T   p(bar)  delta p T (K)   delta T
0.011.03E+002.12E+009.95E-031.21E-04
100 5.48359 71.5565 91.198  1.25218
300 2.62807 162.926 290.324 3.36594
500 16.6356 1048.76 492.616 5.45231
800 59.3245 594.773 799.314 9.18876
100080.2257 626.789 1007.23 11.2159

Thanks in advance,
Shuangxing Dai



--


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


--
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

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[gmx-users] pressure coupling

[Shuangxing Dai]

Hi, all,
 I am trying to do anisotropic coupling using Parrinello-Rahman. I want
to reach the equilibrium state at 1000K, 0.1MPa( 1  bar). However, I find
that the fluctuation is so large ( p=80.22 bar, T=1007.23 K, fluctuation is
626 bar for pressure and 11.21 K for temperature.)  I run energy
minimization first, then Berenderson pressure coupling for 50 ps, finally
Parrinello-Rahman pressure coupling for 50 ps. Anyone has experience on
anisotropic coupling and know why?
  My system has just 4000 atoms. This is my .mdp file:

;define   = -DPOSRES
; RUN CONTROL PARAMETERS =
integrator   = sd
; start time and timestep in ps =
tinit= 0
dt   = 0.001
nsteps   = 5
; number of steps for center of mass motion removal =
nstcomm  = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 0
nstvout  = 0
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 10
nstenergy= 10
; Output frequency and precision for xtc file =
nstxtcout= 10
xtc-precision= 1000
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 20
; ns algorithm (simple or grid) =
ns_type  = grid

;OPTIONS FOR PRESSURE COUPLING
Pcoupl   = Parrinello-Rahman
pcoupltype   = anisotropic
tau_p= 5
compressibility  = 2.1645e-07  2.1645e-07 2.7322e-07 0 0 0
ref_p= 1 1 1 0 0 0
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps  = system
tau_t= 1
ref_t= 1000
; OPTIONS FOR BONDS =
constraints  = hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start  = no
; Relative tolerance of shake =
shake-tol= 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order  = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle  = 30
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw = 1

; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-4
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no




I used the same procedure to reach different state ( like 0.01 K, 100K,
300K, 500K, 800K, 1000K). Only the 0.01 K got the correct average pressure
and small fluctuation.
  T p(bar) delta p T (K) delta T  0.01 1.03E+00 2.12E+00 9.95E-03 1.21E-04
100 5.48359 71.5565 91.198 1.25218  300 2.62807 162.926 290.324 3.36594  500
16.6356 1048.76 492.616 5.45231  800 59.3245 594.773 799.314 9.18876  1000
80.2257 626.789 1007.23 11.2159
Thanks in advance,
Shuangxing Dai
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[gmx-users] Pressure Coupling: Scaling of Coordinates is Occurring - why?

[Christopher Rowan]

Hi Gromacs Users,

Pressure coupling is not supposed to scale the coordinates of my frozen
group, yet it is.  My frozen group is a crystal structure that does not have
any topology assigned to them: no bond, angle, dihedral constants etc.
specified.  I find that a crystal structure gets compressed.  A sample of
the pressure coupling section of my .mdp file is given below:

; PRESSURE COUPLING
pcoupl = parrinello-rahman
pcoupltype = isotropic
tau_p = 50.0
compressibility = 0.1 0.1 0.1 0.1 0.1 0.1
refcoord_scaling = no
ref_p = 1000.0 1000.0 1000.0 0.0 0.0 0.0

I'm using Gromacs 4.0.5.
Any suggestions appreciated,

Chris Rowan
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Re: [gmx-users] Pressure coupling and cut-off

[Justin A. Lemkul]

Yanmei Song wrote:

Dear Justin:

Thank you for your suggestions. using shift for vdwtype helps a lot.

Can I ask you another question? The density of my system is about 8% 
larger than the experimental value. Do you have any suggestions on how 
to reduce the density of the system. Or once the force field and all the 
parameters are fixed, the density is independent of the MD procedure? I 
am using NPT ensemble with the mdp I mentioned before with added vdwtype 
= shift.





Output like density, pressure, energy conservation, etc. are a consequence of 
both the force field parameters and their proper use.  Look into the primary 
literature for the force field you are using and see how well the parameters are 
expected to behave.  A difference of 8% doesn't sound that unreasonable to me, 
but the primary literature will be the judge.


-Justin



On Thu, May 14, 2009 at 4:35 PM, Justin A. Lemkul > wrote:




Yanmei Song wrote:

Dear Justin:

Thanks for your response. Here is the complete my .mdp file:

title   =  pdm
cpp =  /lib/cpp
constraints =  all_bonds
integrator  =  md
dt  =  0.004   ; ps !
nsteps  =  250   ; total 10ns.
nstcomm =  1
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
rlist   =  1.4
rcoulomb=  1.4
rvdw=  1.4
fourierspacing  =  0.20
pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in one groups
Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300
; Energy monitoring
energygrps  =  PDM
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10



The problem you're seeing could be an artifact of the shorter
cutoff.  Have you tried using DispCorr = EnerPres?  Or what about
using a Shift function for vdwtype?  You might see better energy
conservation in that case compared to a plain cutoff.

-Justin


On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Yanmei Song wrote:

   Dear All:

   I have question about the pressure coupling. I have done
a 10ns
   simulation with 19800 atoms for 120 large molecules using the
   following pressure coupling.

   Tcoupl  =  berendsen
   tc_grps =  PDM
   tau_t   =  0.1
   ref_t   =  300

   Pcoupl  =  berendsen
   pcoupltype  =  isotropic
   ;pc-grps=  PDM
   tau_p   =  1.0
   ref_p   =  1.0
   compressibility =  4.5e-5

   Then I did g_energy for the last 3ns and got the results:

   Energy  Average   RMSD Fluct.
Drift  Tot-Drift
 
 ---

   Potential-98061  0  0
  0.616681850.04
   Temperature 303.561109.602109.602
   0.000181791   0.545372
   Pressure (bar)   4.48840.811109.8
-0.169835   -509.506

   For such a long run the pressure drift is still too much and
   seem hasn't approached 1bar. Does it mean the system hasn't
   reach equilibrium yet. I did a similar system by using
the same
   method. it just take 2 or 3ns to reach the equilibrium.
and the
   pressure is around 1.01after the run. The only difference
is the
   cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4
is too
   large to make the system running slower. Or the pressure
   coupling method is not worki

Re: [gmx-users] Pressure coupling and cut-off

[Yanmei Song]

Dear Justin:

Thank you for your suggestions. using shift for vdwtype helps a lot.

Can I ask you another question? The density of my system is about 8% larger
than the experimental value. Do you have any suggestions on how to reduce
the density of the system. Or once the force field and all the parameters
are fixed, the density is independent of the MD procedure? I am using NPT
ensemble with the mdp I mentioned before with added vdwtype = shift.



On Thu, May 14, 2009 at 4:35 PM, Justin A. Lemkul  wrote:

>
>
> Yanmei Song wrote:
>
>> Dear Justin:
>>
>> Thanks for your response. Here is the complete my .mdp file:
>>
>> title   =  pdm
>> cpp =  /lib/cpp
>> constraints =  all_bonds
>> integrator  =  md
>> dt  =  0.004   ; ps !
>> nsteps  =  250   ; total 10ns.
>> nstcomm =  1
>> nstxout =  5
>> nstvout =  5
>> nstfout =  0
>> nstlog  =  5000
>> nstenergy   =  5000
>> nstxtcout   =  25000
>> nstlist =  10
>> ns_type =  grid
>> pbc =  xyz
>> coulombtype =  PME
>> rlist   =  1.4
>> rcoulomb=  1.4
>> rvdw=  1.4
>> fourierspacing  =  0.20
>> pme_order   =  4
>> ewald_rtol  =  1e-5
>> ; Berendsen temperature coupling is on in one groups
>> Tcoupl  =  berendsen
>> tc_grps =  PDM
>> tau_t   =  0.1
>> ref_t   =  300
>> ; Energy monitoring
>> energygrps  =  PDM
>> ; Isotropic pressure coupling is now on
>> Pcoupl  =  berendsen
>> pcoupltype  =  isotropic
>> ;pc-grps=  PDM
>> tau_p   =  1.0
>> ref_p   =  1.0
>> compressibility =  4.5e-5
>>
>> ; Generate velocites is off at 300 K.
>> gen_vel =  yes
>> gen_temp=  300.0
>> gen_seed=  10
>>
>>
>>
> The problem you're seeing could be an artifact of the shorter cutoff.  Have
> you tried using DispCorr = EnerPres?  Or what about using a Shift function
> for vdwtype?  You might see better energy conservation in that case compared
> to a plain cutoff.
>
> -Justin
>
>
>> On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Yanmei Song wrote:
>>
>>Dear All:
>>
>>I have question about the pressure coupling. I have done a 10ns
>>simulation with 19800 atoms for 120 large molecules using the
>>following pressure coupling.
>>
>>Tcoupl  =  berendsen
>>tc_grps =  PDM
>>tau_t   =  0.1
>>ref_t   =  300
>>
>>Pcoupl  =  berendsen
>>pcoupltype  =  isotropic
>>;pc-grps=  PDM
>>tau_p   =  1.0
>>ref_p   =  1.0
>>compressibility =  4.5e-5
>>
>>Then I did g_energy for the last 3ns and got the results:
>>
>>Energy  Average   RMSD Fluct.
>>   Drift  Tot-Drift
>>
>>  
>> ---
>>Potential-98061  0  0
>> 0.616681850.04
>>Temperature 303.561109.602109.602
>>0.000181791   0.545372
>>Pressure (bar)   4.48840.811109.8
>> -0.169835   -509.506
>>
>>For such a long run the pressure drift is still too much and
>>seem hasn't approached 1bar. Does it mean the system hasn't
>>reach equilibrium yet. I did a similar system by using the same
>>method. it just take 2 or 3ns to reach the equilibrium. and the
>>pressure is around 1.01after the run. The only difference is the
>>cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4 is too
>>large to make the system running slower. Or the pressure
>>coupling method is not working well.  Anyone can give me any
>>suggestions?
>>
>>
>>
>>I think it will depend on the interplay of other parameters as well.
>> Posting a complete .mdp file may be more helpful.
>>
>>-Justin
>>
>>--Yanmei Song
>>Ph.D. Candidate
>>Department of Chemical Engineering
>>Arizona State University
>>
>>
>>
>>  
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>

Re: [gmx-users] Pressure coupling and cut-off

[Justin A. Lemkul]

Yanmei Song wrote:

Dear Justin:

Thanks for your response. Here is the complete my .mdp file:

title   =  pdm
cpp =  /lib/cpp
constraints =  all_bonds
integrator  =  md
dt  =  0.004   ; ps !
nsteps  =  250   ; total 10ns.
nstcomm =  1
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
rlist   =  1.4
rcoulomb=  1.4
rvdw=  1.4
fourierspacing  =  0.20
pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in one groups
Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300
; Energy monitoring
energygrps  =  PDM
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10




The problem you're seeing could be an artifact of the shorter cutoff.  Have you 
tried using DispCorr = EnerPres?  Or what about using a Shift function for 
vdwtype?  You might see better energy conservation in that case compared to a 
plain cutoff.


-Justin



On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul > wrote:




Yanmei Song wrote:

Dear All:

I have question about the pressure coupling. I have done a 10ns
simulation with 19800 atoms for 120 large molecules using the
following pressure coupling.

Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300

Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

Then I did g_energy for the last 3ns and got the results:

Energy  Average   RMSD Fluct.
 Drift  Tot-Drift


---
Potential-98061  0  0  
 0.616681850.04

Temperature 303.561109.602109.602
0.000181791   0.545372
Pressure (bar)   4.48840.811109.8
 -0.169835   -509.506

For such a long run the pressure drift is still too much and
seem hasn't approached 1bar. Does it mean the system hasn't
reach equilibrium yet. I did a similar system by using the same
method. it just take 2 or 3ns to reach the equilibrium. and the
pressure is around 1.01after the run. The only difference is the
cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4 is too
large to make the system running slower. Or the pressure
coupling method is not working well.  Anyone can give me any
suggestions?



I think it will depend on the interplay of other parameters as well.
 Posting a complete .mdp file may be more helpful.

-Justin

-- 
Yanmei Song

Ph.D. Candidate
Department of Chemical Engineering
Arizona State University




___
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-- 



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


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Re: [gmx-users] Pressure coupling and cut-off

[Yanmei Song]

Dear Justin:

Thanks for your response. Here is the complete my .mdp file:

title   =  pdm
cpp =  /lib/cpp
constraints =  all_bonds
integrator  =  md
dt  =  0.004   ; ps !
nsteps  =  250   ; total 10ns.
nstcomm =  1
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
rlist   =  1.4
rcoulomb=  1.4
rvdw=  1.4
fourierspacing  =  0.20
pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in one groups
Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300
; Energy monitoring
energygrps  =  PDM
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10



On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul  wrote:

>
>
> Yanmei Song wrote:
>
>> Dear All:
>>
>> I have question about the pressure coupling. I have done a 10ns simulation
>> with 19800 atoms for 120 large molecules using the following pressure
>> coupling.
>>
>> Tcoupl  =  berendsen
>> tc_grps =  PDM
>> tau_t   =  0.1
>> ref_t   =  300
>>
>> Pcoupl  =  berendsen
>> pcoupltype  =  isotropic
>> ;pc-grps=  PDM
>> tau_p   =  1.0
>> ref_p   =  1.0
>> compressibility =  4.5e-5
>>
>> Then I did g_energy for the last 3ns and got the results:
>>
>> Energy  Average   RMSD Fluct.  Drift
>>  Tot-Drift
>>
>> ---
>> Potential-98061  0  00.61668
>>  1850.04
>> Temperature 303.561109.602109.602 0.000181791
>> 0.545372
>> Pressure (bar)   4.48840.811109.8  -0.169835
>> -509.506
>>
>> For such a long run the pressure drift is still too much and seem hasn't
>> approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did
>> a similar system by using the same method. it just take 2 or 3ns to reach
>> the equilibrium. and the pressure is around 1.01after the run. The only
>> difference is the cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4
>> is too large to make the system running slower. Or the pressure coupling
>> method is not working well.  Anyone can give me any suggestions?
>>
>>
>>
> I think it will depend on the interplay of other parameters as well.
>  Posting a complete .mdp file may be more helpful.
>
> -Justin
>
>  --
>> Yanmei Song
>> Ph.D. Candidate
>> Department of Chemical Engineering
>> Arizona State University
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
___
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Re: [gmx-users] Pressure coupling and cut-off

[Justin A. Lemkul]

Yanmei Song wrote:

Dear All:

I have question about the pressure coupling. I have done a 10ns 
simulation with 19800 atoms for 120 large molecules using the following 
pressure coupling.


Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300

Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

Then I did g_energy for the last 3ns and got the results:

Energy  Average   RMSD Fluct.  Drift  
Tot-Drift

---
Potential-98061  0  00.61668
1850.04
Temperature 303.561109.602109.602 0.000181791   
0.545372
Pressure (bar)   4.48840.811109.8  -0.169835   
-509.506


For such a long run the pressure drift is still too much and seem hasn't 
approached 1bar. Does it mean the system hasn't reach equilibrium yet. I 
did a similar system by using the same method. it just take 2 or 3ns to 
reach the equilibrium. and the pressure is around 1.01after the run. The 
only difference is the cutoff changing from 1.2 to 1.4.  Does the cufoff 
of 1.4 is too large to make the system running slower. Or the pressure 
coupling method is not working well.  Anyone can give me any suggestions?





I think it will depend on the interplay of other parameters as well.  Posting a 
complete .mdp file may be more helpful.


-Justin


--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University




___
gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at http://www.gromacs.org/search before posting!
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--


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


___
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[gmx-users] Pressure coupling and cut-off

[Yanmei Song]

Dear All:

I have question about the pressure coupling. I have done a 10ns simulation
with 19800 atoms for 120 large molecules using the following pressure
coupling.

Tcoupl  =  berendsen
tc_grps =  PDM
tau_t   =  0.1
ref_t   =  300

Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps=  PDM
tau_p   =  1.0
ref_p   =  1.0
compressibility =  4.5e-5

Then I did g_energy for the last 3ns and got the results:

Energy  Average   RMSD Fluct.  Drift
Tot-Drift
---
Potential-98061  0  00.61668
1850.04
Temperature 303.561109.602109.602 0.000181791
0.545372
Pressure (bar)   4.48840.811109.8  -0.169835
-509.506

For such a long run the pressure drift is still too much and seem hasn't
approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did
a similar system by using the same method. it just take 2 or 3ns to reach
the equilibrium. and the pressure is around 1.01after the run. The only
difference is the cutoff changing from 1.2 to 1.4.  Does the cufoff of 1.4
is too large to make the system running slower. Or the pressure coupling
method is not working well.  Anyone can give me any suggestions?


-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
___
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Re: [gmx-users] Pressure Coupling Problem

[Lucio Montero]

I don't know the conditions you use with your system, but sometimes there are 
problems when you use pressure coupling in a system with positionally 
restrained or fixed atoms.
Cheers.
 Lucio.


From: Joe Joe 
Sent: Friday, April 10, 2009 12:12 PM
To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Pressure Coupling Problem


I finally figured it out. I went through every parameter step by step and it 
turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs 
would have given me a warning (hint hint). That explains why my P.E. was 10^-5 
instead of 10^-6. Thanks everyone for trying!!!. Sometime the most obvious 
mistake takes some time to figure out. 


Cheers,



Ilya




On Fri, Apr 10, 2009 at 8:05 AM,  wrote:

  Alright, sorry that I wasn't able to help. I'm confused by some apparent 
contradictions in your posts and I'm not sure that I'm going to be useful to 
you here.

  Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html: 
"No matter how much minimization I do the volume of the box expands when run it 
using berendsen pressure coupling with a tau_p -f .1."

  Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041159.html: 
"So I got my small water box (800 waters) to behave stably with pressure 
coupling after more minimization ..."

  Good luck.
  Chris.

  -- original message --


  Nope not an A/nm problem.
  As a simple test I take spc.gro from share/top.
  I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o
  water_center.

  I then solvate with genbox, minimize and run using the mdp file I provided
  earlier.

  No matter how much minimization I do the volume of the box expands when run
  it using berendsen pressure coupling with a tau_p -f .1.

  Ilya


  On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale wrote:

  [Hide Quoted Text]
  So your problem with the small water box was solved simply by adding more
  minimization? I then suspect that all of your problems are simply related to
  a bad starting structure -- and by the sound of it is really is very bad.
  Are you sure that you don't have an angstrom / nm problem here?

  Chris.

  -- original message --

  So I got my small water box (800 waters) to behave stably with pressure
  coupling after more minimization but I still can't get my large system to
  work with pressure coupling. I tried minimizing but I can never get the
  Fmax to be less 102, which is pretty normal for protein/water simulations of
  large proteins, at least from my experience.  I have since run 400 ps NVT
  as ...

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  http://www.gromacs.org/mailman/listinfo/gmx-users
  Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Pressure Coupling Problem

[Joe Joe]

I finally figured it out. I went through every parameter step by step and it
turns our I had epsilon-r set to 80. Not sure why I had that. Wish gromacs
would have given me a warning (hint hint). That explains why my P.E. was
10^-5 instead of 10^-6. Thanks everyone for trying!!!. Sometime the most
obvious mistake takes some time to figure out.
Cheers,

Ilya


On Fri, Apr 10, 2009 at 8:05 AM,  wrote:

> Alright, sorry that I wasn't able to help. I'm confused by some apparent
> contradictions in your posts and I'm not sure that I'm going to be useful to
> you here.
>
> Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html:
> "No matter how much minimization I do the volume of the box expands when run
> it using berendsen pressure coupling with a tau_p -f .1."
>
> Quoting http://www.gromacs.org/pipermail/gmx-users/2009-April/041159.html:
> "So I got my small water box (800 waters) to behave stably with pressure
> coupling after more minimization ..."
>
> Good luck.
> Chris.
>
> -- original message --
>
>
> Nope not an A/nm problem.
> As a simple test I take spc.gro from share/top.
> I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o
> water_center.
>
> I then solvate with genbox, minimize and run using the mdp file I provided
> earlier.
>
> No matter how much minimization I do the volume of the box expands when run
> it using berendsen pressure coupling with a tau_p -f .1.
>
> Ilya
>
>
> On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale  >wrote:
>
> [Hide Quoted Text]
> So your problem with the small water box was solved simply by adding more
> minimization? I then suspect that all of your problems are simply related
> to
> a bad starting structure -- and by the sound of it is really is very bad.
> Are you sure that you don't have an angstrom / nm problem here?
>
> Chris.
>
> -- original message --
>
> So I got my small water box (800 waters) to behave stably with pressure
> coupling after more minimization but I still can't get my large system to
> work with pressure coupling. I tried minimizing but I can never get the
> Fmax to be less 102, which is pretty normal for protein/water simulations
> of
> large proteins, at least from my experience.  I have since run 400 ps NVT
> as ...
>
> ___
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> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>
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[gmx-users] Pressure Coupling Problem

[chris . neale]

Alright, sorry that I wasn't able to help. I'm confused by some  
apparent contradictions in your posts and I'm not sure that I'm going  
to be useful to you here.


Quoting  
http://www.gromacs.org/pipermail/gmx-users/2009-April/041173.html: "No  
matter how much minimization I do the volume of the box expands when  
run it using berendsen pressure coupling with a tau_p -f .1."


Quoting  
http://www.gromacs.org/pipermail/gmx-users/2009-April/041159.html: "So  
I got my small water box (800 waters) to behave stably with pressure  
coupling after more minimization ..."


Good luck.
Chris.

-- original message --


Nope not an A/nm problem.
As a simple test I take spc.gro from share/top.
I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o
water_center.

I then solvate with genbox, minimize and run using the mdp file I provided
earlier.

No matter how much minimization I do the volume of the box expands when run
it using berendsen pressure coupling with a tau_p -f .1.

Ilya


On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale wrote:

[Hide Quoted Text]
So your problem with the small water box was solved simply by adding more
minimization? I then suspect that all of your problems are simply related to
a bad starting structure -- and by the sound of it is really is very bad.
Are you sure that you don't have an angstrom / nm problem here?

Chris.

-- original message --

So I got my small water box (800 waters) to behave stably with pressure
coupling after more minimization but I still can't get my large system to
work with pressure coupling. I tried minimizing but I can never get the
Fmax to be less 102, which is pretty normal for protein/water simulations of
large proteins, at least from my experience.  I have since run 400 ps NVT
as ...

___
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Re: [gmx-users] Pressure Coupling Problem

[Joe Joe]

Nope not an A/nm problem.
As a simple test I take spc.gro from share/top.
I reconfigure the box (i.e. editconf -f spc.gro -d 1.0 -c -bt cubic -o
water_center.

I then solvate with genbox, minimize and run using the mdp file I provided
earlier.

No matter how much minimization I do the volume of the box expands when run
it using berendsen pressure coupling with a tau_p -f .1.

Ilya


On Thu, Apr 9, 2009 at 11:22 AM, Chris Neale wrote:

> So your problem with the small water box was solved simply by adding more
> minimization? I then suspect that all of your problems are simply related to
> a bad starting structure -- and by the sound of it is really is very bad.
> Are you sure that you don't have an angstrom / nm problem here?
>
> Chris.
>
> -- original message --
>
> So I got my small water box (800 waters) to behave stably with pressure
> coupling after more minimization but I still can't get my large system to
> work with pressure coupling. I tried minimizing but I can never get the
> Fmax
> to be less 102, which is pretty normal for protein/water simulations of
> large proteins, at least from my experience.  I have since run 400 ps NVT
> as
> the system (425K atoms) is quite stable. The  is 2E-05. Since I am
> using 4fs time steps gromacs won't let me use a tau_p less than .4. Not
> sure
> what else to do except run NVT, which is what I was going to do after I got
> the density equilibrated. BTW, I am using octahedral PBC, but that should
> not make a difference with respect to P coupling, should it? Below is my
> whole mdp file. As a reminder my density in the system goes from 1.0 - .1
> in
> 10 ps with Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the
> amount of time it takes for my system to expand increases but it still
> expands.
>
> ___
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> Please search the archive at http://www.gromacs.org/search before posting!
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>
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[gmx-users] Pressure Coupling Problem

[Chris Neale]

So your problem with the small water box was solved simply by adding more 
minimization? I then suspect that all of your problems are simply related to a 
bad starting structure -- and by the sound of it is really is very bad. Are you 
sure that you don't have an angstrom / nm problem here?

Chris.

-- original message --

So I got my small water box (800 waters) to behave stably with pressure
coupling after more minimization but I still can't get my large system to
work with pressure coupling. I tried minimizing but I can never get the Fmax
to be less 102, which is pretty normal for protein/water simulations of
large proteins, at least from my experience.  I have since run 400 ps NVT as
the system (425K atoms) is quite stable. The  is 2E-05. Since I am
using 4fs time steps gromacs won't let me use a tau_p less than .4. Not sure
what else to do except run NVT, which is what I was going to do after I got
the density equilibrated. BTW, I am using octahedral PBC, but that should
not make a difference with respect to P coupling, should it? Below is my
whole mdp file. As a reminder my density in the system goes from 1.0 - .1 in
10 ps with Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the
amount of time it takes for my system to expand increases but it still
expands.

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Re: [gmx-users] Pressure Coupling Problem

[Joe Joe]

On Thu, Apr 9, 2009 at 6:36 AM, Justin A. Lemkul  wrote:

>
>
> Joe Joe wrote:
>
>> So I got my small water box (800 waters) to behave stably with pressure
>> coupling after more minimization but I still can't get my large system to
>> work with pressure coupling. I tried minimizing but I can never get the Fmax
>> to be less 10^2, which is pretty normal for protein/water simulations of
>> large proteins, at least from my experience.  I have since run 400 ps NVT as
>> the system (425K atoms) is quite stable. The  is 2E-05. Since I am
>> using 4fs time steps gromacs won't let me use a tau_p less than .4. Not sure
>> what else to do except run NVT, which is what I was going to do after I got
>> the density equilibrated. BTW, I am using octahedral PBC, but that should
>> not make a difference with respect to P coupling, should it? Below is my
>> whole mdp file. As a reminder my density in the system goes from 1.0 - .1 in
>> 10 ps with Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the
>> amount of time it takes for my system to expand increases but it still
>> expands.
>>
>>
> This seems truly bizarre.  How are you measuring the density (g_density,
> g_energy, etc)?


Both g_energy and g_density.


>  What are your box dimensions doing?  To get that kind of sudden change in
> density, your box dimensions would have to expand astronomically?


 Yep.

>
>
> It's also curious that your 425K-atom system only has a PE on the order of
> 10^5; my systems with 100K-200K have around 10^6 - 10^7; are you sure the
> minimization is reasonable, and you are not simply seeing the effects of the
> classic "blowing up" problem?


If that was the case would not the NVT also not behave stably? I also agree
that 10^5 seems to high. Most of that should come from water though,
correct? Why would the water not relax. Maybe I should just expand the box a
bit and see what happens?



>  What does your trajectory show?  If you have multiple proteins or other
> large species present, does minimization of each component individually
> prior to system assembly help?


I have one very large protein (antibody). I did do a gas
phase minimization of the protein prior to solvation and it does not help.
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Re: [gmx-users] Pressure Coupling Problem

[Justin A. Lemkul]

Joe Joe wrote:
So I got my small water box (800 waters) to behave stably with pressure 
coupling after more minimization but I still can't get my large system 
to work with pressure coupling. I tried minimizing but I can never get 
the Fmax to be less 10^2, which is pretty normal for protein/water 
simulations of large proteins, at least from my experience.  I have 
since run 400 ps NVT as the system (425K atoms) is quite stable. The 
 is 2E-05. Since I am using 4fs time steps gromacs won't let me 
use a tau_p less than .4. Not sure what else to do except run NVT, which 
is what I was going to do after I got the density equilibrated. BTW, I 
am using octahedral PBC, but that should not make a difference with 
respect to P coupling, should it? Below is my whole mdp file. As a 
reminder my density in the system goes from 1.0 - .1 in 10 ps with 
Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the amount 
of time it takes for my system to expand increases but it still expands.




This seems truly bizarre.  How are you measuring the density (g_density, 
g_energy, etc)?  What are your box dimensions doing?  To get that kind of sudden 
change in density, your box dimensions would have to expand astronomically?


It's also curious that your 425K-atom system only has a PE on the order of 10^5; 
my systems with 100K-200K have around 10^6 - 10^7; are you sure the minimization 
is reasonable, and you are not simply seeing the effects of the classic "blowing 
up" problem?  What does your trajectory show?  If you have multiple proteins or 
other large species present, does minimization of each component individually 
prior to system assembly help?


-Justin


;
;   File 'mdout.mdp' was generated
;   By user: relly (508)
;   On host: master.simprota.com 
;   At date: Fri Mar  6 20:17:33 2009
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include  =
; e.g.: -DI_Want_Cookies -DMe_Too
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.004
;nsteps   = 25
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; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files 
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simulation_part  = 1
init_step= 0
; mode for center of mass motion removal
comm_mode= linear
; number of steps for center of mass motion removal
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; group(s) for center of mass motion removal
comm_grps= system

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 10
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 12500
nstvout  = 0
nstfout  = 0
; Output frequency for energies to log file and energy file
nstlog   = 10
nstenergy= 10
; Output frequency and precision for xtc file
nstxtcout= 250
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = protein
; Selection of energy groups
energygrps   = Protein SOL

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
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; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = .9
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 80
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Switch
; cut-off lengths
rvdw-switch  = .8
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for t

Re: [gmx-users] Pressure Coupling Problem

[Joe Joe]

So I got my small water box (800 waters) to behave stably with pressure
coupling after more minimization but I still can't get my large system to
work with pressure coupling. I tried minimizing but I can never get the Fmax
to be less 10^2, which is pretty normal for protein/water simulations of
large proteins, at least from my experience.  I have since run 400 ps NVT as
the system (425K atoms) is quite stable. The  is 2E-05. Since I am
using 4fs time steps gromacs won't let me use a tau_p less than .4. Not sure
what else to do except run NVT, which is what I was going to do after I got
the density equilibrated. BTW, I am using octahedral PBC, but that should
not make a difference with respect to P coupling, should it? Below is my
whole mdp file. As a reminder my density in the system goes from 1.0 - .1 in
10 ps with Pcoupl = Berendsen and Tau_p = .4. If I increase Tau_P then the
amount of time it takes for my system to expand increases but it still
expands.
;
;   File 'mdout.mdp' was generated
;   By user: relly (508)
;   On host: master.simprota.com
;   At date: Fri Mar  6 20:17:33 2009
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include  =
; e.g.: -DI_Want_Cookies -DMe_Too
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.004
;nsteps   = 25
nsteps   = 250
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part  = 1
init_step= 0
; mode for center of mass motion removal
comm_mode= linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm_grps= system

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 10
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; TEST PARTICLE INSERTION OPTIONS
rtpi = 0.05

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 12500
nstvout  = 0
nstfout  = 0
; Output frequency for energies to log file and energy file
nstlog   = 10
nstenergy= 10
; Output frequency and precision for xtc file
nstxtcout= 250
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = protein
; Selection of energy groups
energygrps   = Protein SOL

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = .9
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 80
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Switch
; cut-off lengths
rvdw-switch  = .8
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1.e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstl

Re: [gmx-users] Pressure Coupling Problem

[Joe Joe]

On Wed, Apr 8, 2009 at 11:31 AM, Roland Schulz  wrote:

>
>
> On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe  wrote:
>
>> HI Chris,
>>
>> On Tue, Apr 7, 2009 at 9:31 PM,  wrote:
>>
>>> Hi Ilya,
>>>
>>> First thing that comes to mind is that it is strange to couple a
>>> coulombic switching function with PME. While this could possibly be done
>>> correctly, I doubt that it is in fact done in the way that you expect (i.e.
>>> correctly) in gromacs. In fact, I think that grompp/mdrun should probably
>>> throw an error here -- unless it is actually handled in the proper way, and
>>> a developer could help you here to figure out if you are indeed getting what
>>> you desire.
>>>
>>> coulombtype  = PME
>>> rcoulomb-switch  = .9
>>> rcoulomb = 1.0
>>
>>
>> I am pretty sure gromacs ignores the rcoulomb-switch parameter in the case
>> of PME but I will give it a try.
>>
>
> It is indeed supported and does work correctly. But you have to set
> coulombtype PME-Switch. mdp options says:
> "This is mainly useful constant energy simulations. For constant
> temperature simulations the advantage of improved energy conservation is
> usually outweighed by the small loss in accuracy of the electrostatics. "
>
> Roland
>

Yes, my point was that when electrostatics = PME then Gromacs ignores  the
rcoulomb-switch parameter.

>
>
>
>>
>>>
>>> Chris
>>>
>>> -- original message --
>>>
>>> Hi
>>> I am having some pressure coupling issues. I have a fairly large
>>> protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
>>> run NVE it conserves energy with appropriate parameter settings. If I run
>>> NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
>>> Rahman), the system just continuously expands. My parameters are as
>>> follows.
>>> Any ideas?
>>>
>>> Best,
>>>
>>> Ilya
>>>
>>> ;
>>> ;   File 'mdout.mdp' was generated
>>> ;   By user: relly (508)
>>> ;   On host: master.simprota.com
>>> ;   At date: Fri Mar  6 20:17:33 2009
>>> ;
>>>
>>> ; VARIOUS PREPROCESSING OPTIONS
>>> ; Preprocessor information: use cpp syntax.
>>> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
>>> include  =
>>> ; e.g.: -DI_Want_Cookies -DMe_Too
>>> define   =
>>>
>>> ; RUN CONTROL PARAMETERS
>>> integrator   = md
>>> ; Start time and timestep in ps
>>> tinit= 0
>>> dt   = 0.004
>>> ;nsteps   = 25
>>> nsteps   = 250
>>> ; For exact run continuation or redoing part of a run
>>> ; Part index is updated automatically on checkpointing (keeps files
>>> separate)
>>> simulation_part  = 1
>>> init_step= 0
>>> ; mode for center of mass motion removal
>>> comm_mode= linear
>>> ; number of steps for center of mass motion removal
>>> nstcomm  = 1
>>> ; group(s) for center of mass motion removal
>>> comm_grps= system
>>>
>>> ; OUTPUT CONTROL OPTIONS
>>> ; Output frequency for coords (x), velocities (v) and forces (f)
>>> nstxout  = 0
>>> nstvout  = 0
>>> nstfout  = 0
>>>
>>> ; Output frequency for energies to log file and energy file
>>> nstlog   = 10
>>> nstenergy= 10
>>> ; Output frequency and precision for xtc file
>>> nstxtcout= 250
>>> xtc-precision= 1000
>>> ; This selects the subset of atoms for the xtc file. You can
>>> ; select multiple groups. By default all atoms will be written.
>>> xtc-grps = protein
>>> ; Selection of energy groups
>>> energygrps   =
>>>
>>> ; NEIGHBORSEARCHING PARAMETERS
>>> ; nblist update frequency
>>> nstlist  = 5
>>> ; ns algorithm (simple or grid)
>>> ns_type  = grid
>>> ; Periodic boundary conditions: xyz, no, xy
>>> pbc  = xyz
>>> periodic_molecules   = no
>>> ; nblist cut-off
>>> rlist= 1.0
>>>
>>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>> ; Method for doing electrostatics
>>> coulombtype  = PME
>>> rcoulomb-switch  = .9
>>> rcoulomb = 1.0
>>> ; Relative dielectric constant for the medium and the reaction field
>>> epsilon-r= 80
>>> epsilon_rf   = 1
>>> ; Method for doing Van der Waals
>>> vdw-type = Switch
>>> ; cut-off lengths
>>> rvdw-switch  = .9
>>> rvdw = 1.0
>>> ; Apply long range dispersion corrections for Energy and Pressure
>>> DispCorr = EnerPres
>>> ; Extension of the potential lookup tables beyond the cut-off
>>> table-extension  = 1
>>> ; Seperate tables between energy group pairs
>>> energygrp_table  =
>>> ; Spacing for the PME/PPPM FFT grid
>>> fourierspacing   = 0.12
>>> ; FFT grid size, when a value is 0 fourierspacing will be used
>>> fourier_nx   = 0
>>> fourier_ny  

Re: [gmx-users] Pressure Coupling Problem

[Joe Joe]

I tried .1,  and 10 ps tau_p values. I guess I can try smaller values.


On Wed, Apr 8, 2009 at 10:44 AM, Justin A. Lemkul  wrote:

>
>
> Joe Joe wrote:
>
>> Hi Chris,
>>
>> When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I
>> set up the correct constraints. I've tested it and it conserves energy in
>> NVE. I run all he sims with constraints=all-bonds. I am now running a single
>> water box (800 water molecules) with 1s time steps and the volume keeps
>> blowing up.
>>
>
> In addition to what Chris has been saying about constraints, consider your
> pressure coupling settings themselves
>
> Pcoupl   = Berendsen
> Pcoupltype   = Isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p= 10
> compressibility  = 4.5e-5
> ref_p= 1.01325
>
> A 10-ps relaxation time for a system that is not necessarily
> well-equilibrated is too weak, I think.  Try 1.0 - 2.0 ps for tau_p.  If
> your system is expanding rapidly in as little as 5 ps, I would think you
> lack appropriate pressure regulation.
>
> -Justin
>
>  Thanks,
>>
>> Ilya
>>
>>
>> On Wed, Apr 8, 2009 at 8:37 AM, > chris.ne...@utoronto.ca>> wrote:
>>
>>Hi Ilya,
>>
>>If you did include the entire mdp file then you have a time step of
>>4 fs and no constraints (other than water). For a timestep of 2 fs,
>>you should constrain all-bonds (or some would say at least h-bonds)
>>and for 4 fs then you should also constrain angles involving
>>hydrogens (need a new .itp file for this).
>>
>>Can you try with a 1 fs timestep and see how it goes? Still, I am
>>surprised that everything works out at NVT, but this is certainly
>>worth the test.
>>
>>Do you have other systems running fine with these mdp options in NVT?
>>
>>Chris.
>>
>>-- original message --
>>
>>HI Chris,
>>
>>On Tue, Apr 7, 2009 at 9:31 PM, >> wrote:
>>
>>Hi Ilya,
>>
>>First thing that comes to mind is that it is strange to couple a
>>coulombic
>>switching function with PME. While this could possibly be done
>>correctly, I
>>doubt that it is in fact done in the way that you expect (i.e.
>>correctly) in
>>gromacs. In fact, I think that grompp/mdrun should probably
>>throw an error
>>here -- unless it is actually handled in the proper way, and a
>>developer
>>could help you here to figure out if you are indeed getting what
>>you desire.
>>
>>coulombtype  = PME
>>rcoulomb-switch  = .9
>>rcoulomb = 1.0
>>
>>
>>
>>I am pretty sure gromacs ignores the rcoulomb-switch parameter in
>>the case
>>of PME but I will give it a try.
>>
>>
>>
>>However, it is not clear to me that this should cause a system to
>>"continuously expand".
>>
>>Still, you do not give very good information about what you mean by
>>"continuously expand". Can you please provide some information
>>on that? e.g.
>>amount of time and total volume change.
>>
>>
>>
>>My box density goes from ~1.0 to .5 in 5 ps with a compressibility
>>of 5E-05.
>> It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06.
>>In both
>>case the slope of density(t) is negative and never levels off.
>>
>>
>>
>>Chris
>>
>>-- original message --
>>
>>Hi
>>I am having some pressure coupling issues. I have a fairly large
>>protein/water system 400K+ atoms. It minimizes just fine (F <
>>1000). If I
>>run NVE it conserves energy with appropriate parameter settings.
>>If I run
>>NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or
>> Parinello
>>Rahman), the system just continuously expands. My parameters are as
>>follows.
>>Any ideas?
>>
>>Best,
>>
>>Ilya
>>
>>;
>>;   File 'mdout.mdp' was generated
>>;   By user: relly (508)
>>;   On host: master.simprota.com 
>>
>>;   At date: Fri Mar  6 20:17:33 2009
>>;
>>
>>; VARIOUS PREPROCESSING OPTIONS
>>; Preprocessor information: use cpp syntax.
>>; e.g.: -I/home/joe/doe -I/home/mary/hoe
>>include  =
>>; e.g.: -DI_Want_Cookies -DMe_Too
>>define   =
>>
>>; RUN CONTROL PARAMETERS
>>integrator   = md
>>; Start time and timestep in ps
>>tinit= 0
>>dt   = 0.004
>>;nsteps   = 25
>>nsteps   = 250
>>; For exact run continuation or redoing part of a run
>>; Part index is updated automatically on checkpointing (keeps files
>>separate)
>>

Re: [gmx-users] Pressure Coupling Problem

[Joe Joe]

Yeah I only gave a partial. Tried to remove the QM params. I do use
constraints = all-bonds.


On Wed, Apr 8, 2009 at 9:18 AM,  wrote:

> You say "I run all he sims with constraints=all-bonds", but I don't see
> that in the mdp options that you provided. I even put your text in a file
> and grepped for it just to be sure. Did you only give us a partial mdp file?
>
> Try adding this to your mdp file:
>
> constraints =  all-bonds  ; REMOVE_FOR_EM
> constraint_algorithm=  lincs  ; REMOVE_FOR_EM
> lincs-iter  =  1  ; REMOVE_FOR_EM
> lincs-order =  6  ; REMOVE_FOR_EM
>
> see, for example,
> http://www.gromacs.org/pipermail/gmx-users/2008-October/037545.html
> http://www.gromacs.org/pipermail/gmx-users/2008-November/037673.html
>
> --- original message ---
>
>
> Hi Chris,
> When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I
> set up the correct constraints. I've tested it and it conserves energy in
> NVE. I run all he sims with constraints=all-bonds. I am now running a
> single
> water box (800 water molecules) with 1s time steps and the volume keeps
> blowing up.
>
> Thanks,
>
> Ilya
>
>
> On Wed, Apr 8, 2009 at 8:37 AM,  wrote:
>
>  Hi Ilya,
>>
>> If you did include the entire mdp file then you have a time step of 4 fs
>> and no constraints (other than water). For a timestep of 2 fs, you should
>> constrain all-bonds (or some would say at least h-bonds) and for 4 fs then
>> you should also constrain angles involving hydrogens (need a new .itp file
>> for this).
>>
>> Can you try with a 1 fs timestep and see how it goes? Still, I am
>> surprised
>> that everything works out at NVT, but this is certainly worth the test.
>>
>> Do you have other systems running fine with these mdp options in NVT?
>>
>> Chris.
>>
>> -- original message --
>>
>> HI Chris,
>>
>> On Tue, Apr 7, 2009 at 9:31 PM,  wrote:
>>
>>  Hi Ilya,
>>
>>>
>>> First thing that comes to mind is that it is strange to couple a
>>> coulombic
>>> switching function with PME. While this could possibly be done correctly,
>>> I
>>> doubt that it is in fact done in the way that you expect (i.e. correctly)
>>> in
>>> gromacs. In fact, I think that grompp/mdrun should probably throw an
>>> error
>>> here -- unless it is actually handled in the proper way, and a developer
>>> could help you here to figure out if you are indeed getting what you
>>> desire.
>>>
>>> coulombtype  = PME
>>> rcoulomb-switch  = .9
>>> rcoulomb = 1.0
>>>
>>>
>>
>> I am pretty sure gromacs ignores the rcoulomb-switch parameter in the case
>> of PME but I will give it a try.
>>
>>
>>
>>> However, it is not clear to me that this should cause a system to
>>> "continuously expand".
>>>
>>> Still, you do not give very good information about what you mean by
>>> "continuously expand". Can you please provide some information on that?
>>> e.g.
>>> amount of time and total volume change.
>>>
>>>
>>
>> My box density goes from ~1.0 to .5 in 5 ps with a compressibility of
>> 5E-05.
>>  It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06. In
>> both
>> case the slope of density(t) is negative and never levels off.
>>
>>
>>
>>  Chris
>>>
>>> -- original message --
>>>
>>> Hi
>>> I am having some pressure coupling issues. I have a fairly large
>>> protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
>>> run NVE it conserves energy with appropriate parameter settings. If I run
>>> NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
>>> Rahman), the system just continuously expands. My parameters are as
>>> follows.
>>> Any ideas?
>>>
>>> Best,
>>>
>>> Ilya
>>>
>>> ;
>>> ;   File 'mdout.mdp' was generated
>>> ;   By user: relly (508)
>>> ;   On host: master.simprota.com
>>> ;   At date: Fri Mar  6 20:17:33 2009
>>> ;
>>>
>>> ; VARIOUS PREPROCESSING OPTIONS
>>> ; Preprocessor information: use cpp syntax.
>>> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
>>> include  =
>>> ; e.g.: -DI_Want_Cookies -DMe_Too
>>> define   =
>>>
>>> ; RUN CONTROL PARAMETERS
>>> integrator   = md
>>> ; Start time and timestep in ps
>>> tinit= 0
>>> dt   = 0.004
>>> ;nsteps   = 25
>>> nsteps   = 250
>>> ; For exact run continuation or redoing part of a run
>>> ; Part index is updated automatically on checkpointing (keeps files
>>> separate)
>>> simulation_part  = 1
>>> init_step= 0
>>> ; mode for center of mass motion removal
>>> comm_mode= linear
>>> ; number of steps for center of mass motion removal
>>> nstcomm  = 1
>>> ; group(s) for center of mass motion removal
>>> comm_grps= system
>>>
>>> ; OUTPUT CONTROL OPTIONS
>>> ; Output frequency for coords (x), velocities (v) and forces (f)
>>> nstxout  = 0
>>> nstvout   

Re: [gmx-users] Pressure Coupling Problem

[Roland Schulz]

On Wed, Apr 8, 2009 at 7:53 AM, Joe Joe  wrote:

> HI Chris,
>
> On Tue, Apr 7, 2009 at 9:31 PM,  wrote:
>
>> Hi Ilya,
>>
>> First thing that comes to mind is that it is strange to couple a coulombic
>> switching function with PME. While this could possibly be done correctly, I
>> doubt that it is in fact done in the way that you expect (i.e. correctly) in
>> gromacs. In fact, I think that grompp/mdrun should probably throw an error
>> here -- unless it is actually handled in the proper way, and a developer
>> could help you here to figure out if you are indeed getting what you desire.
>>
>> coulombtype  = PME
>> rcoulomb-switch  = .9
>> rcoulomb = 1.0
>
>
> I am pretty sure gromacs ignores the rcoulomb-switch parameter in the case
> of PME but I will give it a try.
>

It is indeed supported and does work correctly. But you have to set
coulombtype PME-Switch. mdp options says:
"This is mainly useful constant energy simulations. For constant temperature
simulations the advantage of improved energy conservation is usually
outweighed by the small loss in accuracy of the electrostatics. "

Roland


>
>>
>> Chris
>>
>> -- original message --
>>
>> Hi
>> I am having some pressure coupling issues. I have a fairly large
>> protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
>> run NVE it conserves energy with appropriate parameter settings. If I run
>> NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
>> Rahman), the system just continuously expands. My parameters are as
>> follows.
>> Any ideas?
>>
>> Best,
>>
>> Ilya
>>
>> ;
>> ;   File 'mdout.mdp' was generated
>> ;   By user: relly (508)
>> ;   On host: master.simprota.com
>> ;   At date: Fri Mar  6 20:17:33 2009
>> ;
>>
>> ; VARIOUS PREPROCESSING OPTIONS
>> ; Preprocessor information: use cpp syntax.
>> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
>> include  =
>> ; e.g.: -DI_Want_Cookies -DMe_Too
>> define   =
>>
>> ; RUN CONTROL PARAMETERS
>> integrator   = md
>> ; Start time and timestep in ps
>> tinit= 0
>> dt   = 0.004
>> ;nsteps   = 25
>> nsteps   = 250
>> ; For exact run continuation or redoing part of a run
>> ; Part index is updated automatically on checkpointing (keeps files
>> separate)
>> simulation_part  = 1
>> init_step= 0
>> ; mode for center of mass motion removal
>> comm_mode= linear
>> ; number of steps for center of mass motion removal
>> nstcomm  = 1
>> ; group(s) for center of mass motion removal
>> comm_grps= system
>>
>> ; OUTPUT CONTROL OPTIONS
>> ; Output frequency for coords (x), velocities (v) and forces (f)
>> nstxout  = 0
>> nstvout  = 0
>> nstfout  = 0
>>
>> ; Output frequency for energies to log file and energy file
>> nstlog   = 10
>> nstenergy= 10
>> ; Output frequency and precision for xtc file
>> nstxtcout= 250
>> xtc-precision= 1000
>> ; This selects the subset of atoms for the xtc file. You can
>> ; select multiple groups. By default all atoms will be written.
>> xtc-grps = protein
>> ; Selection of energy groups
>> energygrps   =
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> ; nblist update frequency
>> nstlist  = 5
>> ; ns algorithm (simple or grid)
>> ns_type  = grid
>> ; Periodic boundary conditions: xyz, no, xy
>> pbc  = xyz
>> periodic_molecules   = no
>> ; nblist cut-off
>> rlist= 1.0
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> ; Method for doing electrostatics
>> coulombtype  = PME
>> rcoulomb-switch  = .9
>> rcoulomb = 1.0
>> ; Relative dielectric constant for the medium and the reaction field
>> epsilon-r= 80
>> epsilon_rf   = 1
>> ; Method for doing Van der Waals
>> vdw-type = Switch
>> ; cut-off lengths
>> rvdw-switch  = .9
>> rvdw = 1.0
>> ; Apply long range dispersion corrections for Energy and Pressure
>> DispCorr = EnerPres
>> ; Extension of the potential lookup tables beyond the cut-off
>> table-extension  = 1
>> ; Seperate tables between energy group pairs
>> energygrp_table  =
>> ; Spacing for the PME/PPPM FFT grid
>> fourierspacing   = 0.12
>> ; FFT grid size, when a value is 0 fourierspacing will be used
>> fourier_nx   = 0
>> fourier_ny   = 0
>> fourier_nz   = 0
>> ; EWALD/PME/PPPM parameters
>> pme_order= 4
>> ewald_rtol   = 1.e-05
>> ewald_geometry   = 3d
>> epsilon_surface  = 0
>> optimize_fft = no
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>> ; Temperature coupling
>> Tcoupl 

Re: [gmx-users] Pressure Coupling Problem

[Justin A. Lemkul]

Joe Joe wrote:

Hi Chris,

When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. 
I set up the correct constraints. I've tested it and it conserves energy 
in NVE. I run all he sims with constraints=all-bonds. I am now running a 
single water box (800 water molecules) with 1s time steps and the volume 
keeps blowing up. 



In addition to what Chris has been saying about constraints, consider your 
pressure coupling settings themselves


Pcoupl   = Berendsen
Pcoupltype   = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 10
compressibility  = 4.5e-5
ref_p= 1.01325

A 10-ps relaxation time for a system that is not necessarily well-equilibrated 
is too weak, I think.  Try 1.0 - 2.0 ps for tau_p.  If your system is expanding 
rapidly in as little as 5 ps, I would think you lack appropriate pressure 
regulation.


-Justin


Thanks,

Ilya


On Wed, Apr 8, 2009 at 8:37 AM, > wrote:


Hi Ilya,

If you did include the entire mdp file then you have a time step of
4 fs and no constraints (other than water). For a timestep of 2 fs,
you should constrain all-bonds (or some would say at least h-bonds)
and for 4 fs then you should also constrain angles involving
hydrogens (need a new .itp file for this).

Can you try with a 1 fs timestep and see how it goes? Still, I am
surprised that everything works out at NVT, but this is certainly
worth the test.

Do you have other systems running fine with these mdp options in NVT?

Chris.

-- original message --

HI Chris,

On Tue, Apr 7, 2009 at 9:31 PM, http://utoronto.ca>> wrote:

Hi Ilya,

First thing that comes to mind is that it is strange to couple a
coulombic
switching function with PME. While this could possibly be done
correctly, I
doubt that it is in fact done in the way that you expect (i.e.
correctly) in
gromacs. In fact, I think that grompp/mdrun should probably
throw an error
here -- unless it is actually handled in the proper way, and a
developer
could help you here to figure out if you are indeed getting what
you desire.

coulombtype  = PME
rcoulomb-switch  = .9
rcoulomb = 1.0



I am pretty sure gromacs ignores the rcoulomb-switch parameter in
the case
of PME but I will give it a try.



However, it is not clear to me that this should cause a system to
"continuously expand".

Still, you do not give very good information about what you mean by
"continuously expand". Can you please provide some information
on that? e.g.
amount of time and total volume change.



My box density goes from ~1.0 to .5 in 5 ps with a compressibility
of 5E-05.
 It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06.
In both
case the slope of density(t) is negative and never levels off.



Chris

-- original message --

Hi
I am having some pressure coupling issues. I have a fairly large
protein/water system 400K+ atoms. It minimizes just fine (F <
1000). If I
run NVE it conserves energy with appropriate parameter settings.
If I run
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
Rahman), the system just continuously expands. My parameters are as
follows.
Any ideas?

Best,

Ilya

;
;   File 'mdout.mdp' was generated
;   By user: relly (508)
;   On host: master.simprota.com 
;   At date: Fri Mar  6 20:17:33 2009
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include  =
; e.g.: -DI_Want_Cookies -DMe_Too
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.004
;nsteps   = 25
nsteps   = 250
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part  = 1
init_step= 0
; mode for center of mass motion removal
comm_mode= linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm_grps= system

; OUTPUT CONTROL OPTIONS
; Output frequency for co

[gmx-users] Pressure Coupling Problem

[chris . neale]

You say "I run all he sims with constraints=all-bonds", but I don't  
see that in the mdp options that you provided. I even put your text in  
a file and grepped for it just to be sure. Did you only give us a  
partial mdp file?


Try adding this to your mdp file:

constraints =  all-bonds  ; REMOVE_FOR_EM
constraint_algorithm=  lincs  ; REMOVE_FOR_EM
lincs-iter  =  1  ; REMOVE_FOR_EM
lincs-order =  6  ; REMOVE_FOR_EM

see, for example,
http://www.gromacs.org/pipermail/gmx-users/2008-October/037545.html
http://www.gromacs.org/pipermail/gmx-users/2008-November/037673.html

--- original message ---


Hi Chris,
When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I
set up the correct constraints. I've tested it and it conserves energy in
NVE. I run all he sims with constraints=all-bonds. I am now running a single
water box (800 water molecules) with 1s time steps and the volume keeps
blowing up.

Thanks,

Ilya


On Wed, Apr 8, 2009 at 8:37 AM,  wrote:


Hi Ilya,

If you did include the entire mdp file then you have a time step of 4 fs
and no constraints (other than water). For a timestep of 2 fs, you should
constrain all-bonds (or some would say at least h-bonds) and for 4 fs then
you should also constrain angles involving hydrogens (need a new .itp file
for this).

Can you try with a 1 fs timestep and see how it goes? Still, I am surprised
that everything works out at NVT, but this is certainly worth the test.

Do you have other systems running fine with these mdp options in NVT?

Chris.

-- original message --

HI Chris,

On Tue, Apr 7, 2009 at 9:31 PM,  wrote:

 Hi Ilya,


First thing that comes to mind is that it is strange to couple a coulombic
switching function with PME. While this could possibly be done correctly,
I
doubt that it is in fact done in the way that you expect (i.e. correctly)
in
gromacs. In fact, I think that grompp/mdrun should probably throw an error
here -- unless it is actually handled in the proper way, and a developer
could help you here to figure out if you are indeed getting what you
desire.

coulombtype  = PME
rcoulomb-switch  = .9
rcoulomb = 1.0




I am pretty sure gromacs ignores the rcoulomb-switch parameter in the case
of PME but I will give it a try.




However, it is not clear to me that this should cause a system to
"continuously expand".

Still, you do not give very good information about what you mean by
"continuously expand". Can you please provide some information on that?
e.g.
amount of time and total volume change.




My box density goes from ~1.0 to .5 in 5 ps with a compressibility of
5E-05.
 It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06. In
both
case the slope of density(t) is negative and never levels off.




Chris

-- original message --

Hi
I am having some pressure coupling issues. I have a fairly large
protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
run NVE it conserves energy with appropriate parameter settings. If I run
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
Rahman), the system just continuously expands. My parameters are as
follows.
Any ideas?

Best,

Ilya

;
;   File 'mdout.mdp' was generated
;   By user: relly (508)
;   On host: master.simprota.com
;   At date: Fri Mar  6 20:17:33 2009
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include  =
; e.g.: -DI_Want_Cookies -DMe_Too
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.004
;nsteps   = 25
nsteps   = 250
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part  = 1
init_step= 0
; mode for center of mass motion removal
comm_mode= linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm_grps= system

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 0
nstvout  = 0
nstfout  = 0

; Output frequency for energies to log file and energy file
nstlog   = 10
nstenergy= 10
; Output frequency and precision for xtc file
nstxtcout= 250
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = protein
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algori

Re: [gmx-users] Pressure Coupling Problem

[Joe Joe]

Hi Chris,
When I create the topology for the 4fs timestep I use pdb2gmx -vsite h. I
set up the correct constraints. I've tested it and it conserves energy in
NVE. I run all he sims with constraints=all-bonds. I am now running a single
water box (800 water molecules) with 1s time steps and the volume keeps
blowing up.

Thanks,

Ilya


On Wed, Apr 8, 2009 at 8:37 AM,  wrote:

> Hi Ilya,
>
> If you did include the entire mdp file then you have a time step of 4 fs
> and no constraints (other than water). For a timestep of 2 fs, you should
> constrain all-bonds (or some would say at least h-bonds) and for 4 fs then
> you should also constrain angles involving hydrogens (need a new .itp file
> for this).
>
> Can you try with a 1 fs timestep and see how it goes? Still, I am surprised
> that everything works out at NVT, but this is certainly worth the test.
>
> Do you have other systems running fine with these mdp options in NVT?
>
> Chris.
>
> -- original message --
>
> HI Chris,
>
> On Tue, Apr 7, 2009 at 9:31 PM,  wrote:
>
>  Hi Ilya,
>>
>> First thing that comes to mind is that it is strange to couple a coulombic
>> switching function with PME. While this could possibly be done correctly,
>> I
>> doubt that it is in fact done in the way that you expect (i.e. correctly)
>> in
>> gromacs. In fact, I think that grompp/mdrun should probably throw an error
>> here -- unless it is actually handled in the proper way, and a developer
>> could help you here to figure out if you are indeed getting what you
>> desire.
>>
>> coulombtype  = PME
>> rcoulomb-switch  = .9
>> rcoulomb = 1.0
>>
>
>
> I am pretty sure gromacs ignores the rcoulomb-switch parameter in the case
> of PME but I will give it a try.
>
>
>>
>> However, it is not clear to me that this should cause a system to
>> "continuously expand".
>>
>> Still, you do not give very good information about what you mean by
>> "continuously expand". Can you please provide some information on that?
>> e.g.
>> amount of time and total volume change.
>>
>
>
> My box density goes from ~1.0 to .5 in 5 ps with a compressibility of
> 5E-05.
>  It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06. In
> both
> case the slope of density(t) is negative and never levels off.
>
>
>
>> Chris
>>
>> -- original message --
>>
>> Hi
>> I am having some pressure coupling issues. I have a fairly large
>> protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
>> run NVE it conserves energy with appropriate parameter settings. If I run
>> NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
>> Rahman), the system just continuously expands. My parameters are as
>> follows.
>> Any ideas?
>>
>> Best,
>>
>> Ilya
>>
>> ;
>> ;   File 'mdout.mdp' was generated
>> ;   By user: relly (508)
>> ;   On host: master.simprota.com
>> ;   At date: Fri Mar  6 20:17:33 2009
>> ;
>>
>> ; VARIOUS PREPROCESSING OPTIONS
>> ; Preprocessor information: use cpp syntax.
>> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
>> include  =
>> ; e.g.: -DI_Want_Cookies -DMe_Too
>> define   =
>>
>> ; RUN CONTROL PARAMETERS
>> integrator   = md
>> ; Start time and timestep in ps
>> tinit= 0
>> dt   = 0.004
>> ;nsteps   = 25
>> nsteps   = 250
>> ; For exact run continuation or redoing part of a run
>> ; Part index is updated automatically on checkpointing (keeps files
>> separate)
>> simulation_part  = 1
>> init_step= 0
>> ; mode for center of mass motion removal
>> comm_mode= linear
>> ; number of steps for center of mass motion removal
>> nstcomm  = 1
>> ; group(s) for center of mass motion removal
>> comm_grps= system
>>
>> ; OUTPUT CONTROL OPTIONS
>> ; Output frequency for coords (x), velocities (v) and forces (f)
>> nstxout  = 0
>> nstvout  = 0
>> nstfout  = 0
>>
>> ; Output frequency for energies to log file and energy file
>> nstlog   = 10
>> nstenergy= 10
>> ; Output frequency and precision for xtc file
>> nstxtcout= 250
>> xtc-precision= 1000
>> ; This selects the subset of atoms for the xtc file. You can
>> ; select multiple groups. By default all atoms will be written.
>> xtc-grps = protein
>> ; Selection of energy groups
>> energygrps   =
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> ; nblist update frequency
>> nstlist  = 5
>> ; ns algorithm (simple or grid)
>> ns_type  = grid
>> ; Periodic boundary conditions: xyz, no, xy
>> pbc  = xyz
>> periodic_molecules   = no
>> ; nblist cut-off
>> rlist= 1.0
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> ; Method for doing electrostatics
>> coulombtype  = PME
>> rcoulomb-switch 

[gmx-users] Pressure Coupling Problem

[chris . neale]

Hi Ilya,

If you did include the entire mdp file then you have a time step of 4  
fs and no constraints (other than water). For a timestep of 2 fs, you  
should constrain all-bonds (or some would say at least h-bonds) and  
for 4 fs then you should also constrain angles involving hydrogens  
(need a new .itp file for this).


Can you try with a 1 fs timestep and see how it goes? Still, I am  
surprised that everything works out at NVT, but this is certainly  
worth the test.


Do you have other systems running fine with these mdp options in NVT?

Chris.

-- original message --

HI Chris,

On Tue, Apr 7, 2009 at 9:31 PM,  wrote:


Hi Ilya,

First thing that comes to mind is that it is strange to couple a coulombic
switching function with PME. While this could possibly be done correctly, I
doubt that it is in fact done in the way that you expect (i.e. correctly) in
gromacs. In fact, I think that grompp/mdrun should probably throw an error
here -- unless it is actually handled in the proper way, and a developer
could help you here to figure out if you are indeed getting what you desire.

coulombtype  = PME
rcoulomb-switch  = .9
rcoulomb = 1.0



I am pretty sure gromacs ignores the rcoulomb-switch parameter in the case
of PME but I will give it a try.




However, it is not clear to me that this should cause a system to
"continuously expand".

Still, you do not give very good information about what you mean by
"continuously expand". Can you please provide some information on that? e.g.
amount of time and total volume change.



My box density goes from ~1.0 to .5 in 5 ps with a compressibility of 5E-05.
 It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06. In both
case the slope of density(t) is negative and never levels off.




Chris

-- original message --

Hi
I am having some pressure coupling issues. I have a fairly large
protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
run NVE it conserves energy with appropriate parameter settings. If I run
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
Rahman), the system just continuously expands. My parameters are as
follows.
Any ideas?

Best,

Ilya

;
;   File 'mdout.mdp' was generated
;   By user: relly (508)
;   On host: master.simprota.com
;   At date: Fri Mar  6 20:17:33 2009
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include  =
; e.g.: -DI_Want_Cookies -DMe_Too
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.004
;nsteps   = 25
nsteps   = 250
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part  = 1
init_step= 0
; mode for center of mass motion removal
comm_mode= linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm_grps= system

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 0
nstvout  = 0
nstfout  = 0

; Output frequency for energies to log file and energy file
nstlog   = 10
nstenergy= 10
; Output frequency and precision for xtc file
nstxtcout= 250
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = protein
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = .9
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 80
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Switch
; cut-off lengths
rvdw-switch  = .9
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_

Re: [gmx-users] Pressure Coupling Problem

[Joe Joe]

HI Chris,

On Tue, Apr 7, 2009 at 9:31 PM,  wrote:

> Hi Ilya,
>
> First thing that comes to mind is that it is strange to couple a coulombic
> switching function with PME. While this could possibly be done correctly, I
> doubt that it is in fact done in the way that you expect (i.e. correctly) in
> gromacs. In fact, I think that grompp/mdrun should probably throw an error
> here -- unless it is actually handled in the proper way, and a developer
> could help you here to figure out if you are indeed getting what you desire.
>
> coulombtype  = PME
> rcoulomb-switch  = .9
> rcoulomb = 1.0


I am pretty sure gromacs ignores the rcoulomb-switch parameter in the case
of PME but I will give it a try.

>
>
> However, it is not clear to me that this should cause a system to
> "continuously expand".
>
> Still, you do not give very good information about what you mean by
> "continuously expand". Can you please provide some information on that? e.g.
> amount of time and total volume change.


My box density goes from ~1.0 to .5 in 5 ps with a compressibility of 5E-05.
 It goes from ~1.0 to .94 in 300 ps with a compressibility of 5E-06. In both
case the slope of density(t) is negative and never levels off.


>
> Chris
>
> -- original message --
>
> Hi
> I am having some pressure coupling issues. I have a fairly large
> protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
> run NVE it conserves energy with appropriate parameter settings. If I run
> NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
> Rahman), the system just continuously expands. My parameters are as
> follows.
> Any ideas?
>
> Best,
>
> Ilya
>
> ;
> ;   File 'mdout.mdp' was generated
> ;   By user: relly (508)
> ;   On host: master.simprota.com
> ;   At date: Fri Mar  6 20:17:33 2009
> ;
>
> ; VARIOUS PREPROCESSING OPTIONS
> ; Preprocessor information: use cpp syntax.
> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
> include  =
> ; e.g.: -DI_Want_Cookies -DMe_Too
> define   =
>
> ; RUN CONTROL PARAMETERS
> integrator   = md
> ; Start time and timestep in ps
> tinit= 0
> dt   = 0.004
> ;nsteps   = 25
> nsteps   = 250
> ; For exact run continuation or redoing part of a run
> ; Part index is updated automatically on checkpointing (keeps files
> separate)
> simulation_part  = 1
> init_step= 0
> ; mode for center of mass motion removal
> comm_mode= linear
> ; number of steps for center of mass motion removal
> nstcomm  = 1
> ; group(s) for center of mass motion removal
> comm_grps= system
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout  = 0
> nstvout  = 0
> nstfout  = 0
>
> ; Output frequency for energies to log file and energy file
> nstlog   = 10
> nstenergy= 10
> ; Output frequency and precision for xtc file
> nstxtcout= 250
> xtc-precision= 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps = protein
> ; Selection of energy groups
> energygrps   =
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist  = 5
> ; ns algorithm (simple or grid)
> ns_type  = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc  = xyz
> periodic_molecules   = no
> ; nblist cut-off
> rlist= 1.0
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype  = PME
> rcoulomb-switch  = .9
> rcoulomb = 1.0
> ; Relative dielectric constant for the medium and the reaction field
> epsilon-r= 80
> epsilon_rf   = 1
> ; Method for doing Van der Waals
> vdw-type = Switch
> ; cut-off lengths
> rvdw-switch  = .9
> rvdw = 1.0
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension  = 1
> ; Seperate tables between energy group pairs
> energygrp_table  =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing   = 0.12
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> ; EWALD/PME/PPPM parameters
> pme_order= 4
> ewald_rtol   = 1.e-05
> ewald_geometry   = 3d
> epsilon_surface  = 0
> optimize_fft = no
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl 

[gmx-users] Pressure Coupling Problem

[Joe Joe]

Hi
I am having some pressure coupling issues. I have a fairly large
protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
run NVE it conserves energy with appropriate parameter settings. If I run
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
Rahman), the system just continuously expands. My parameters are as follows.
Any ideas?

Best,

Ilya

;
;   File 'mdout.mdp' was generated
;   By user: relly (508)
;   On host: master.simprota.com
;   At date: Fri Mar  6 20:17:33 2009
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include  =
; e.g.: -DI_Want_Cookies -DMe_Too
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.004
;nsteps   = 25
nsteps   = 250
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part  = 1
init_step= 0
; mode for center of mass motion removal
comm_mode= linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm_grps= system

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 0
nstvout  = 0
nstfout  = 0

; Output frequency for energies to log file and energy file
nstlog   = 10
nstenergy= 10
; Output frequency and precision for xtc file
nstxtcout= 250
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = protein
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = .9
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 80
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Switch
; cut-off lengths
rvdw-switch  = .9
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1.e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl   = V-rescale
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 298.0
; Pressure coupling
Pcoupl   = Berendsen
Pcoupltype   = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 10
compressibility  = 4.5e-5
ref_p= 1.01325
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed= 815131
___
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[gmx-users] Pressure Coupling Problem

[chris . neale]

Hi Ilya,

First thing that comes to mind is that it is strange to couple a  
coulombic switching function with PME. While this could possibly be  
done correctly, I doubt that it is in fact done in the way that you  
expect (i.e. correctly) in gromacs. In fact, I think that grompp/mdrun  
should probably throw an error here -- unless it is actually handled  
in the proper way, and a developer could help you here to figure out  
if you are indeed getting what you desire.


coulombtype  = PME
rcoulomb-switch  = .9
rcoulomb = 1.0

However, it is not clear to me that this should cause a system to  
"continuously expand".


Still, you do not give very good information about what you mean by  
"continuously expand". Can you please provide some information on  
that? e.g. amount of time and total volume change.


Chris

-- original message --

Hi
I am having some pressure coupling issues. I have a fairly large
protein/water system 400K+ atoms. It minimizes just fine (F < 1000). If I
run NVE it conserves energy with appropriate parameter settings. If I run
NVT it is stable. When I turn on Pcoupl (i.e. Berendsen or Parinello
Rahman), the system just continuously expands. My parameters are as follows.
Any ideas?

Best,

Ilya

;
;   File 'mdout.mdp' was generated
;   By user: relly (508)
;   On host: master.simprota.com
;   At date: Fri Mar  6 20:17:33 2009
;

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include  =
; e.g.: -DI_Want_Cookies -DMe_Too
define   =

; RUN CONTROL PARAMETERS
integrator   = md
; Start time and timestep in ps
tinit= 0
dt   = 0.004
;nsteps   = 25
nsteps   = 250
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps files
separate)
simulation_part  = 1
init_step= 0
; mode for center of mass motion removal
comm_mode= linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm_grps= system

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 0
nstvout  = 0
nstfout  = 0

; Output frequency for energies to log file and energy file
nstlog   = 10
nstenergy= 10
; Output frequency and precision for xtc file
nstxtcout= 250
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps = protein
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 5
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz, no, xy
pbc  = xyz
periodic_molecules   = no
; nblist cut-off
rlist= 1.0

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = .9
rcoulomb = 1.0
; Relative dielectric constant for the medium and the reaction field
epsilon-r= 80
epsilon_rf   = 1
; Method for doing Van der Waals
vdw-type = Switch
; cut-off lengths
rvdw-switch  = .9
rvdw = 1.0
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Seperate tables between energy group pairs
energygrp_table  =
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters
pme_order= 4
ewald_rtol   = 1.e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
Tcoupl   = V-rescale
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 298.0
; Pressure coupling
Pcoupl   = Berendsen
Pcoupltype   = Isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p= 10
compressibility  = 4.5e-5
ref_p= 1.01325
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No
; Random seed for Andersen thermostat
andersen_seed= 815131
---

[gmx-users] Pressure coupling

[Matteus Lindgren]

Hi all!

I am quite new to Gromacs and am wondering why I can´t see any box
fluctuations during a NPT run of protein + urea solvent in dodecahedron. In
the energy output file I can see that the Box-X,Y,Z values only fluctuate
<1%. 

However the pressure average is reasonably close to the ref_p value, 1.7
instead of 1.0 during 20ns. Should there not be any box fluctuations with
the parrinello-rahman algorithm? 

 

I use the input settings specified below.

title= Dyna

cpp  = /usr/bin/cpp

constraints  = hbonds

constraint_algorithm = lincs

lincs_iter   = 1

integrator   = md

dt   = 0.002

nsteps   = 800

nstxout  = 400

nstvout  = 3000

nstlog   = 250

nstenergy= 250

nstxtcout= 250

xtc_grps = 

energygrps   = Protein  SOLUREA CL-

nstlist  = 5

ns_type  = grid

rlist= 1.1

coulombtype  = PME

rcoulomb = 1.1

rvdw = 1.4

fourierspacing   = 0.14

pme_order= 6

optimize_fft = yes

tcoupl   = nose-hoover

tc-grps  = Protein  SOLUREA CL-

tau_t= 0.5  0.5  0.5   0.0

ref_t= 308  308  308   308

Pcoupl   = parrinello-rahman

tau_p= 1.0

compressibility  = 4.5e-5

ref_p= 1.0

 

Thank you!

Regards

 

Matteus Lindgren 

Graduate student 

 

Department of Chemistry
Umeå University
SE-901 87 Umeå, Sweden
Tel: +46 (0)90 786 53 68
e-mail:   [EMAIL PROTECTED]

 

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[gmx-users] pressure coupling for self-assembly of bilayer

[LeeHwan-kyu]

Dear GMX-users,

I'm trying to do self-assembly of bilayer. I'm using coarse-grained model 
(MARTINI), and there are 1280 CG lipids and 30110 CG waters. I followed 
procedures of Marrink and de Vries's atomistic simulations of the bilayer 
self-assembly.  So, I simulated the randomly-positioned system with isotropic 
pressures for a while, and then run the system with anisotropic pressure (shown 
below).  I've tried this a couple of times, but I always got tilted multiple 
bilayers (due to anisotropic pressure, the box x,y,z dimensions become even 
awkward.).   How can I get only one bilayer (normal to z-direction) ?   Do I 
need to apply other pressure couplings?  Or, am I using too much water?
 
Thanks for your help in advance.

best,
Hwankyu.


tau_p= 0.2   0.2   0.2   0.2   0.2   0.2
compressibility   = 3e-5 3e-5 3e-5 3e-5 3e-5 3e-5 
ref_p= 1.0   1.0   1.0   1.0   1.0   1.0
---
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[gmx-users] Pressure Coupling for DPPC Bilayers

[Sona Aramyan]

Hello,

 Would the following be a reasonable way to implement
anisotropic pressure coupling, for a 128 DPPC /3655
water bilayer with an aminoacid on it:

 ; Pressure coupling is on
 Pcoupl = parrinello-rahman 
 pcoupltype = anisotropic 
 tau_p = 1.0 1.0 1.0 0 0 0
 compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
 ref_p = 1.0 1.0 1.0 0 0 0


Beforehand thank you very very much.


  

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Re: [gmx-users] pressure coupling for bilayers

[Xavier Periole]

semiisotropic is more indicated for bilayers.

 pragya chohan <[EMAIL PROTECTED]> wrote:


hi i want to rum a NPT ensemble on my bilayer+protein system. What is the 
best pcoupletype to use. I have seen some posts on gmx user group advising 
anisotriopic type with 
tau_p 5.0 ps

cpmpressibility: 4.5e-5 4.5e-5 4.5e-5 0.0  0.0 0.0

Another suggestion is welcome.
Thanks in advance
Pragya

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-
XAvier Periole - PhD

1- Institute of Molecular Assemblies
 City University of New York - USA
2- Molecular Dynamics-Group
 University of Groningen - The Netherlands
http://md.chem.rug.nl/~periole
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[gmx-users] pressure coupling for bilayers

[pragya chohan]

hi i want to rum a NPT ensemble on my bilayer+protein system. What is the best 
pcoupletype to use. I have seen some posts on gmx user group advising 
anisotriopic type with 
tau_p 5.0 ps
cpmpressibility: 4.5e-5 4.5e-5 4.5e-5 0.0  0.0 0.0

Another suggestion is welcome.
Thanks in advance
Pragya

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[gmx-users] Pressure coupling and tau_p values

[chris . neale]

For example, a 3ns simulation using a tau_p of 0.5 I get
a surface tension of 30 dynes/cm and using a tau_p of 5.0 I get a surface
tension of 25 dynes/cm.


First thing that comes to mind is that your area per lipid is not at  
equilibrium. Assuming that your bilayer normal lies in the Z  
dimension, plot your xy area vs. simulation time. My bet is that it is  
not converged and that the run using a tau_p of 0.5 is approaching  
convergence faster than the run using a tau_p of 5.0. Once it is  
converged, I would recommend something more like 20ns for a production  
run.



Is this difference negligible?


Test that out yourself. Do some repeats, or perhaps take the 3ns  
snapshot from the simulation at tau_p of 0.5 and continue it using a  
tau_p of 5.0. Also take the 3ns snapshot from the simulation at tau_p  
of 5.0 and continue it using a tau_p of 0.5.



Therefore, is it more reliable when simulating a lipid
bilayer system to use a short tau_p ~0.5ps or a longer tau_p ~ 5.0ps?


Sorry, I don't know the answer to that one.

Chris.

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[gmx-users] Pressure coupling and tau_p values

[toma0052]

Hello,
 I am simulating a lipid bilayer system under a shear stress, in which I
am interested in looking at the surface tension.  I have done a number of
simulations in an NPT ensemble using semiisotropic Berendsen pressure
coupling.  For a system such as this, I am wondering what would be an optimal
tau_p because I seem to be getting slightly different results dependent on
the value I choose.  For example, a 3ns simulation using a tau_p of 0.5 I get
a surface tension of 30 dynes/cm and using a tau_p of 5.0 I get a surface
tension of 25 dynes/cm.  Is this difference negligible?
 I have looked into this a bit, and I have seen a number of publications
in which people have used Berendsen pressure coupling in a lipid bilayer
system with a coupling constant of 0.5 or 1.0ps.  However, in the mailing
list, there are some posts in which it is recommended that one use a tau_p of
5.0ps to 10.0ps due to semiisotropic coupling not having the averaging effect
of isotropic coupling and using a small coupling time can add excessive noise
to the system.  Therefore, is it more reliable when simulating a lipid
bilayer system to use a short tau_p ~0.5ps or a longer tau_p ~ 5.0ps? 

Thank you,
Mike Tomasini

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Re: [gmx-users] Pressure Coupling

[George Abadir]

Thank you very much for the reply, and I'll try to better search the 
board first :)

Cheers,
George

Dallas B. Warren wrote:


Issue like this has been discussed previously, try searching the
emailing list for a solution first before posting.  Means you get your
answer faster :-)

Pressure is a macroscopic property that is being monitored and adjusted
on a microscopic scale.

A variation of that order is entirely normal.  How much and quickly it
varies depends on what type of coupling you use and the coupling
constants.  My own simulations oscillate between roughly 400 bar and
-400 bar.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.


 



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RE: [gmx-users] Pressure Coupling

[Dallas B. Warren]

Issue like this has been discussed previously, try searching the
emailing list for a solution first before posting.  Means you get your
answer faster :-)

Pressure is a macroscopic property that is being monitored and adjusted
on a microscopic scale.

A variation of that order is entirely normal.  How much and quickly it
varies depends on what type of coupling you use and the coupling
constants.  My own simulations oscillate between roughly 400 bar and
-400 bar.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
-
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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[gmx-users] Pressure Coupling

[George Abadir]

Hi,
I want to fix the pressure during the simulation so I use pressure 
coupling. I set the reference potential to 1 (the unit is bar as the 
manual says). Nevertheless, the log file shows much higher pressures 
(can reach the order of  1e+03 and again it seems the unit is bar). 
Moreover, it fluctuates alot, both for Berendsen and Parrinello-Rahman 
coupling. Can anybody help me to identify the reason?

Thank you very much,
Regards,
George
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Re: [gmx-users] Pressure coupling question

[David van der Spoel]

toma0052 wrote:

Hello,
 I am simulating a lipid bilayer system, and am having some trouble
understanding the pressure output.  When I run a simulation, even when I do
not add any perturbations or fix any atoms, the pressure oscillations are
quite large.  The temperature coupling seems fine.  After about 1ps, the
system is near the reference temperature, and the oscillations are only about
1 or 2 degrees.  So, I expected something, roughly, similar with the
pressure.  For the pressure, however, my reference pressure is 1.0 bar, but
the pressure in the system after a few picoseconds seems to range from -400
to 400 bar.  Is this normal?  Do I just need to wait longer?  Does this mean
that I did not run the energy minimization long enough and there are some
high forces?  Is there something else that I am doing wrong?
 In my mdp file, the pressure coupling looks like:
Pcoupl   = berendsen
Pcoupltype   = isotropic
tau_p= 0.5
compressibility  = 4e-5
ref_p= 1.0

I have also tried Parrinello-Rahman pressure coupling with the same result.

Thanks
Mike

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this is normal.
increase your system size to reduce the fluctuations. scales as sqrt(n) :(.

--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Pressure coupling question

[toma0052]

Hello,
 I am simulating a lipid bilayer system, and am having some trouble
understanding the pressure output.  When I run a simulation, even when I do
not add any perturbations or fix any atoms, the pressure oscillations are
quite large.  The temperature coupling seems fine.  After about 1ps, the
system is near the reference temperature, and the oscillations are only about
1 or 2 degrees.  So, I expected something, roughly, similar with the
pressure.  For the pressure, however, my reference pressure is 1.0 bar, but
the pressure in the system after a few picoseconds seems to range from -400
to 400 bar.  Is this normal?  Do I just need to wait longer?  Does this mean
that I did not run the energy minimization long enough and there are some
high forces?  Is there something else that I am doing wrong?
 In my mdp file, the pressure coupling looks like:
Pcoupl   = berendsen
Pcoupltype   = isotropic
tau_p= 0.5
compressibility  = 4e-5
ref_p= 1.0

I have also tried Parrinello-Rahman pressure coupling with the same result.

Thanks
Mike

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Re: [gmx-users] Pressure coupling appears to produce errors on the P655+ aix 5.2

[David van der Spoel]

Arthur Roberts wrote:

Hi, All,

I would like to thank Carsten Kutzner, Erik Lindahl,
and David van der Spoel for their advise with my
previous problem with not getting any data with mdrun.
 It turned out to be due to the fourier spacing and
the PME order.  In addition, David van der Spoel's
suggestion of using a water shell was quite useful for
troubleshooting.

I have a new problem:

When pressure coupling is used with mdrun, I get the
following error: 


Step 209  Warning: pressure scaling more than 1%, mu:
1.02233 1.02233 1.02233

I tried lengthening the tau_p to 4, but it didn't help
as recommended for a similar problem in the mail
archives.



is the system well minimized and equilibrated?
you can try running without pressure coupling for a while.
then you can try running without PME for testing only..


Details of the problem can be found here:

http://cetus.mchem.washington.edu/pub/supercomputer/Pressure%20causes%20errors.html

Best wishes,
Art
University of Washington
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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] Pressure coupling appears to produce errors on the P655+ aix 5.2

[Arthur Roberts]

Hi, All,

I would like to thank Carsten Kutzner, Erik Lindahl,
and David van der Spoel for their advise with my
previous problem with not getting any data with mdrun.
 It turned out to be due to the fourier spacing and
the PME order.  In addition, David van der Spoel's
suggestion of using a water shell was quite useful for
troubleshooting.

I have a new problem:

When pressure coupling is used with mdrun, I get the
following error: 

Step 209  Warning: pressure scaling more than 1%, mu:
1.02233 1.02233 1.02233

I tried lengthening the tau_p to 4, but it didn't help
as recommended for a similar problem in the mail
archives.

Details of the problem can be found here:

http://cetus.mchem.washington.edu/pub/supercomputer/Pressure%20causes%20errors.html

Best wishes,
Art
University of Washington
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Re: [gmx-users] Pressure Coupling for Lipid Bilayers

[Erik Lindahl]

Hi,


On May 11, 2006, at 6:05 PM, Arneh Babakhani wrote:


Hello,

Would the following be a reasonable way to implement semiisotropic  
pressure coupling, for a 128 DMPC membrane:


; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 1.0 1.0
compressibility = 4.5e-5 1.0e-30
ref_p = 1.0 1.0


I would use slower scaling, e.g. tau_p = 10ps.  The inherent  
relaxation is on the order of nanoseconds anyway, so by using a too  
short time you only add noise and risk risk system crashes due to  
excessively hard scaling.


However, you should be aware that semi-isotropic scaling might affect  
the properties if the membrane since it removes the x-y fluctuations.  
On the other hand, anisotropic scaling probably over-estimates them  
due to PBC.


It was a hack I introduced a long time ago when 64 lipid systems were  
common, and I'm still not sure whether it's better or worse than  
anisotropic scaling...


Cheers,

Erik


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[gmx-users] Pressure Coupling for Lipid Bilayers

[Arneh Babakhani]

Hello,

Would the following be a reasonable way to implement semiisotropic 
pressure coupling, for a 128 DMPC membrane:


; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = semiisotropic
tau_p = 1.0 1.0
compressibility = 4.5e-5 1.0e-30
ref_p = 1.0 1.0

[I'm not asking whether this will produce the right membrane 
properties.  I know there's some trial & error involved in this. I'm 
just wondering if this is one possible way to use pressure]. 


Thanks,

Arneh
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