[gmx-users] Semiisotropic pressure coupling problem

[congchen]

 

Dear Gromacs users,
  I am doing a simulation on CO2/water interface. Two separate simulations (NPT) have been done sucessfully for pure CO2 and pure water systems. Then two CO2 gro files and one water gro files were connected into one single gro files for CO2/water interface (CO2/water/CO2).
  The CO2/water system was simulated in NVT ensemble first with water molecules fixed in positions for 500ps,  and then the position constraints were removed and further 500ps simulation run were made. The temperature were coupled with v-rescale method and the average value was exactly the same as the target temperature. The CO2/water system was further simulated in NPT ensemble for 3000ps, but the result seems quite bad. The average values of temperature and pressure are 344.7K and -6.89249e+02 bar, respectively, which are quite different from the targets.
  The reason may be that the system is far from equilibrium, but the simulation time for 3ns is enough for my opinion.
  I would be grateful if anyone could give me some advice. The .mdp file is listed as follows.
title    = chcwaaa;;; run control;;integrator   = md   ;a leap-frog integrator for integrating Newton's equations of motiontinit    = 0    ; default, starting time for your rundt   = 0.001    ; time step for integration, default 0.001 psnsteps   = 300   ; maximum number of steps to integrate or minimize, -1 is no maximuminit-step    = 0    ; the starting step. t=tinit + dt(init-step + i)comm-mode    = Linear   ; remove center of mass translation; Angular: remove center of mass translation and rotation around the center of massnstcomm  = 100  ; frequency for center of mass motion removalcomm-grps    = system ; groups for center of mass motion removal, default is the whole system;;; output control;;nstxout  = 5000 ; frequency to write coordinates to output trajectory file, the last coordinates are always writtennstvout  = 5000 ; frequency to write velocities to output trajectorynstfout  = 0    ; frequency to write forces to output trajectorynstlog   = 5000 ; frequency to write energies to log filenstcalcenergy    = 100  ; default, frequency for calculating energies.nstenergy    = 300  ; frequency to write energies to energy file, should be a multiple of nstcalcenergynstxtcout    = 300  ; frequency to write coordinates to xtc trajectoryxtc-precision    = 1000 ; precision to write to xtc trajectory, defaultxtc-grps = system   ; default the whole systemenergygrps   = system   ; groups to write to energy file;;; neighbor searching;;cutoff-scheme    = Verlet   ; generate a pair list with buffering.nstlist  = 10   ; default, frequency to update the neighbor listns-type  = grid ; make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list.pbc  = xyzperiodic-molecules   = no   ; molecules are finite, defaultverlet-buffer-drift  = 0.005    ; This sets the target energy drift per particle caused by the Verlet buffer, which indirectly sets rlist.rlist    = 1  ; With cutoff-scheme=Verlet, this is by default set by the verlet-buffer-drift option and the value of rlist is ignorednstcalclr    = 1;;; electrostatics;;coulombtype  = PME  ;Fast smooth Particle-Mesh Ewald (SPME) electrostaticscoulomb-modifier = Potential-shift-Verletrcoulomb = 1.6  ;distance for the Coulomb cut-off ;;; vdw;;vdwtype  = Cut-offvdw-modifier = Potential-shift-Verletrvdw = 1.6DispCorr = EnerPres  ;apply long range dispersion corrections for Energy and Pressure ;;; Ewald;;fourierspacing   = 0.12  ;pme-order    = 4ewald-rtol   

Re: [gmx-users] Semiisotropic Pressure coupling with PR

[Sai Pooja]

Its basically a melting process and there is ample of published data on this
(not related to gromacs though). The only reason for using freeze-dimensions
was to avoid using pbc=xy in combination with walls since I thought the
extra interactions due to the walls might make the simulations
computationally intensive.

The data I have obtained from these runs doesn't seem to match with an npt
MC simulation(fortran based in-house code) and the data from the MC
simulation looks more credible when compared to published results.

Pooja

On Thu, Jul 15, 2010 at 10:21 AM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>>
>> 1. Pressure
>> For my initial configuration, I run a long nvt run. This gives me a
>> pressure. Then I run an npt simulation at this prerssure.
>> The idea is to do expansion runs(decrease pressure so that the system
>> expands) to get a P vs density curve.
>> For example, after I determine the pressure of the initial configuration
>> from the long nvt run, say Pinit, I choose a set of pressures - Pinit, P1,
>> P2, PN s.t Pinit>P1,>P2...(eg. 74, 72, 70, 69.50). Then for each
>> pressure I run an npt simulation till the average converges.
>>
>>
>> 2. Freeze-dimension
>> Is there a better alternative for running simulations for a planar system?
>>
>>
> Maybe you want to use "pbc = xy" or walls?  Is there any literature
> precedent for what you want to do, or perhaps an alternate procedure?
>
> -Justin
>
>
>> Pooja
>>
>>
>> On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Sai Pooja wrote:
>>
>>
>>
>>
>>   Do you run any equilibration prior to applying these parameters?
>>Both N-H and P-R allow for wide fluctuations in temperature and
>>   pressure, respectively, which are exacerbated by systems that
>> are
>>   not sufficiently equilibrated.  Hence it could take a very
>>long time
>>   if you do not equilibrate well using, i.e. a weak coupling
>>scheme first.
>>
>>
>>I usually start with a pressure nearby. For example, I start
>>with a system which was equilibrated at p=71 and then run npt at
>>p=69. Is that not sufficient?
>>
>>
>>How do you determine the pressure before the simulation has begun?
>> Moreover, freezing your system in one dimension can certainly
>>complicate matters, since that is a non-equilibrium restraint on the
>>dynamics.  That could be a factor.
>>
>>-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
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>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
>>
>>
>>
>>
>> --
>> 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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>



-- 
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Re: [gmx-users] Semiisotropic Pressure coupling with PR

[Justin A. Lemkul]

Sai Pooja wrote:


1. Pressure
For my initial configuration, I run a long nvt run. This gives me a 
pressure. Then I run an npt simulation at this prerssure. 

The idea is to do expansion runs(decrease pressure so that the system 
expands) to get a P vs density curve. 

For example, after I determine the pressure of the initial configuration 
from the long nvt run, say Pinit, I choose a set of pressures - Pinit, 
P1, P2, PN s.t Pinit>P1,>P2...(eg. 74, 72, 70, 69.50). Then for 
each pressure I run an npt simulation till the average converges.



2. Freeze-dimension
Is there a better alternative for running simulations for a planar system?



Maybe you want to use "pbc = xy" or walls?  Is there any literature precedent 
for what you want to do, or perhaps an alternate procedure?


-Justin



Pooja

On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul > wrote:




Sai Pooja wrote:




   Do you run any equilibration prior to applying these parameters?
Both N-H and P-R allow for wide fluctuations in temperature and
   pressure, respectively, which are exacerbated by systems that are
   not sufficiently equilibrated.  Hence it could take a very
long time
   if you do not equilibrate well using, i.e. a weak coupling
scheme first.


I usually start with a pressure nearby. For example, I start
with a system which was equilibrated at p=71 and then run npt at
p=69. Is that not sufficient?


How do you determine the pressure before the simulation has begun?
 Moreover, freezing your system in one dimension can certainly
complicate matters, since that is a non-equilibrium restraint on the
dynamics.  That could be a factor.

-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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Please search the archive at http://www.gromacs.org/search before
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--
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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Re: [gmx-users] Semiisotropic Pressure coupling with PR

[Sai Pooja]

1. Pressure
For my initial configuration, I run a long nvt run. This gives me a
pressure. Then I run an npt simulation at this prerssure.

The idea is to do expansion runs(decrease pressure so that the system
expands) to get a P vs density curve.

For example, after I determine the pressure of the initial configuration
from the long nvt run, say Pinit, I choose a set of pressures - Pinit, P1,
P2, PN s.t Pinit>P1,>P2...(eg. 74, 72, 70, 69.50). Then for each
pressure I run an npt simulation till the average converges.


2. Freeze-dimension
Is there a better alternative for running simulations for a planar system?


Pooja

On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
> 
>
>
> Do you run any equilibration prior to applying these parameters?
>> Both N-H and P-R allow for wide fluctuations in temperature and
>>pressure, respectively, which are exacerbated by systems that are
>>not sufficiently equilibrated.  Hence it could take a very long time
>>if you do not equilibrate well using, i.e. a weak coupling scheme
>> first.
>>
>>
>> I usually start with a pressure nearby. For example, I start with a system
>> which was equilibrated at p=71 and then run npt at p=69. Is that not
>> sufficient?
>>
>>
> How do you determine the pressure before the simulation has begun?
>  Moreover, freezing your system in one dimension can certainly complicate
> matters, since that is a non-equilibrium restraint on the dynamics.  That
> could be a factor.
>
> -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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before 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
>



-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
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http://lists.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] Semiisotropic Pressure coupling with PR

[Justin A. Lemkul]

Sai Pooja wrote:




Do you run any equilibration prior to applying these parameters?
 Both N-H and P-R allow for wide fluctuations in temperature and
pressure, respectively, which are exacerbated by systems that are
not sufficiently equilibrated.  Hence it could take a very long time
if you do not equilibrate well using, i.e. a weak coupling scheme first.


I usually start with a pressure nearby. For example, I start with a 
system which was equilibrated at p=71 and then run npt at p=69. Is that 
not sufficient?




How do you determine the pressure before the simulation has begun?  Moreover, 
freezing your system in one dimension can certainly complicate matters, since 
that is a non-equilibrium restraint on the dynamics.  That could be a factor.


-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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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Re: [gmx-users] Semiisotropic Pressure coupling with PR

[Sai Pooja]

Reply inline...

On Thu, Jul 15, 2010 at 9:54 AM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>> Reply inline...
>>
>>
>> On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Sai Pooja wrote:
>>
>>Hi,
>>
>>I have a system of 3600 LJ particles in a plane (using
>>freeze-dimension option in z). I am running npt runs using
>>Semi-isotropic pressure coupling with Parrinello-Rahman
>>barostat. I have a few concerns:
>>
>>1) On the gromacs website, a webpage mentions that this type of
>>pressure coupling may not be accurate
>>
>>
>>Please provide a link when making this kind of statement.
>>
>> http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman
>><
>> http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman
>> >
>>
>
> Bugzilla entry 14 is ancient, and has long since been resolved:
>
>
> http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0#Resolved_issues
>
>
>
>>2) It takes a really long time for the system to reach the
>>reference pressure  > 500ns. Particularly the Pxx, Pyy terms are
>>very different and take an extremely long time to converge to a
>>common value.
>>
>>integrator   = md
>>dt   = 0.001
>>nsteps   = 5000
>>
>>; OUTPUT CONTROL OPTIONS
>>nstxout  = 0  ; No output, except for last frame
>>(coordinates)
>>nstvout  = 0; No output, except for last frame
>>(velocities)
>>nstfout  = 0; No output, except for last frame
>>(forces)
>>nstlog   = 100   ; Write every nth step to the log
>>nstenergy= 100 ; Write energies at every n step
>>nstxtcout= 100 ; Do not write a compressed tr
>>
>>; NEIGHBORSEARCHING PARAMETERS
>>nstlist  = 10
>>ns-type  = Grid
>>pbc  = xyz
>>rlist= 0.9
>>
>>; OPTIONS FOR ELECTROSTATICS AND VDW
>>coulombtype  = Cut-off
>>rcoulomb = 1.1225
>>vdw-type = User
>>rvdw = 1.1225
>>table-extension  = 0
>>
>>; Temperature coupling
>>tcoupl   = nose-hoover
>>tc-grps  = ARAR
>>tau_t= 0.1
>>ref_t= 120.2717
>>
>>; Pressure coupling
>>pcoupl   = Parrinello-Rahman
>>pcoupltype   = semiisotropic
>>tau-p= 1.0  1.0
>>compressibility  = 1e-5  0   ;Dont know
>>ref-p= 69 0
>>
>>
>>;Generate velocities for startup run
>>gen_vel  =no
>>gen_temp =120.2717
>>gen_seed =-1
>>
>> ;Non equilibrium MD steps
>> freezegrps  =ARAR
>> freezedim   =N N Y
>> ;Constraints
>> constraints = all-bonds
>> constraint_algorithm= Lincs
>> lincs_order = 4
>> lincs_iter  = 1
>> lincs_warnangle = 90  ;unconstrained_start= no
>> ;shake_tol  = 0.0001
>>
>>
> Do you run any equilibration prior to applying these parameters?  Both N-H
> and P-R allow for wide fluctuations in temperature and pressure,
> respectively, which are exacerbated by systems that are not sufficiently
> equilibrated.  Hence it could take a very long time if you do not
> equilibrate well using, i.e. a weak coupling scheme first.
>
>
I usually start with a pressure nearby. For example, I start with a system
which was equilibrated at p=71 and then run npt at p=69. Is that not
sufficient?

Pooja


> -Justin
>
>
>>
>>
>>What was your equilibration protocol?  What are your .mdp settings?
>>
>>-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
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>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.grom

Re: [gmx-users] Semiisotropic Pressure coupling with PR

[Justin A. Lemkul]

Sai Pooja wrote:

Reply inline...

On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul > wrote:




Sai Pooja wrote:

Hi,

I have a system of 3600 LJ particles in a plane (using
freeze-dimension option in z). I am running npt runs using
Semi-isotropic pressure coupling with Parrinello-Rahman
barostat. I have a few concerns:

1) On the gromacs website, a webpage mentions that this type of
pressure coupling may not be accurate


Please provide a link when making this kind of statement.

http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman




Bugzilla entry 14 is ancient, and has long since been resolved:

http://www.gromacs.org/About_Gromacs/Release_Notes/Revisions_in_4.0#Resolved_issues



2) It takes a really long time for the system to reach the
reference pressure  > 500ns. Particularly the Pxx, Pyy terms are
very different and take an extremely long time to converge to a
common value.

integrator   = md
dt   = 0.001
nsteps   = 5000

; OUTPUT CONTROL OPTIONS
nstxout  = 0  ; No output, except for last frame
(coordinates)
nstvout  = 0; No output, except for last frame
(velocities)
nstfout  = 0; No output, except for last frame
(forces)
nstlog   = 100   ; Write every nth step to the log
nstenergy= 100 ; Write energies at every n step
nstxtcout= 100 ; Do not write a compressed tr

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 10
ns-type  = Grid
pbc  = xyz
rlist= 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = Cut-off
rcoulomb = 1.1225
vdw-type = User
rvdw = 1.1225
table-extension  = 0

; Temperature coupling
tcoupl   = nose-hoover
tc-grps  = ARAR
tau_t= 0.1
ref_t= 120.2717

; Pressure coupling
pcoupl   = Parrinello-Rahman
pcoupltype   = semiisotropic
tau-p= 1.0  1.0
compressibility  = 1e-5  0   ;Dont know
ref-p= 69 0


;Generate velocities for startup run
gen_vel  =no
gen_temp =120.2717
gen_seed =-1

;Non equilibrium MD steps
freezegrps  =ARAR
freezedim   =N N Y 


;Constraints
constraints = all-bonds
constraint_algorithm= Lincs
lincs_order = 4
lincs_iter  = 1
lincs_warnangle = 90  
;unconstrained_start= no

;shake_tol  = 0.0001



Do you run any equilibration prior to applying these parameters?  Both N-H and 
P-R allow for wide fluctuations in temperature and pressure, respectively, which 
are exacerbated by systems that are not sufficiently equilibrated.  Hence it 
could take a very long time if you do not equilibrate well using, i.e. a weak 
coupling scheme first.


-Justin




 


What was your equilibration protocol?  What are your .mdp settings?

-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


-- 
gmx-users mailing listgmx-users@gromacs.org


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
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




--
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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please sear

Re: [gmx-users] Semiisotropic Pressure coupling with PR

[Sai Pooja]

Reply inline...

On Thu, Jul 15, 2010 at 9:41 AM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>> Hi,
>>
>> I have a system of 3600 LJ particles in a plane (using freeze-dimension
>> option in z). I am running npt runs using Semi-isotropic pressure coupling
>> with Parrinello-Rahman barostat. I have a few concerns:
>>
>> 1) On the gromacs website, a webpage mentions that this type of pressure
>> coupling may not be accurate
>>
>>
> Please provide a link when making this kind of statement.
>
> http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Barostat&highlight=parrinello-rahman
>
>  2) It takes a really long time for the system to reach the reference
>> pressure  > 500ns. Particularly the Pxx, Pyy terms are very different and
>> take an extremely long time to converge to a common value.
>>
>>  integrator   = md
> dt   = 0.001
> nsteps   = 5000
>
> ; OUTPUT CONTROL OPTIONS
> nstxout  = 0  ; No output, except for last frame
> (coordinates)
> nstvout  = 0; No output, except for last frame
> (velocities)
> nstfout  = 0; No output, except for last frame (forces)
> nstlog   = 100   ; Write every nth step to the log
> nstenergy= 100 ; Write energies at every n step
> nstxtcout= 100 ; Do not write a compressed tr
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist  = 10
> ns-type  = Grid
> pbc  = xyz
> rlist= 0.9
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = Cut-off
> rcoulomb = 1.1225
> vdw-type = User
> rvdw = 1.1225
> table-extension  = 0
>
> ; Temperature coupling
> tcoupl   = nose-hoover
> tc-grps  = ARAR
> tau_t= 0.1
> ref_t= 120.2717
>
> ; Pressure coupling
> pcoupl   = Parrinello-Rahman
> pcoupltype   = semiisotropic
> tau-p= 1.0  1.0
> compressibility  = 1e-5  0   ;Dont know
> ref-p= 69 0
>
>
> ;Generate velocities for startup run
> gen_vel  =no
> gen_temp =120.2717
> gen_seed =-1
>
> ;Non equilibrium MD steps
freezegrps  =ARAR
freezedim   =N N Y

;Constraints
constraints = all-bonds
constraint_algorithm= Lincs
lincs_order = 4
lincs_iter  = 1
lincs_warnangle = 90
;unconstrained_start= no
;shake_tol  = 0.0001





> What was your equilibration protocol?  What are your .mdp settings?
>
> -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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>



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Re: [gmx-users] Semiisotropic Pressure coupling with PR

[Justin A. Lemkul]

Sai Pooja wrote:

Hi,

I have a system of 3600 LJ particles in a plane (using freeze-dimension 
option in z). I am running npt runs using Semi-isotropic pressure 
coupling with Parrinello-Rahman barostat. I have a few concerns:


1) On the gromacs website, a webpage mentions that this type of pressure 
coupling may not be accurate




Please provide a link when making this kind of statement.

2) It takes a really long time for the system to reach the reference 
pressure  > 500ns. Particularly the Pxx, Pyy terms are very different 
and take an extremely long time to converge to a common value.




What was your equilibration protocol?  What are your .mdp settings?

-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] Semiisotropic Pressure coupling with PR

[Sai Pooja]

Hi,

I have a system of 3600 LJ particles in a plane (using freeze-dimension
option in z). I am running npt runs using Semi-isotropic pressure coupling
with Parrinello-Rahman barostat. I have a few concerns:

1) On the gromacs website, a webpage mentions that this type of pressure
coupling may not be accurate

2) It takes a really long time for the system to reach the reference
pressure  > 500ns. Particularly the Pxx, Pyy terms are very different and
take an extremely long time to converge to a common value.

Pooja

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

[Justin A. Lemkul]

Yongchul Chung wrote:


Also note that haphazardly changing the vdwtype or rvdw can have
negative impacts on your simulation, depending on your chosen force
field's sensitivity to these parameters.


Thank you for pointing this out. I am relatively new to this method so 
am taking "figure out as I go" approach.


Well, if something "works" doesn't mean it's "right."  I would recommend doing 
some textbook reading, and the primary literature for the force field you've 
chosen.  It will save you a lot of time in the long run.  Remember that when 
publishing, you may have to defend any or all of your chosen parameters.  With 
the right background work, you won't have to improvise these choices and face 
unnecessary criticism :)


-Justin

--


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


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Re: [gmx-users] semiisotropic pressure coupling

[Yongchul Chung]

On Sun, Oct 25, 2009 at 6:38 PM, Justin A. Lemkul  wrote:

>
>
> Yongchul Chung wrote:
>
>> Hello gmx-users,
>>
>> I am running an NPT simulation with 100 molecules of n-alkane and trying
>> to impose uni-axial pressure of these molecules using semiisotropic option
>> in grompp.mdp.
>> However, as the box seems to distort significantly due to the imposed
>> pressure which leads to the following error message:
>>
>> ---
>> Program mdrun, VERSION 4.0.5
>> Source code file: ns.c, line: 2295
>>
>> Fatal error:
>> One of the box vectors has become shorter than twice the cut-off length or
>> box_yy-|box_zy| or box_zz has become smaller than the cut-off.
>> ---
>>
>> I tried all vdwtype options to see whether this would mitigate the issues
>> but was unsuccessful.
>> is there any other options in gromacs that I can use to impose uniaxial
>> stress? Or does anyone had any similar problems related to semi-isotropic
>> pressure coupling?
>> Thank you in advance.
>>
>>
> It seems to me that your system is simply too small to perform this kind of
> operation.  By applying 1000 bar of pressure to such a small system, you can
> certainly expect the box size to deform and get smaller.  Perhaps a larger
> number of molecules (and thus a larger box) will give you a reasonably-sized
> box once the 1000 bar of pressure has been applied and the system
> equilibrated.
>

Yes I think I should increase my simulation size as pointed out by Mark.


> Also note that haphazardly changing the vdwtype or rvdw can have negative
> impacts on your simulation, depending on your chosen force field's
> sensitivity to these parameters.
>

Thank you for pointing this out. I am relatively new to this method so am
taking "figure out as I go" approach.


-Justin
>
>  This is my grompp.mdp file configuration:
>> integrator  =  md
>> dt  =  0.001 ; ps !
>> nsteps  =  100 ; nstcomm =  1
>> nstxout =  250 ; collect data every 0.5 ps
>> nstvout =  1000
>> nstfout =  0
>> nstlog  =  10
>> nstenergy   =  10
>> nstlist =  10
>> ns_type =  grid
>> rlist   =  0.9
>>
>> coulombtype=  PME
>> rcoulomb=  0.9
>> vdwtype =  switch
>> rvdw=  0.7
>> rvdw_switch =  0.0
>>
>> fourierspacing  =  0.12
>> fourier_nx  =  0
>> fourier_ny  =  0
>> fourier_nz  =  0
>> pme_order  =  4
>> ewald_rtol  =  1e-5
>> optimize_fft  =  yes
>> ; temperature coupling is on
>> Tcoupl  =  v-rescale
>> ; Groups to couple separately
>> tc-grps  = System
>> ; Time constant (ps) and reference temperature (K)
>> tau_t= 0.1
>> ref_t= 300
>> ; Generate velocites is on at 300 K.
>> gen_vel =  yes
>> gen_temp=  300.0
>> gen_seed=  173529
>> constraints  = all-bonds
>>
>> ; pressure coupling is on
>> pcoupl = parrinello-rahman
>> pcoupltype = semiisotropic
>>
>> tau_p = 0.5
>> compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction
>> ref_p = 1.0 1000.0  ;x/y-direction, z-direction
>>
>>
>>
>> --
>> Yongchul "Greg" Chung
>> Graduate Student
>> Dept. of Chemical Engineering, Case Western Reserve University
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>> 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
>
> 
>
> ___
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>



-- 
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
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Re: [gmx-users] semiisotropic pressure coupling

[Yongchul Chung]

On Sun, Oct 25, 2009 at 6:28 PM, Mark Abraham wrote:

> Yongchul Chung wrote:
>
>> Hello gmx-users,
>>
>> I am running an NPT simulation with 100 molecules of n-alkane and trying
>> to impose uni-axial pressure of these molecules using semiisotropic option
>> in grompp.mdp.
>> However, as the box seems to distort significantly due to the imposed
>> pressure which leads to the following error message:
>>
>> ---
>> Program mdrun, VERSION 4.0.5
>> Source code file: ns.c, line: 2295
>>
>> Fatal error:
>> One of the box vectors has become shorter than twice the cut-off length or
>> box_yy-|box_zy| or box_zz has become smaller than the cut-off.
>> ---
>>
>
> You're imposing 1000 bar of pressure along the z-axis. Surely you should
> expect distortion?
>
> You should do some maths and work out the expected density of the box under
> such pressure. You still need a box large enough that the maximum cut-off
> length can be satisfied, so that sets the minimum number of molecules you
> need, and thus the initial size of the box.
>
>
Thanks for the input. I should do this.




>
>  I tried all vdwtype options to see whether this would mitigate the issues
>> but was unsuccessful.
>>
>
> Don't fool with .mdp settings hoping it'll magically work. Read how they
> work, and you might have understood why the minimum image convention
> requires that the condition that provoked the above error does not arise.
>
> Mark
>
 is there any other options in gromacs that I can use to impose uniaxial
>> stress? Or does anyone had any similar problems related to semi-isotropic
>> pressure coupling?
>> Thank you in advance.
>>
>> This is my grompp.mdp file configuration:
>> integrator  =  md
>> dt  =  0.001 ; ps !
>> nsteps  =  100 ; nstcomm =  1
>> nstxout =  250 ; collect data every 0.5 ps
>> nstvout =  1000
>> nstfout =  0
>> nstlog  =  10
>> nstenergy   =  10
>> nstlist =  10
>> ns_type =  grid
>> rlist   =  0.9
>>
>> coulombtype=  PME
>> rcoulomb=  0.9
>> vdwtype =  switch
>> rvdw=  0.7
>> rvdw_switch =  0.0
>>
>> fourierspacing  =  0.12
>> fourier_nx  =  0
>> fourier_ny  =  0
>> fourier_nz  =  0
>> pme_order  =  4
>> ewald_rtol  =  1e-5
>> optimize_fft  =  yes
>> ; temperature coupling is on
>> Tcoupl  =  v-rescale
>> ; Groups to couple separately
>> tc-grps  = System
>> ; Time constant (ps) and reference temperature (K)
>> tau_t= 0.1
>> ref_t= 300
>> ; Generate velocites is on at 300 K.
>> gen_vel =  yes
>> gen_temp=  300.0
>> gen_seed=  173529
>> constraints  = all-bonds
>>
>> ; pressure coupling is on
>> pcoupl = parrinello-rahman
>> pcoupltype = semiisotropic
>>
>> tau_p = 0.5
>> compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction
>> ref_p = 1.0 1000.0  ;x/y-direction, z-direction
>>
>>
>>
>> --
>> Yongchul "Greg" Chung
>> Graduate Student
>> Dept. of Chemical Engineering, Case Western Reserve University
>>
>>
>> 
>>
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>>
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-- 
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
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Re: [gmx-users] semiisotropic pressure coupling

[Justin A. Lemkul]

Yongchul Chung wrote:

Hello gmx-users,

I am running an NPT simulation with 100 molecules of n-alkane and trying 
to impose uni-axial pressure of these molecules using semiisotropic 
option in grompp.mdp.
However, as the box seems to distort significantly due to the imposed 
pressure which leads to the following error message:


---
Program mdrun, VERSION 4.0.5
Source code file: ns.c, line: 2295

Fatal error:
One of the box vectors has become shorter than twice the cut-off length 
or box_yy-|box_zy| or box_zz has become smaller than the cut-off.

---

I tried all vdwtype options to see whether this would mitigate the 
issues but was unsuccessful.
is there any other options in gromacs that I can use to impose uniaxial 
stress? Or does anyone had any similar problems related to 
semi-isotropic pressure coupling?

Thank you in advance.



It seems to me that your system is simply too small to perform this kind of 
operation.  By applying 1000 bar of pressure to such a small system, you can 
certainly expect the box size to deform and get smaller.  Perhaps a larger 
number of molecules (and thus a larger box) will give you a reasonably-sized box 
once the 1000 bar of pressure has been applied and the system equilibrated.


Also note that haphazardly changing the vdwtype or rvdw can have negative 
impacts on your simulation, depending on your chosen force field's sensitivity 
to these parameters.


-Justin


This is my grompp.mdp file configuration:
integrator  =  md
dt  =  0.001 ; ps !
nsteps  =  100 ; 
nstcomm =  1

nstxout =  250 ; collect data every 0.5 ps
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  0.9

coulombtype=  PME
rcoulomb=  0.9
vdwtype =  switch
rvdw=  0.7
rvdw_switch =  0.0

fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order  =  4
ewald_rtol  =  1e-5
optimize_fft  =  yes
; temperature coupling is on
Tcoupl  =  v-rescale
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
constraints  = all-bonds

; pressure coupling is on
pcoupl = parrinello-rahman
pcoupltype = semiisotropic

tau_p = 0.5
compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction
ref_p = 1.0 1000.0  ;x/y-direction, z-direction



--
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve 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] semiisotropic pressure coupling

[Mark Abraham]

Yongchul Chung wrote:

Hello gmx-users,

I am running an NPT simulation with 100 molecules of n-alkane and trying 
to impose uni-axial pressure of these molecules using semiisotropic 
option in grompp.mdp.
However, as the box seems to distort significantly due to the imposed 
pressure which leads to the following error message:


---
Program mdrun, VERSION 4.0.5
Source code file: ns.c, line: 2295

Fatal error:
One of the box vectors has become shorter than twice the cut-off length 
or box_yy-|box_zy| or box_zz has become smaller than the cut-off.

---


You're imposing 1000 bar of pressure along the z-axis. Surely you should 
expect distortion?


You should do some maths and work out the expected density of the box 
under such pressure. You still need a box large enough that the maximum 
cut-off length can be satisfied, so that sets the minimum number of 
molecules you need, and thus the initial size of the box.


I tried all vdwtype options to see whether this would mitigate the 
issues but was unsuccessful.


Don't fool with .mdp settings hoping it'll magically work. Read how they 
work, and you might have understood why the minimum image convention 
requires that the condition that provoked the above error does not arise.


Mark

is there any other options in gromacs that I can use to impose uniaxial 
stress? Or does anyone had any similar problems related to 
semi-isotropic pressure coupling?

Thank you in advance.

This is my grompp.mdp file configuration:
integrator  =  md
dt  =  0.001 ; ps !
nsteps  =  100 ; 
nstcomm =  1

nstxout =  250 ; collect data every 0.5 ps
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  0.9

coulombtype=  PME
rcoulomb=  0.9
vdwtype =  switch
rvdw=  0.7
rvdw_switch =  0.0

fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order  =  4
ewald_rtol  =  1e-5
optimize_fft  =  yes
; temperature coupling is on
Tcoupl  =  v-rescale
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
constraints  = all-bonds

; pressure coupling is on
pcoupl = parrinello-rahman
pcoupltype = semiisotropic

tau_p = 0.5
compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction
ref_p = 1.0 1000.0  ;x/y-direction, z-direction



--
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University




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[gmx-users] semiisotropic pressure coupling

[Yongchul Chung]

Hello gmx-users,

I am running an NPT simulation with 100 molecules of n-alkane and trying to
impose uni-axial pressure of these molecules using semiisotropic option in
grompp.mdp.
However, as the box seems to distort significantly due to the imposed
pressure which leads to the following error message:

---
Program mdrun, VERSION 4.0.5
Source code file: ns.c, line: 2295

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.
---

I tried all vdwtype options to see whether this would mitigate the issues
but was unsuccessful.
is there any other options in gromacs that I can use to impose uniaxial
stress? Or does anyone had any similar problems related to semi-isotropic
pressure coupling?
Thank you in advance.

This is my grompp.mdp file configuration:
integrator  =  md
dt  =  0.001 ; ps !
nsteps  =  100 ;
nstcomm =  1
nstxout =  250 ; collect data every 0.5 ps
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  0.9

coulombtype=  PME
rcoulomb=  0.9
vdwtype =  switch
rvdw=  0.7
rvdw_switch =  0.0

fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order  =  4
ewald_rtol  =  1e-5
optimize_fft  =  yes
; temperature coupling is on
Tcoupl  =  v-rescale
; Groups to couple separately
tc-grps  = System
; Time constant (ps) and reference temperature (K)
tau_t= 0.1
ref_t= 300
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
constraints  = all-bonds

; pressure coupling is on
pcoupl = parrinello-rahman
pcoupltype = semiisotropic

tau_p = 0.5
compressibility = 7.10e-5 7.10e-5 ;x/y-direction, z-direction
ref_p = 1.0 1000.0  ;x/y-direction, z-direction



-- 
Yongchul "Greg" Chung
Graduate Student
Dept. of Chemical Engineering, Case Western Reserve University
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[gmx-users] Semiisotropic pressure coupling & comm_grps (VCM)

[Alok]

Dear All,

I have two basic questions regarding membrane protein simulation. First 
regarding Semiisotropic pressure coupling (NPAT) and second regarding comm_grpp 
(VCM).

1) If I want to use NPAT ensemble (x/y dimensions of bilayer to be fixed) then 
is following the correct way to define?

Pcoupl   =  Berendsen
Pcoupltype=  semiisotropic
tau_p =   2.0 2.0 
compressibility =   04.5e-5
ref_p =  1.0  1.0

2) I want to remove center of mass translation so in following which one is 
better?

a)comm_mode=  Linear
   nstcomm   =  1
   comm_grps  =  Protein_POP ; (both protein and lipid 
are together)

b)comm_mode=  Linear
   nstcomm   =  1
   comm_grps  =  Protein POP ; (protein and lipid 
separately)



Thanks a lot

Best Regards,
Alok___
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