Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-21 Thread Justin Lemkul 



On 4/21/16 6:57 AM, Tuhin Samanta wrote:

please check it...

[ moleculetype ]
; molname   nrexcl
HOD 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
  1  opls_116   1HOD OW  1  -0.8476
  2  opls_117   1HOD HW  1   0.4238
  3  opls_805   1HOD DW  1   0.4238

#ifndef FLEXIBLE
; [ settles ]
; OWfunct   doh dhh
  ; 10.101   0.16500

;[ exclusions ]
;1  2   3
;2  1   3
;3  1   2
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.1 345000  0.1 345000
1   3   1   0.102   266292  0.102   266292

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   105.7   583 105.7   583



Of course this crashes - you're trying to use a 2-fs time step without any 
constraints.  Reduce dt or treat the water model as rigid.


-Justin


Thanks,
Tuhin

On Thu, Apr 21, 2016 at 3:20 PM, Justin Lemkul  wrote:




On 4/21/16 3:32 AM, Tuhin Samanta wrote:


The topology file for my system - HOD System like that ---



#include "oplsaa.ff/forcefield.itp"

; Include hod topology
#include "hod.itp"

[ system ]
;Name
HOD

[ molecules ]
; Compound#mols
HOD102

.mdp file is like that -

(FOR Energy minimization)

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 0.1   ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 20; Maximum number of (minimization) steps
to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list
and
long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
constraints = none

For Equilibritaion (NVT)

title   =  NVT equilibration of W10 RM
cpp = /lib/cpp
include = -I../top
integrator  = md; leap-frog integrator
nsteps  = 50   ; 2 * 1 = 20 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100  ; save coordinates every 0.1 ns
nstvout = 100  ; save velocities every 0.1 ns
nstenergy   = 100 ; save energies every 0.1 ns
nstlog  = 100  ; update log file every 0.1 ns
; Bond parameters
continuation= yes   ; continuation from previous run
constraint_algorithm = lincs; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 10 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
optimize_fft= yes
; Temperature coupling is on
tcoupl  = Berendsen ; modified Berendsen thermostat
tc-grps = System; two coupling groups - more accurate
tau_t   = 1.0   ; time constant, in ps
ref_t   = 300   ; reference temperature, one for each
group
; 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


Please take a look . I am getting the error like that -- 4 particles
communicated to PME node 4 are more than 2/3 times the cut-off out of the
domain decomposition cell of their charge group in dimension x. This
usually means that your system is not well equilibrated.

If you want I can send you my .itp file also.



Yes, that's actually rather important; the .top itself just #includes

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-21 Thread Tuhin Samanta 
please check it...

[ moleculetype ]
; molname   nrexcl
HOD 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1  opls_116   1HOD OW  1  -0.8476
 2  opls_117   1HOD HW  1   0.4238
 3  opls_805   1HOD DW  1   0.4238

#ifndef FLEXIBLE
; [ settles ]
; OWfunct   doh dhh
 ; 10.101   0.16500

;[ exclusions ]
;1  2   3
;2  1   3
;3  1   2
#else
[ bonds ]
; i j   funct   length  force.c.
1   2   1   0.1 345000  0.1 345000
1   3   1   0.102   266292  0.102   266292

[ angles ]
; i j   k   funct   angle   force.c.
2   1   3   1   105.7   583 105.7   583

Thanks,
Tuhin

On Thu, Apr 21, 2016 at 3:20 PM, Justin Lemkul  wrote:

>
>
> On 4/21/16 3:32 AM, Tuhin Samanta wrote:
>
>> The topology file for my system - HOD System like that ---
>>
>>
>>
>> #include "oplsaa.ff/forcefield.itp"
>>
>> ; Include hod topology
>> #include "hod.itp"
>>
>> [ system ]
>> ;Name
>> HOD
>>
>> [ molecules ]
>> ; Compound#mols
>> HOD102
>>
>> .mdp file is like that -
>>
>> (FOR Energy minimization)
>>
>> ; minim.mdp - used as input into grompp to generate em.tpr
>> ; Parameters describing what to do, when to stop and what to save
>> integrator  = steep ; Algorithm (steep = steepest descent
>> minimization)
>> emtol   = 0.1   ; Stop minimization when the maximum force
>> < 1000.0 kJ/mol/nm
>> emstep  = 0.01  ; Energy step size
>> nsteps  = 20; Maximum number of (minimization) steps
>> to
>> perform
>>
>> ; Parameters describing how to find the neighbors of each atom and how to
>> calculate the interactions
>> nstlist = 1 ; Frequency to update the neighbor list
>> and
>> long range forces
>> ns_type = grid  ; Method to determine neighbor list
>> (simple, grid)
>> rlist   = 1.0   ; Cut-off for making neighbor list (short
>> range forces)
>> coulombtype = PME   ; Treatment of long range electrostatic
>> interactions
>> rcoulomb= 1.0   ; Short-range electrostatic cut-off
>> rvdw= 1.0   ; Short-range Van der Waals cut-off
>> pbc = xyz   ; Periodic Boundary Conditions (yes/no)
>> constraints = none
>>
>> For Equilibritaion (NVT)
>>
>> title   =  NVT equilibration of W10 RM
>> cpp = /lib/cpp
>> include = -I../top
>> integrator  = md; leap-frog integrator
>> nsteps  = 50   ; 2 * 1 = 20 ns
>> dt  = 0.002 ; 2 fs
>> ; Output control
>> nstxout = 100  ; save coordinates every 0.1 ns
>> nstvout = 100  ; save velocities every 0.1 ns
>> nstenergy   = 100 ; save energies every 0.1 ns
>> nstlog  = 100  ; update log file every 0.1 ns
>> ; Bond parameters
>> continuation= yes   ; continuation from previous run
>> constraint_algorithm = lincs; holonomic constraints
>> constraints = none ; all bonds (even heavy atom-H bonds)
>> constrained
>> lincs_iter  = 1 ; accuracy of LINCS
>> lincs_order = 4 ; also related to accuracy
>> ; Neighborsearching
>> ns_type = grid  ; search neighboring grid cells
>> nstlist = 10 ; 10 fs
>> rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
>> rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
>> rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
>> ; Electrostatics
>> coulombtype = PME   ; Particle Mesh Ewald for long-range
>> electrostatics
>> pme_order   = 4 ; cubic interpolation
>> fourierspacing  = 0.16  ; grid spacing for FFT
>> optimize_fft= yes
>> ; Temperature coupling is on
>> tcoupl  = Berendsen ; modified Berendsen thermostat
>> tc-grps = System; two coupling groups - more accurate
>> tau_t   = 1.0   ; time constant, in ps
>> ref_t   = 300   ; reference temperature, one for each
>> group
>> ; 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
>>
>>
>> Please take a look . I am getting the error like that -- 4 particles
>> communicated to PME node 4 are more than 2/3 times the cut-off out of the
>> domain decomposition cell of their charge group in dimension x. This
>> usually means that your system is not well equilibrated.
>>
>> If you want I can

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-21 Thread Justin Lemkul 



On 4/21/16 3:32 AM, Tuhin Samanta wrote:

The topology file for my system - HOD System like that ---



#include "oplsaa.ff/forcefield.itp"

; Include hod topology
#include "hod.itp"

[ system ]
;Name
HOD

[ molecules ]
; Compound#mols
HOD102

.mdp file is like that -

(FOR Energy minimization)

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 0.1   ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 20; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and
long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
constraints = none

For Equilibritaion (NVT)

title   =  NVT equilibration of W10 RM
cpp = /lib/cpp
include = -I../top
integrator  = md; leap-frog integrator
nsteps  = 50   ; 2 * 1 = 20 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100  ; save coordinates every 0.1 ns
nstvout = 100  ; save velocities every 0.1 ns
nstenergy   = 100 ; save energies every 0.1 ns
nstlog  = 100  ; update log file every 0.1 ns
; Bond parameters
continuation= yes   ; continuation from previous run
constraint_algorithm = lincs; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 10 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
optimize_fft= yes
; Temperature coupling is on
tcoupl  = Berendsen ; modified Berendsen thermostat
tc-grps = System; two coupling groups - more accurate
tau_t   = 1.0   ; time constant, in ps
ref_t   = 300   ; reference temperature, one for each group
; 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


Please take a look . I am getting the error like that -- 4 particles
communicated to PME node 4 are more than 2/3 times the cut-off out of the
domain decomposition cell of their charge group in dimension x. This
usually means that your system is not well equilibrated.

If you want I can send you my .itp file also.



Yes, that's actually rather important; the .top itself just #includes the .itp 
and therefore contains no useful information.


-Justin


Tuhin


On Wed, Apr 20, 2016 at 10:52 PM, Justin Lemkul  wrote:




On 4/20/16 1:20 PM, Tuhin Samanta wrote:


I have done the energy minimization many times by taking previously
minimized structure.



A box of water should be basically impossible to break.  Either your .mdp
or topology has problems.  Since you've provided neither, there's not much
anyone can do to help you.  The diagnostic walkthrough that Mark linked is
the best source of figuring it out.  Short of that, provide us with your
input topology and .mdp (copied and pasted if small enough for an email, or
linked to a file-sharing service otherwise).

-Justin





On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham 
wrote:

Hi,


On Wed, 20 Apr 2016 19:04 Tuhin Samanta 
wrote:

Thank Mark for your suggestion.


I was trying to resolve the problem 
" 4 particles communicated to PME node 4 are more than 2/3 times the
cut-off out of the

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-21 Thread Tuhin Samanta 
The topology file for my system - HOD System like that ---



#include "oplsaa.ff/forcefield.itp"

; Include hod topology
#include "hod.itp"

[ system ]
;Name
HOD

[ molecules ]
; Compound#mols
HOD102

.mdp file is like that -

(FOR Energy minimization)

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep ; Algorithm (steep = steepest descent
minimization)
emtol   = 0.1   ; Stop minimization when the maximum force
< 1000.0 kJ/mol/nm
emstep  = 0.01  ; Energy step size
nsteps  = 20; Maximum number of (minimization) steps to
perform

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and
long range forces
ns_type = grid  ; Method to determine neighbor list
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list (short
range forces)
coulombtype = PME   ; Treatment of long range electrostatic
interactions
rcoulomb= 1.0   ; Short-range electrostatic cut-off
rvdw= 1.0   ; Short-range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions (yes/no)
constraints = none

For Equilibritaion (NVT)

title   =  NVT equilibration of W10 RM
cpp = /lib/cpp
include = -I../top
integrator  = md; leap-frog integrator
nsteps  = 50   ; 2 * 1 = 20 ns
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100  ; save coordinates every 0.1 ns
nstvout = 100  ; save velocities every 0.1 ns
nstenergy   = 100 ; save energies every 0.1 ns
nstlog  = 100  ; update log file every 0.1 ns
; Bond parameters
continuation= yes   ; continuation from previous run
constraint_algorithm = lincs; holonomic constraints
constraints = none ; all bonds (even heavy atom-H bonds) constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 10 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
optimize_fft= yes
; Temperature coupling is on
tcoupl  = Berendsen ; modified Berendsen thermostat
tc-grps = System; two coupling groups - more accurate
tau_t   = 1.0   ; time constant, in ps
ref_t   = 300   ; reference temperature, one for each group
; 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


Please take a look . I am getting the error like that -- 4 particles
communicated to PME node 4 are more than 2/3 times the cut-off out of the
domain decomposition cell of their charge group in dimension x. This
usually means that your system is not well equilibrated.

If you want I can send you my .itp file also.

Tuhin


On Wed, Apr 20, 2016 at 10:52 PM, Justin Lemkul  wrote:

>
>
> On 4/20/16 1:20 PM, Tuhin Samanta wrote:
>
>> I have done the energy minimization many times by taking previously
>> minimized structure.
>>
>>
> A box of water should be basically impossible to break.  Either your .mdp
> or topology has problems.  Since you've provided neither, there's not much
> anyone can do to help you.  The diagnostic walkthrough that Mark linked is
> the best source of figuring it out.  Short of that, provide us with your
> input topology and .mdp (copied and pasted if small enough for an email, or
> linked to a file-sharing service otherwise).
>
> -Justin
>
>
>
>>
>> On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham 
>> wrote:
>>
>> Hi,
>>>
>>> On Wed, 20 Apr 2016 19:04 Tuhin Samanta 
>>> wrote:
>>>
>>> Thank Mark for your suggestion.

 I was trying to resolve the problem 
 " 4 particles communicated to PME node 4 are more than 2/3 times the
 cut-off out of the domain decomposition cell of their charge group in
 dimension x.
 This usually means that your system

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-20 Thread Justin Lemkul 



On 4/20/16 1:20 PM, Tuhin Samanta wrote:

I have done the energy minimization many times by taking previously
minimized structure.



A box of water should be basically impossible to break.  Either your .mdp or 
topology has problems.  Since you've provided neither, there's not much anyone 
can do to help you.  The diagnostic walkthrough that Mark linked is the best 
source of figuring it out.  Short of that, provide us with your input topology 
and .mdp (copied and pasted if small enough for an email, or linked to a 
file-sharing service otherwise).


-Justin




On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham 
wrote:


Hi,

On Wed, 20 Apr 2016 19:04 Tuhin Samanta 
wrote:


Thank Mark for your suggestion.

I was trying to resolve the problem 
" 4 particles communicated to PME node 4 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated."

First of all I have done the energy minimization for long times for

proper

equilibriuation.



Then what did you change? You may need to be more gentle.

Secondly by changing rcut and PME mesh girding I have tried a lot. But it's

showing same error message.



Those suggestions are made for perhaps improving performance, which is
unrelated to your error. They just both happen to use the word PME...

So can you please tell me any specific solution for this problem.




They're all at http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Mark

Thanking you,

Tuhin


On Wed, Apr 20, 2016 at 2:21 PM, Mark Abraham 
wrote:


Hi,

The information message and the actual error are separated in your log

file

with a bunch of punctuation because they're logically separate.

Anyway, there should also have been a link to
http://www.gromacs.org/Documentation/Errors which suggests some

strategies

for this issue.

Mark

On Wed, 20 Apr 2016 09:00 Tuhin Samanta 
wrote:


Hello ,

My system involves water molecules in a box of 5x5x5 nm3. When I was

doing

the simulation for energy minimization I  got n error message --

The optimal PME mesh load for parallel simulations is below 0.5
   and for highly parallel simulations between 0.25 and 0.33,
   for higher performance, increase the cut-off and the PME grid

spacing


  4 particles communicated to PME node 4 are more than 2/3 times the

cut-off

out of the domain decomposition cell of their charge group in

dimension

x.

This usually means that your system is not well equilibrated.

I have changed the cut off and grid spacing but still it's showing

the

error message. I know it is the problem with the parallelization.

Also

I

have  gone through the user forum's discussion.  So can anyone please
suggest me how to get rid of that problem.


Thank you so much.
Best regards,
Tuhin
--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users

or

send a mail to gmx-users-requ...@gromacs.org.


--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.


--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.


--
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

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

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

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

==
--
Gromacs Users mailing list

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

* Can't post? Read

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-20 Thread Mark Abraham 
That's just the first stage of an equilibration. See
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
for suggestions

Mark

On Wed, 20 Apr 2016 19:20 Tuhin Samanta  wrote:

> I have done the energy minimization many times by taking previously
> minimized structure.
>
>
>
> On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > On Wed, 20 Apr 2016 19:04 Tuhin Samanta 
> > wrote:
> >
> > > Thank Mark for your suggestion.
> > >
> > > I was trying to resolve the problem 
> > > " 4 particles communicated to PME node 4 are more than 2/3 times the
> > > cut-off out of the domain decomposition cell of their charge group in
> > > dimension x.
> > > This usually means that your system is not well equilibrated."
> > >
> > > First of all I have done the energy minimization for long times for
> > proper
> > > equilibriuation.
> > >
> >
> > Then what did you change? You may need to be more gentle.
> >
> > Secondly by changing rcut and PME mesh girding I have tried a lot. But
> it's
> > > showing same error message.
> > >
> >
> > Those suggestions are made for perhaps improving performance, which is
> > unrelated to your error. They just both happen to use the word PME...
> >
> > So can you please tell me any specific solution for this problem.
> > >
> >
> > They're all at
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> >
> > Mark
> >
> > Thanking you,
> > > Tuhin
> > >
> > >
> > > On Wed, Apr 20, 2016 at 2:21 PM, Mark Abraham <
> mark.j.abra...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > The information message and the actual error are separated in your
> log
> > > file
> > > > with a bunch of punctuation because they're logically separate.
> > > >
> > > > Anyway, there should also have been a link to
> > > > http://www.gromacs.org/Documentation/Errors which suggests some
> > > strategies
> > > > for this issue.
> > > >
> > > > Mark
> > > >
> > > > On Wed, 20 Apr 2016 09:00 Tuhin Samanta 
> > > > wrote:
> > > >
> > > > > Hello ,
> > > > >
> > > > > My system involves water molecules in a box of 5x5x5 nm3. When I
> was
> > > > doing
> > > > > the simulation for energy minimization I  got n error message --
> > > > >
> > > > > The optimal PME mesh load for parallel simulations is below 0.5
> > > > >   and for highly parallel simulations between 0.25 and 0.33,
> > > > >   for higher performance, increase the cut-off and the PME grid
> > spacing
> > > > >
> > > > >  4 particles communicated to PME node 4 are more than 2/3 times the
> > > > cut-off
> > > > > out of the domain decomposition cell of their charge group in
> > dimension
> > > > x.
> > > > > This usually means that your system is not well equilibrated.
> > > > >
> > > > > I have changed the cut off and grid spacing but still it's showing
> > the
> > > > > error message. I know it is the problem with the parallelization.
> > Also
> > > I
> > > > > have  gone through the user forum's discussion.  So can anyone
> please
> > > > > suggest me how to get rid of that problem.
> > > > >
> > > > >
> > > > > Thank you so much.
> > > > > Best regards,
> > > > > Tuhin
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-20 Thread Tuhin Samanta 
I have done the energy minimization many times by taking previously
minimized structure.



On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham 
wrote:

> Hi,
>
> On Wed, 20 Apr 2016 19:04 Tuhin Samanta 
> wrote:
>
> > Thank Mark for your suggestion.
> >
> > I was trying to resolve the problem 
> > " 4 particles communicated to PME node 4 are more than 2/3 times the
> > cut-off out of the domain decomposition cell of their charge group in
> > dimension x.
> > This usually means that your system is not well equilibrated."
> >
> > First of all I have done the energy minimization for long times for
> proper
> > equilibriuation.
> >
>
> Then what did you change? You may need to be more gentle.
>
> Secondly by changing rcut and PME mesh girding I have tried a lot. But it's
> > showing same error message.
> >
>
> Those suggestions are made for perhaps improving performance, which is
> unrelated to your error. They just both happen to use the word PME...
>
> So can you please tell me any specific solution for this problem.
> >
>
> They're all at http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> Mark
>
> Thanking you,
> > Tuhin
> >
> >
> > On Wed, Apr 20, 2016 at 2:21 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > The information message and the actual error are separated in your log
> > file
> > > with a bunch of punctuation because they're logically separate.
> > >
> > > Anyway, there should also have been a link to
> > > http://www.gromacs.org/Documentation/Errors which suggests some
> > strategies
> > > for this issue.
> > >
> > > Mark
> > >
> > > On Wed, 20 Apr 2016 09:00 Tuhin Samanta 
> > > wrote:
> > >
> > > > Hello ,
> > > >
> > > > My system involves water molecules in a box of 5x5x5 nm3. When I was
> > > doing
> > > > the simulation for energy minimization I  got n error message --
> > > >
> > > > The optimal PME mesh load for parallel simulations is below 0.5
> > > >   and for highly parallel simulations between 0.25 and 0.33,
> > > >   for higher performance, increase the cut-off and the PME grid
> spacing
> > > >
> > > >  4 particles communicated to PME node 4 are more than 2/3 times the
> > > cut-off
> > > > out of the domain decomposition cell of their charge group in
> dimension
> > > x.
> > > > This usually means that your system is not well equilibrated.
> > > >
> > > > I have changed the cut off and grid spacing but still it's showing
> the
> > > > error message. I know it is the problem with the parallelization.
> Also
> > I
> > > > have  gone through the user forum's discussion.  So can anyone please
> > > > suggest me how to get rid of that problem.
> > > >
> > > >
> > > > Thank you so much.
> > > > Best regards,
> > > > Tuhin
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-20 Thread Mark Abraham 
Hi,

On Wed, 20 Apr 2016 19:04 Tuhin Samanta  wrote:

> Thank Mark for your suggestion.
>
> I was trying to resolve the problem 
> " 4 particles communicated to PME node 4 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated."
>
> First of all I have done the energy minimization for long times for proper
> equilibriuation.
>

Then what did you change? You may need to be more gentle.

Secondly by changing rcut and PME mesh girding I have tried a lot. But it's
> showing same error message.
>

Those suggestions are made for perhaps improving performance, which is
unrelated to your error. They just both happen to use the word PME...

So can you please tell me any specific solution for this problem.
>

They're all at http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Mark

Thanking you,
> Tuhin
>
>
> On Wed, Apr 20, 2016 at 2:21 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > The information message and the actual error are separated in your log
> file
> > with a bunch of punctuation because they're logically separate.
> >
> > Anyway, there should also have been a link to
> > http://www.gromacs.org/Documentation/Errors which suggests some
> strategies
> > for this issue.
> >
> > Mark
> >
> > On Wed, 20 Apr 2016 09:00 Tuhin Samanta 
> > wrote:
> >
> > > Hello ,
> > >
> > > My system involves water molecules in a box of 5x5x5 nm3. When I was
> > doing
> > > the simulation for energy minimization I  got n error message --
> > >
> > > The optimal PME mesh load for parallel simulations is below 0.5
> > >   and for highly parallel simulations between 0.25 and 0.33,
> > >   for higher performance, increase the cut-off and the PME grid spacing
> > >
> > >  4 particles communicated to PME node 4 are more than 2/3 times the
> > cut-off
> > > out of the domain decomposition cell of their charge group in dimension
> > x.
> > > This usually means that your system is not well equilibrated.
> > >
> > > I have changed the cut off and grid spacing but still it's showing the
> > > error message. I know it is the problem with the parallelization. Also
> I
> > > have  gone through the user forum's discussion.  So can anyone please
> > > suggest me how to get rid of that problem.
> > >
> > >
> > > Thank you so much.
> > > Best regards,
> > > Tuhin
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-20 Thread Tuhin Samanta 
Thank Mark for your suggestion.

I was trying to resolve the problem 
" 4 particles communicated to PME node 4 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated."

First of all I have done the energy minimization for long times for proper
equilibriuation.
Secondly by changing rcut and PME mesh girding I have tried a lot. But it's
showing same error message.

So can you please tell me any specific solution for this problem.


Thanking you,
Tuhin


On Wed, Apr 20, 2016 at 2:21 PM, Mark Abraham 
wrote:

> Hi,
>
> The information message and the actual error are separated in your log file
> with a bunch of punctuation because they're logically separate.
>
> Anyway, there should also have been a link to
> http://www.gromacs.org/Documentation/Errors which suggests some strategies
> for this issue.
>
> Mark
>
> On Wed, 20 Apr 2016 09:00 Tuhin Samanta 
> wrote:
>
> > Hello ,
> >
> > My system involves water molecules in a box of 5x5x5 nm3. When I was
> doing
> > the simulation for energy minimization I  got n error message --
> >
> > The optimal PME mesh load for parallel simulations is below 0.5
> >   and for highly parallel simulations between 0.25 and 0.33,
> >   for higher performance, increase the cut-off and the PME grid spacing
> >
> >  4 particles communicated to PME node 4 are more than 2/3 times the
> cut-off
> > out of the domain decomposition cell of their charge group in dimension
> x.
> > This usually means that your system is not well equilibrated.
> >
> > I have changed the cut off and grid spacing but still it's showing the
> > error message. I know it is the problem with the parallelization. Also I
> > have  gone through the user forum's discussion.  So can anyone please
> > suggest me how to get rid of that problem.
> >
> >
> > Thank you so much.
> > Best regards,
> > Tuhin
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

2016-04-20 Thread Mark Abraham 
Hi,

The information message and the actual error are separated in your log file
with a bunch of punctuation because they're logically separate.

Anyway, there should also have been a link to
http://www.gromacs.org/Documentation/Errors which suggests some strategies
for this issue.

Mark

On Wed, 20 Apr 2016 09:00 Tuhin Samanta  wrote:

> Hello ,
>
> My system involves water molecules in a box of 5x5x5 nm3. When I was doing
> the simulation for energy minimization I  got n error message --
>
> The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing
>
>  4 particles communicated to PME node 4 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
>
> I have changed the cut off and grid spacing but still it's showing the
> error message. I know it is the problem with the parallelization. Also I
> have  gone through the user forum's discussion.  So can anyone please
> suggest me how to get rid of that problem.
>
>
> Thank you so much.
> Best regards,
> Tuhin
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

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

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.