Re: [gmx-users] pressure scaling more than 1%

[Justin A. Lemkul]

杜波 wrote:


Dear teacher,

when i do remd in the npt ensemble.
it will be bomb when it run a little time .
and the dt is 0.00144,(in my opinion ,it is small enough , in this 
condition , the simlution time is about one month )


how could i do except using a small dt.


Please consult:

http://www.gromacs.org/Documentation/Errors#Pressure_scaling_more_than_1.25
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Without seeing your .mdp file, there's little more to be said.  Please also 
search the list archive; such issues have been asked and solved hundreds of 
times over and there is certainly some useful information already available.


Also note that high-temperature replicates in REMD may be unstable in an NPT 
ensemble, largely because the algorithms break down.


-Justin


thanks!!

step 112000, will finish Sun Dec 11 03:59:40 2011
Step 112002  Warning: pressure scaling more than 1%, mu: 48937.5 48937.5 
48937.5


---
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: nsgrid.c, line: 549

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value 1792617862. It should have been within [ 0 .. 
330578952 ]


For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


regards,

Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com 



--


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 scaling more than 1%

[杜波]

Dear teacher,

when i do remd in the npt ensemble.
it will be bomb when it run a little time .
and the dt is 0.00144,(in my opinion ,it is small enough , in this
condition , the simlution time is about one month )

how could i do except using a small dt.
thanks!!

step 112000, will finish Sun Dec 11 03:59:40 2011
Step 112002  Warning: pressure scaling more than 1%, mu: 48937.5 48937.5
48937.5

---
Program mdrun_mpi_4.5.5, VERSION 4.5.5
Source code file: nsgrid.c, line: 549

Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value 1792617862. It should have been within [ 0 ..
330578952 ]

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


regards,

Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com
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Re: [gmx-users] pressure scaling more than 1%

[Justin A. Lemkul]

Sebastian Waltz wrote:

Hi all,

my simulation runs well for the first 70 steps with a
step size of 0.001ps and when I get the warning that the
pressure scaling is more than 1% every 1 step or so.
So, is my tau_p of 0.2 to small or is the equillibration
not done well enough.


Possibly, have you tried larger values?  Usually something on the order of 
1.0-5.0 ps is more typical.



I am simulating a small peptide in CHCl3 with an handmade
CHCl3 model. 



If you're seeing instabilities, it could also be related to the topology.  Have 
you thoroughly validated the parameters you're using for CHCl3?


-Justin


 title= ttt
cpp =  /lib/cpp
include = -I../top
constraints =  none
;define  =  -DFLEX_SPC
;define  =  -DPOSRES; for possition
restraints
integrator  =  md   
emtol   =  100.0
emstep  =  0.005
dt  =  0.001; ps !
nsteps  =  200  ; total 2 ns
nstcomm =  1

nstxout =  0
nstvout =  0
nstfout =  10   
nstlog  =  0
nstenergy   =  10   
nstxtcout   =  10

xtc_grps= Protein+PTS+AIC 


nstlist =  5
ns_type =  grid 
rlist   =  1.2  

coulombtype =  PME  
rcoulomb=  1.2  
rvdw=  1.2  
fourierspacing  =  0.12 
pme_order   =  4
optimize_fft=  yes

Tcoupl  =  berendsen
tc-grps =  Protein+PTS+AIC CHCl3
tau_t   =  0.1 0.1 
ref_t   =  300 300


energygrps  =  Protein+PTS+AIC CHCl3

Pcoupl  =  berendsen
tau_p   =  0.2
compressibility =  5.4e-5
ref_p   =  1.0

gen_vel =  yes
gen_temp=  300
gen_seed=  913529


Thanks


--


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 scaling more than 1%

[Sebastian Waltz]

Hi all,

my simulation runs well for the first 70 steps with a
step size of 0.001ps and when I get the warning that the
pressure scaling is more than 1% every 1 step or so.
So, is my tau_p of 0.2 to small or is the equillibration
not done well enough.
I am simulating a small peptide in CHCl3 with an handmade
CHCl3 model. 

 title= ttt
cpp =  /lib/cpp
include = -I../top
constraints =  none
;define  =  -DFLEX_SPC
;define  =  -DPOSRES; for possition
restraints
integrator  =  md   
emtol   =  100.0
emstep  =  0.005
dt  =  0.001; ps !
nsteps  =  200  ; total 2 ns
nstcomm =  1

nstxout =  0
nstvout =  0
nstfout =  10   
nstlog  =  0
nstenergy   =  10   
nstxtcout   =  10

xtc_grps= Protein+PTS+AIC 

nstlist =  5
ns_type =  grid 
rlist   =  1.2  

coulombtype =  PME  
rcoulomb=  1.2  
rvdw=  1.2  
fourierspacing  =  0.12 
pme_order   =  4
optimize_fft=  yes

Tcoupl  =  berendsen
tc-grps =  Protein+PTS+AIC CHCl3
tau_t   =  0.1 0.1 
ref_t   =  300 300

energygrps  =  Protein+PTS+AIC CHCl3

Pcoupl  =  berendsen
tau_p   =  0.2
compressibility =  5.4e-5
ref_p   =  1.0

gen_vel =  yes
gen_temp=  300
gen_seed=  913529


Thanks
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Re: [gmx-users] pressure scaling more than 1%

[van Bemmelen]

Hi Wang Qin,

It sounds to me like (part of) your structure immediately starts collapsing 
during equilibration. So I have a couple of suggestions:

1) It may help to take a look at the trajectory file from those first 500 
steps, to see what's really going on physically.
2) Please make sure you also do your minimization run with the free energy 
paramters turned ON.
3) For equilibration runs, I'd suggest using Berendsen temperature coupling 
(with tau_t=0.2 or larger) instead of Nosé-Hoover, combined with the gen_vel 
mdp-option to generate initial velocities at 300K. Then, you may switch to 
Nosé-Hoover for your production run, with a tau_t of at least 0.5. Running with 
NH T-coupling on a system that's far from equilibrium can give very serious 
problems, resulting in various stange errors and crashes.

Apart from the above, I really don't see big problems in your mdp-file. Also, 
your strategy of taking the output structure from the previous lambda=0.9 (and 
re-minimize and re-equilibrate) sounds fine to me.

But maybe someone else with more experience has something to add to this. :-)

Grtz,
Jeroen


>From: "Wang Qin" <[EMAIL PROTECTED]>
>Subject: Re: [gmx-users] pressure scaling more than 1%
>To: "Discussion list for GROMACS users" 
>Message-ID:
>   <[EMAIL PROTECTED]>
>Content-Type: text/plain; charset="iso-8859-1"
>
>The system is a protein binding with one ligand and the ligand 
>mutates to
>another one. The problem is found when lamda=1. First of all I 
>run a energy
>minimization using an initial structure from the product of 
>lamda=0.9. Then
>the problem happens when I run a equilibrium.
>Here is the mdp option:
>cpp  =/usr/bin/cpp
>integrator   =
>md
>
>tinit= 0
>dt   = 0.002
>nsteps   = 5
>nstcomm  = 1
>nstxout  = 0
>nstvout  = 0
>nstfout  = 0
>nstlog   = 500
>nstenergy=
>100
>
>nstxtcout= 5000
>xtc-precision= 1000
>nstlist  = 1
>ns_type  = grid
>
>
>Pcoupl   = berendsen
>tau_p= 1.0
>compressibility  = 4.5e-05
>ref_p= 1.0
>
>
>tcoupl   = nose-hoover
>tc_grps  = system
>tau_t= 0.1
>ref_t= 300
>
>constraints  = none
>constraint-algorithm =
>lincs
>
>shake-tol= 0.0001
>lincs-order  = 12
>lincs-warnangle  =
>30
>
>coulombtype  =
>pme
>
>rcoulomb = 1.0
>
>epsilon-r=
>1
>
>vdw-type =
>switch
>
>rvdw-switch  = 1.0
>rvdw = 1.3
>DispCorr  =
>EnerPres
>
>fourierspacing   = 0.08
>
>fourier_nx   = 0
>fourier_ny   = 0
>fourier_nz   = 0
>
>
>pme_order= 6
>ewald_rtol   = 1e-05
>epsilon_surface  = 0
>optimize_fft = yes
>
>
>free_energy  = yes
>init_lambda  = 1.0
>delta_lambda = 0
>sc_alpha =0.5
>sc-power =1.0
>sc-sigma = 0.3
>
>
>Thanks.
>
>
>On 8/8/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
>>
>> Wang Qin wrote:
>> > Dear all,
>> >   I am trying to do a FEP. In the equilibrium 
>step, it fails
>> > after about 500 steps with a warnning:  pressure scaling 
>more than 1%,
>> > mu: 1.06718 1.06718 1.06718. I searched the old discussion 
>about it and
>> > then try to increase the tau_p to 2 till 10. But it just 
>goes futher but
>> > still meets the problem at the end.
>> >   Any idea about it?
>>
>> Not unless you tell us how you prepared this system. Almost certainly
>> the initial structure is too far from the constant-P 
>equilibrium state.
>> Follow the kind of things that the tutorial material does, and also
>> check out this link
>> http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
>>
>> Mark
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Re: [gmx-users] pressure scaling more than 1%

[Wang Qin]

The system is a protein binding with one ligand and the ligand mutates to
another one. The problem is found when lamda=1. First of all I run a energy
minimization using an initial structure from the product of lamda=0.9. Then
the problem happens when I run a equilibrium.
Here is the mdp option:
cpp  =/usr/bin/cpp
integrator   =
md

tinit= 0
dt   = 0.002
nsteps   = 5
nstcomm  = 1
nstxout  = 0
nstvout  = 0
nstfout  = 0
nstlog   = 500
nstenergy=
100

nstxtcout= 5000
xtc-precision= 1000
nstlist  = 1
ns_type  = grid


Pcoupl   = berendsen
tau_p= 1.0
compressibility  = 4.5e-05
ref_p= 1.0


tcoupl   = nose-hoover
tc_grps  = system
tau_t= 0.1
ref_t= 300

constraints  = none
constraint-algorithm =
lincs

shake-tol= 0.0001
lincs-order  = 12
lincs-warnangle  =
30

coulombtype  =
pme

rcoulomb = 1.0

epsilon-r=
1

vdw-type =
switch

rvdw-switch  = 1.0
rvdw = 1.3
DispCorr  =
EnerPres

fourierspacing   = 0.08

fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0


pme_order= 6
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = yes


free_energy  = yes
init_lambda  = 1.0
delta_lambda = 0
sc_alpha =0.5
sc-power =1.0
sc-sigma = 0.3


Thanks.


On 8/8/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
>
> Wang Qin wrote:
> > Dear all,
> >   I am trying to do a FEP. In the equilibrium step, it fails
> > after about 500 steps with a warnning:  pressure scaling more than 1%,
> > mu: 1.06718 1.06718 1.06718. I searched the old discussion about it and
> > then try to increase the tau_p to 2 till 10. But it just goes futher but
> > still meets the problem at the end.
> >   Any idea about it?
>
> Not unless you tell us how you prepared this system. Almost certainly
> the initial structure is too far from the constant-P equilibrium state.
> Follow the kind of things that the tutorial material does, and also
> check out this link
> http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
>
> Mark
> ___
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Re: [gmx-users] pressure scaling more than 1%

[Mark Abraham]

Wang Qin wrote:

Dear all,
  I am trying to do a FEP. In the equilibrium step, it fails 
after about 500 steps with a warnning:  pressure scaling more than 1%, 
mu: 1.06718 1.06718 1.06718. I searched the old discussion about it and 
then try to increase the tau_p to 2 till 10. But it just goes futher but 
still meets the problem at the end.

  Any idea about it?


Not unless you tell us how you prepared this system. Almost certainly 
the initial structure is too far from the constant-P equilibrium state. 
Follow the kind of things that the tutorial material does, and also 
check out this link 
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation


Mark
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[gmx-users] pressure scaling more than 1%

[Wang Qin]

Dear all,
  I am trying to do a FEP. In the equilibrium step, it fails after
about 500 steps with a warnning:  pressure scaling more than 1%, mu: 1.06718
1.06718 1.06718. I searched the old discussion about it and then try to
increase the tau_p to 2 till 10. But it just goes futher but still meets the
problem at the end.
  Any idea about it?

Regards,
Qin
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Re: [gmx-users] pressure scaling more than 1%

[Mark Abraham]

james zhang wrote:

Hi,
 
I try to compress a box at a high pressure, but the box alwasys 
collapsed after several steps.
 
And I get the error:  /pressure scaling more than 1%/
 
How can I get over this problem.


Probably, doing the pressure increase gradually will help.

Mark
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Re: [gmx-users] pressure scaling more than 1%

[james zhang]

ok, Thanks a lot
On 10/1/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
james zhang wrote:> Hi,>> I try to compress a box at a high pressure, but the box alwasys
> collapsed after several steps.>> And I get the error:  /pressure scaling more than 1%/>> How can I get over this problem.>increase tau_p> Thanks in advance.
>>> --> Sincerely yours,> James jianzhang> Department of Mechanical and Chemical Engineering> North Carolina Agricultural and Technical State University> 1601 East Market Street
> Greensboro, NC 27411 >> ___> gmx-users mailing list
gmx-users@gromacs.org> http://www.gromacs.org/mailman/listinfo/gmx-users> Please don't post (un)subscribe requests to the list. Use the
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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, Swedenphone:  46 18 471 4205  fax: 46 18 511 755[EMAIL PROTECTED][EMAIL PROTECTED]
   http://folding.bmc.uu.se___gmx-users mailing list
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-- Sincerely yours,James jianzhangDepartment of Mechanical and Chemical Engineering North Carolina Agricultural and Technical State University 1601 East Market Street 
Greensboro, NC 27411 [EMAIL PROTECTED] or [EMAIL PROTECTED]http://www.ncat.edu/~jzhang
 
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Re: [gmx-users] pressure scaling more than 1%

[David van der Spoel]

james zhang wrote:

Hi,
 
I try to compress a box at a high pressure, but the box alwasys 
collapsed after several steps.
 
And I get the error:  /pressure scaling more than 1%/
 
How can I get over this problem.
 




increase tau_p


Thanks in advance.


--
Sincerely yours,
James jianzhang
Department of Mechanical and Chemical Engineering
North Carolina Agricultural and Technical State University
1601 East Market Street
Greensboro, NC 27411
 





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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 scaling more than 1%

[james zhang]

Hi,
 
I try to compress a box at a high pressure, but the box alwasys collapsed after several steps.
 
And I get the error:  pressure scaling more than 1%
 
How can I get over this problem.
 
Thanks in advance.
-- Sincerely yours,James jianzhangDepartment of Mechanical and Chemical Engineering North Carolina Agricultural and Technical State University 1601 East Market Street Greensboro, NC 27411 
 
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