Re: [gmx-users] System expansion

[Dr. Vitaly Chaban]

Hi Oliver -

Hmm. Did you try to start from (a little bit) different configurations
on the problematic machine? Or re-install gromacs there, perhaps?

Dr. Vitaly Chaban





On Thu, Jun 20, 2013 at 3:44 PM, Oliver Schillinger
wrote:

> Dear Gromacs users,
>
> I experience a very strange problem.
> I have a well equilibrated system consisting of a protein, a ligand, ions
> and water. On most machines I run my simulations on, everything is just
> fine. Except for one compute cluster, where the system undergoes an extreme
> expansion when I use the md-vv integrator for an NPT-simulation. To give
> you an impression I uploaded a short video showing the first 100
> picoseconds of the run to my Dropbox:
> https://www.dropbox.com/s/**d1ef94bbns0hasr/explode.mpg
>
> The system expands so heavily that it consists mainly of vacuum.
> If I switch the integrator from md-vv to md, everything is fine again.
> The same simulation (same .mdp file, same starting positions and
> velocities from previous simulation) runs fine with the md-vv integrator on
> our GPU-cluster.
>
> The .mdp file can be downloaded here:
> https://www.dropbox.com/s/**k9it6eiqb259o59/explode.mdp
>
> I have no idea if it is me who is doing something wrond, a bug in Gromacs,
> a problem with the cluster or something else.
> Any suggestions and ideas are appreciated.
>
> Regards,
> Oliver
>
> --
> Oliver Schillinger
> Master's student
>
> Forschungszentrum Juelich GmbH
> 52425 Juelich | Germany
>
> Building 5.8v, Room 3010
> Phone: 02461-61-9532
>
> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
> Prof. Dr. Sebastian M. Schmidt
> --
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[gmx-users] System expansion

[Oliver Schillinger]

Dear Gromacs users,

I experience a very strange problem.
I have a well equilibrated system consisting of a protein, a ligand, 
ions and water. On most machines I run my simulations on, everything is 
just fine. Except for one compute cluster, where the system undergoes an 
extreme expansion when I use the md-vv integrator for an NPT-simulation. 
To give you an impression I uploaded a short video showing the first 100 
picoseconds of the run to my Dropbox:

https://www.dropbox.com/s/d1ef94bbns0hasr/explode.mpg

The system expands so heavily that it consists mainly of vacuum.
If I switch the integrator from md-vv to md, everything is fine again.
The same simulation (same .mdp file, same starting positions and 
velocities from previous simulation) runs fine with the md-vv integrator 
on our GPU-cluster.


The .mdp file can be downloaded here:
https://www.dropbox.com/s/k9it6eiqb259o59/explode.mdp

I have no idea if it is me who is doing something wrond, a bug in 
Gromacs, a problem with the cluster or something else.

Any suggestions and ideas are appreciated.

Regards,
Oliver

--
Oliver Schillinger
Master's student

Forschungszentrum Juelich GmbH
52425 Juelich | Germany

Building 5.8v, Room 3010
Phone: 02461-61-9532

Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
--
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Re: [gmx-users] System broken after energy minimization

[Tsjerk Wassenaar]

Hey :

When increasing the system size like that, make sure that all molecules in
the original box are whole (trjconv -pbc mol). Only then can you, e.g., use
genconf to double the system.

Cheers,

Tsjerk


On Sat, Jun 15, 2013 at 1:49 PM, Justin Lemkul  wrote:

>
>
> On 6/15/13 6:21 AM, Kieu Thu Nguyen wrote:
>
>> Dear users,
>>
>> I make a rectangle bilayer by doubling two equilibrated cubic boxes. But
>> after minimizing, the system have been crashed. I do not understand why. I
>> attach the em.mdp below
>>
>>
> The list does not allow attachments.  Either copy and paste or provide a
> link to where the file can be downloaded.  The .mdp file may or may not be
> useful.  You should carefully inspect the starting configuration for atomic
> overlap, and then otherwise follow the instructions described here:
>
> http://www.gromacs.org/**Documentation/Terminology/**
> Blowing_Up#Diagnosing_an_**Unstable_System
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] System broken after energy minimization

[Justin Lemkul]

On 6/15/13 6:21 AM, Kieu Thu Nguyen wrote:

Dear users,

I make a rectangle bilayer by doubling two equilibrated cubic boxes. But
after minimizing, the system have been crashed. I do not understand why. I
attach the em.mdp below



The list does not allow attachments.  Either copy and paste or provide a link to 
where the file can be downloaded.  The .mdp file may or may not be useful.  You 
should carefully inspect the starting configuration for atomic overlap, and then 
otherwise follow the instructions described here:


http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] System broken after energy minimization

[Kieu Thu Nguyen]

Dear users,

I make a rectangle bilayer by doubling two equilibrated cubic boxes. But
after minimizing, the system have been crashed. I do not understand why. I
attach the em.mdp below

Thankful for any help !
Thu
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Re: [gmx-users] System equilibrium problems

[Parker de Waal]

Hi Mark,

Thanks for your response,

Currently I'm using the gromos53a6 force field because it is compatible
with heme cofactor found within P450.
I'll look through the literature again to double check my settings for my
NvT, NpT and energy minimization steps
as well, however any further insight would be greatly appreciated!

Parker


On Fri, Jun 14, 2013 at 4:13 AM, Mark Abraham wrote:

> On Thu, Jun 13, 2013 at 11:59 PM, Parker de Waal
> wrote:
>
> > Hi everyone,
> >
> > I recently tried to perform an 25 ns simulation on 12 nodes and was
> greeted
> > with this error around 3.2 ns into the run.
> >
> > '3 particles communicated to PME node 9 are more than 2/3 times the
> cut-off
> > out of the domain decomposition cell of their charge group in dimension
> y.'
> >
> > To my knowledge the system has reached equilibrium as shown by energy
> > minimization, nvt and npt runs prior to the md run. The only thing that
> > concerns me is the Pressure average of 1.9
> >
>
> This is normal, see
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
>
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> >
> ---
> > Potential   -921529  3200094074.9-214425
> >  (kJ/mol)
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> >
> ---
> > Temperature 300.033   0.161.57434  -0.790469  (K)
> >
> > Energy  Average   Err.Est.   RMSD  Tot-Drift
> >
> >
> ---
> > Pressure1.94649   0.3291.45451.28586
>  (bar)
> > Density 1012.96  0.037   0.778484 -0.0126246
> >  (kg/m^3)
> >
> > Additionally here is a link to my md.mdp file
> >
> https://gist.github.com/ParkerdeWaal/d472bac58aa9cebfc23e#file-gistfile1-sh
>
>
> Seems fine, apart from fourierspacing being rather more lax than normal. Be
> sure your settings are compatible with those used for your force field.
>
> Mark
>
>
> >
> >
> > Any input would be greatly appreciated!
> > Parker
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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> >
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Re: [gmx-users] System equilibrium problems

[Mark Abraham]

On Thu, Jun 13, 2013 at 11:59 PM, Parker de Waal
wrote:

> Hi everyone,
>
> I recently tried to perform an 25 ns simulation on 12 nodes and was greeted
> with this error around 3.2 ns into the run.
>
> '3 particles communicated to PME node 9 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.'
>
> To my knowledge the system has reached equilibrium as shown by energy
> minimization, nvt and npt runs prior to the md run. The only thing that
> concerns me is the Pressure average of 1.9
>

This is normal, see
http://www.gromacs.org/Documentation/Terminology/Pressure


>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Potential   -921529  3200094074.9-214425
>  (kJ/mol)
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Temperature 300.033   0.161.57434  -0.790469  (K)
>
> Energy  Average   Err.Est.   RMSD  Tot-Drift
>
> ---
> Pressure1.94649   0.3291.45451.28586  (bar)
> Density 1012.96  0.037   0.778484 -0.0126246
>  (kg/m^3)
>
> Additionally here is a link to my md.mdp file
> https://gist.github.com/ParkerdeWaal/d472bac58aa9cebfc23e#file-gistfile1-sh


Seems fine, apart from fourierspacing being rather more lax than normal. Be
sure your settings are compatible with those used for your force field.

Mark


>
>
> Any input would be greatly appreciated!
> Parker
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] System equilibrium problems

[Parker de Waal]

Hi everyone,

I recently tried to perform an 25 ns simulation on 12 nodes and was greeted
with this error around 3.2 ns into the run.

'3 particles communicated to PME node 9 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.'

To my knowledge the system has reached equilibrium as shown by energy
minimization, nvt and npt runs prior to the md run. The only thing that
concerns me is the Pressure average of 1.9

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Potential   -921529  3200094074.9-214425
 (kJ/mol)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Temperature 300.033   0.161.57434  -0.790469  (K)

Energy  Average   Err.Est.   RMSD  Tot-Drift
---
Pressure1.94649   0.3291.45451.28586  (bar)
Density 1012.96  0.037   0.778484 -0.0126246
 (kg/m^3)

Additionally here is a link to my md.mdp file
https://gist.github.com/ParkerdeWaal/d472bac58aa9cebfc23e#file-gistfile1-sh

Any input would be greatly appreciated!
Parker
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Re: [gmx-users] System does not heat up to 300K.

[Marc Hoemberger]

Thanks, I must have confused the units for the simulated annealing
parameters.


On Tue, Jun 11, 2013 at 2:12 PM, Dr. Vitaly Chaban wrote:

> According to your MD parameters, your system should attain T=300K at the
> 300th
> nanosecond.
>
> Since you have run only for 50 * 0.002 ps = 1ns, you got T=1K, since
> temperature elevates linearly, based on your setup.
>
>
> Dr. Vitaly Chaban
>
>
>
>
> On Tue, Jun 11, 2013 at 8:07 PM, Marc Hömberger  wrote:
>
> > Hi,
> >
> > I have a system setup (minimized etc.) and wanted to heat this system
> > gradually with simulated annealing. I set up the mdp file as you can see
> > below (simulated annealing part is marked bold). But when the heating is
> > finished, the log file tells me that the temperature of the system is
> only
> > 1K (see below).
> >
> > Can someone tell me what I am doing wrong?
> >
> >
> > Best,
> > Marc
> >
> > ; PREPROCESSING *
> > ;include=
> > ;define =
> > ; RUN CONTROL ***
> > dt  = 0.002 ; timestep, 2 fs
> > integrator  = md; leap-frog integrator
> > nsteps  = 50 ; 2 * 50 = 1000 ps
> > tinit   = 0 ; starting time, ps
> > init_step   = 0 ; starting step
> > comm-mode   = linear; remove COM translation
> > nstcomm = 10; freq steps comm-mode
> > comm-grps   = system; groups COM removal ; protein
> > nstcalcenergy   = -1; freq calc ener; default =
> nstlist
> > ; DYNAMICS **
> > ;### Initial velocity assignment
> > gen_vel = yes   ; assign velocities from Maxwell
> > distribution
> > gen_temp= 300   ; temperature for Maxwell
> > distribution
> > gen_seed= -1; random generator seed; -1 from
> > job ID
> > ; OUTPUT CONTROL 
> > ;### xtc
> > nstxtcout   = 2500  ; .xtc freq write coor
> > xtc-precision   = 1000  ; .xtc precision
> > xtc_grps= system; .xtc saved groups
> > ;### trr
> > nstxout = 50; .trr freq write coor
> > nstvout = 50; .trr freq write vel
> > nstfout = 0 ; .trr freq write forces
> > ;### log
> > nstlog  = 2500  ; .log freq write ener
> > ;### edr
> > nstenergy   = 2500  ; .edr freq write ener; =
> > i*nstcalcenergy
> > energygrps  = protein non-protein   ; .edr saved groups
> > ; NON-BONDED INTERACTIONS ***
> > ns_type = grid  ; search neighbor grid cells
> > nstlist = 10; freq update NB list
> >
> > vdwtype = switch; switching function for VdW
> > coulombtype = PME   ; PME for long-range
> electrostatics
> > rvdw_switch = 0.9   ; switching dist VdW
> > rvdw= 1.0   ; cutoff VdW
> > rcoulomb= 1.2   ; cutoff elec
> > rlist   = 1.2   ; cutoff NB list; must = rcoulomb
> > when PME
> >
> > epsilon-r   = 1 ; dielectric const
> > DispCorr= EnerPres  ; Long-range VdW dispersion
> > correction
> >
> > ;### PME & Ewald
> > ewald_rtol  = 1.0e-5; direct space tolerance;
> > 1.0e-6/2.2e-5
> > fourierspacing  = 0.12  ; max grid spacing for FFT
> > pme_order   = 6 ; interpolation order; depends on
> > cutoff
> > ewald_geometry  = 3d; Ewald in 3d
> > epsilon_surface = 0 ; dipole correction for 3d Ewald
> > optimize_fft= yes   ; start-up FFT grid optimization
> > ; BOUNDARY CONTROL **
> > pbc = xyz   ; 3-D PBC
> > ; CONSTRAINTS CONTROL ***
> > constraints = all-bonds ; all bonds (even heavy atom-H
> > bonds) constrained
> > continuation= no; constraints applied to initial
> > conf
> > constraint_algorithm = lincs; holonomic constraints
> > lincs_iter  = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > lincs_warnangle = 30; max allowed bond angle before
> > warning
> > ; TEMPERATURE CONTROL ***
> > tcoupl  = nose-hoover   ; Nose-Hoover T-coupling;
> v-rescale
> > tc-grps = s

Re: [gmx-users] System does not heat up to 300K.

[Dr. Vitaly Chaban]

According to your MD parameters, your system should attain T=300K at the 300th
nanosecond.

Since you have run only for 50 * 0.002 ps = 1ns, you got T=1K, since
temperature elevates linearly, based on your setup.


Dr. Vitaly Chaban




On Tue, Jun 11, 2013 at 8:07 PM, Marc Hömberger  wrote:

> Hi,
>
> I have a system setup (minimized etc.) and wanted to heat this system
> gradually with simulated annealing. I set up the mdp file as you can see
> below (simulated annealing part is marked bold). But when the heating is
> finished, the log file tells me that the temperature of the system is only
> 1K (see below).
>
> Can someone tell me what I am doing wrong?
>
>
> Best,
> Marc
>
> ; PREPROCESSING *
> ;include=
> ;define =
> ; RUN CONTROL ***
> dt  = 0.002 ; timestep, 2 fs
> integrator  = md; leap-frog integrator
> nsteps  = 50 ; 2 * 50 = 1000 ps
> tinit   = 0 ; starting time, ps
> init_step   = 0 ; starting step
> comm-mode   = linear; remove COM translation
> nstcomm = 10; freq steps comm-mode
> comm-grps   = system; groups COM removal ; protein
> nstcalcenergy   = -1; freq calc ener; default = nstlist
> ; DYNAMICS **
> ;### Initial velocity assignment
> gen_vel = yes   ; assign velocities from Maxwell
> distribution
> gen_temp= 300   ; temperature for Maxwell
> distribution
> gen_seed= -1; random generator seed; -1 from
> job ID
> ; OUTPUT CONTROL 
> ;### xtc
> nstxtcout   = 2500  ; .xtc freq write coor
> xtc-precision   = 1000  ; .xtc precision
> xtc_grps= system; .xtc saved groups
> ;### trr
> nstxout = 50; .trr freq write coor
> nstvout = 50; .trr freq write vel
> nstfout = 0 ; .trr freq write forces
> ;### log
> nstlog  = 2500  ; .log freq write ener
> ;### edr
> nstenergy   = 2500  ; .edr freq write ener; =
> i*nstcalcenergy
> energygrps  = protein non-protein   ; .edr saved groups
> ; NON-BONDED INTERACTIONS ***
> ns_type = grid  ; search neighbor grid cells
> nstlist = 10; freq update NB list
>
> vdwtype = switch; switching function for VdW
> coulombtype = PME   ; PME for long-range electrostatics
> rvdw_switch = 0.9   ; switching dist VdW
> rvdw= 1.0   ; cutoff VdW
> rcoulomb= 1.2   ; cutoff elec
> rlist   = 1.2   ; cutoff NB list; must = rcoulomb
> when PME
>
> epsilon-r   = 1 ; dielectric const
> DispCorr= EnerPres  ; Long-range VdW dispersion
> correction
>
> ;### PME & Ewald
> ewald_rtol  = 1.0e-5; direct space tolerance;
> 1.0e-6/2.2e-5
> fourierspacing  = 0.12  ; max grid spacing for FFT
> pme_order   = 6 ; interpolation order; depends on
> cutoff
> ewald_geometry  = 3d; Ewald in 3d
> epsilon_surface = 0 ; dipole correction for 3d Ewald
> optimize_fft= yes   ; start-up FFT grid optimization
> ; BOUNDARY CONTROL **
> pbc = xyz   ; 3-D PBC
> ; CONSTRAINTS CONTROL ***
> constraints = all-bonds ; all bonds (even heavy atom-H
> bonds) constrained
> continuation= no; constraints applied to initial
> conf
> constraint_algorithm = lincs; holonomic constraints
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> lincs_warnangle = 30; max allowed bond angle before
> warning
> ; TEMPERATURE CONTROL ***
> tcoupl  = nose-hoover   ; Nose-Hoover T-coupling; v-rescale
> tc-grps = system; two coupling groups - more
> accurate
> tau_t   = 0.6   ; coupling time constant at equil,
> in ps
> ref_t   = 300   ; reference temperature, one for
> each group, in K
> ; PRESSURE CONTROL **
> pcoupl  = Parrinello-Rah

Re: [gmx-users] System does not heat up to 300K.

[Justin Lemkul]

On 6/11/13 2:07 PM, Marc Hömberger wrote:

Hi,

I have a system setup (minimized etc.) and wanted to heat this system
gradually with simulated annealing. I set up the mdp file as you can see
below (simulated annealing part is marked bold). But when the heating is
finished, the log file tells me that the temperature of the system is only
1K (see below).

Can someone tell me what I am doing wrong?



You've specified heating to 300K over 300,000 ps (300 ns), thus 1 K per 1 ns. 
Your simulation calls for 1 ns of time, thus 1 K should be achieved.


-Justin



Best,
Marc

; PREPROCESSING *
;include=
;define =
; RUN CONTROL ***
dt  = 0.002 ; timestep, 2 fs
integrator  = md; leap-frog integrator
nsteps  = 50 ; 2 * 50 = 1000 ps
tinit   = 0 ; starting time, ps
init_step   = 0 ; starting step
comm-mode   = linear; remove COM translation
nstcomm = 10; freq steps comm-mode
comm-grps   = system; groups COM removal ; protein
nstcalcenergy   = -1; freq calc ener; default = nstlist
; DYNAMICS **
;### Initial velocity assignment
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell
distribution
gen_seed= -1; random generator seed; -1 from
job ID
; OUTPUT CONTROL 
;### xtc
nstxtcout   = 2500  ; .xtc freq write coor
xtc-precision   = 1000  ; .xtc precision
xtc_grps= system; .xtc saved groups
;### trr
nstxout = 50; .trr freq write coor
nstvout = 50; .trr freq write vel
nstfout = 0 ; .trr freq write forces
;### log
nstlog  = 2500  ; .log freq write ener
;### edr
nstenergy   = 2500  ; .edr freq write ener; =
i*nstcalcenergy
energygrps  = protein non-protein   ; .edr saved groups
; NON-BONDED INTERACTIONS ***
ns_type = grid  ; search neighbor grid cells
nstlist = 10; freq update NB list

vdwtype = switch; switching function for VdW
coulombtype = PME   ; PME for long-range electrostatics
rvdw_switch = 0.9   ; switching dist VdW
rvdw= 1.0   ; cutoff VdW
rcoulomb= 1.2   ; cutoff elec
rlist   = 1.2   ; cutoff NB list; must = rcoulomb
when PME

epsilon-r   = 1 ; dielectric const
DispCorr= EnerPres  ; Long-range VdW dispersion
correction

;### PME & Ewald
ewald_rtol  = 1.0e-5; direct space tolerance;
1.0e-6/2.2e-5
fourierspacing  = 0.12  ; max grid spacing for FFT
pme_order   = 6 ; interpolation order; depends on
cutoff
ewald_geometry  = 3d; Ewald in 3d
epsilon_surface = 0 ; dipole correction for 3d Ewald
optimize_fft= yes   ; start-up FFT grid optimization
; BOUNDARY CONTROL **
pbc = xyz   ; 3-D PBC
; CONSTRAINTS CONTROL ***
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
continuation= no; constraints applied to initial
conf
constraint_algorithm = lincs; holonomic constraints
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
lincs_warnangle = 30; max allowed bond angle before
warning
; TEMPERATURE CONTROL ***
tcoupl  = nose-hoover   ; Nose-Hoover T-coupling; v-rescale
tc-grps = system; two coupling groups - more
accurate
tau_t   = 0.6   ; coupling time constant at equil,
in ps
ref_t   = 300   ; reference temperature, one for
each group, in K
; PRESSURE CONTROL **
pcoupl  = Parrinello-Rahman ; Pressure coupling on in
NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 1.0   ; coupling time constant at equil,
in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility

[gmx-users] System does not heat up to 300K.

[Marc Hömberger]

Hi,

I have a system setup (minimized etc.) and wanted to heat this system
gradually with simulated annealing. I set up the mdp file as you can see
below (simulated annealing part is marked bold). But when the heating is
finished, the log file tells me that the temperature of the system is only
1K (see below).

Can someone tell me what I am doing wrong?


Best,
Marc

; PREPROCESSING *
;include=
;define =
; RUN CONTROL ***
dt  = 0.002 ; timestep, 2 fs
integrator  = md; leap-frog integrator
nsteps  = 50 ; 2 * 50 = 1000 ps
tinit   = 0 ; starting time, ps
init_step   = 0 ; starting step
comm-mode   = linear; remove COM translation
nstcomm = 10; freq steps comm-mode
comm-grps   = system; groups COM removal ; protein
nstcalcenergy   = -1; freq calc ener; default = nstlist
; DYNAMICS **
;### Initial velocity assignment
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell
distribution
gen_seed= -1; random generator seed; -1 from
job ID
; OUTPUT CONTROL 
;### xtc
nstxtcout   = 2500  ; .xtc freq write coor
xtc-precision   = 1000  ; .xtc precision
xtc_grps= system; .xtc saved groups
;### trr
nstxout = 50; .trr freq write coor
nstvout = 50; .trr freq write vel
nstfout = 0 ; .trr freq write forces
;### log
nstlog  = 2500  ; .log freq write ener
;### edr
nstenergy   = 2500  ; .edr freq write ener; =
i*nstcalcenergy
energygrps  = protein non-protein   ; .edr saved groups
; NON-BONDED INTERACTIONS ***
ns_type = grid  ; search neighbor grid cells
nstlist = 10; freq update NB list

vdwtype = switch; switching function for VdW
coulombtype = PME   ; PME for long-range electrostatics
rvdw_switch = 0.9   ; switching dist VdW
rvdw= 1.0   ; cutoff VdW
rcoulomb= 1.2   ; cutoff elec
rlist   = 1.2   ; cutoff NB list; must = rcoulomb
when PME

epsilon-r   = 1 ; dielectric const
DispCorr= EnerPres  ; Long-range VdW dispersion
correction

;### PME & Ewald
ewald_rtol  = 1.0e-5; direct space tolerance;
1.0e-6/2.2e-5
fourierspacing  = 0.12  ; max grid spacing for FFT
pme_order   = 6 ; interpolation order; depends on
cutoff
ewald_geometry  = 3d; Ewald in 3d
epsilon_surface = 0 ; dipole correction for 3d Ewald
optimize_fft= yes   ; start-up FFT grid optimization
; BOUNDARY CONTROL **
pbc = xyz   ; 3-D PBC
; CONSTRAINTS CONTROL ***
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
continuation= no; constraints applied to initial
conf
constraint_algorithm = lincs; holonomic constraints
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
lincs_warnangle = 30; max allowed bond angle before
warning
; TEMPERATURE CONTROL ***
tcoupl  = nose-hoover   ; Nose-Hoover T-coupling; v-rescale
tc-grps = system; two coupling groups - more
accurate
tau_t   = 0.6   ; coupling time constant at equil,
in ps
ref_t   = 300   ; reference temperature, one for
each group, in K
; PRESSURE CONTROL **
pcoupl  = Parrinello-Rahman ; Pressure coupling on in
NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 1.0   ; coupling time constant at equil,
in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water at 1 atm, bar^-1
; SIMULATED ANNEALING **
*annealing   = single; type of 

Re: [gmx-users] system hangs while running perl distances.pl

[Justin Lemkul]

On 5/12/13 6:40 AM, Arunima Shilpi wrote:

Respected Sir
  many many thanks for your reply to my last mail. while running

trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep

I selected group 0 for the system...

but while i run perl distances.pl

it says processing file 236...and than the system hangs, no more
blinking along the terminal... while when I run indivdual file for distance
calculation i am able to run the command

g_dist -s pull.tpr -f conf1.gro -n index.ndx -o dist1.xvg < groups.txt

i request you to kindly guide me to debug the error



If the script any any Gromacs commands it calls run fine for 235 frames, there 
is no Gromacs-related reason that it should stop.  Try running the command 
yourself for the problematic frame and see if there is an issue.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] system hangs while running perl distances.pl

[Arunima Shilpi]

Respected Sir
 many many thanks for your reply to my last mail. while running

trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep

I selected group 0 for the system...

but while i run perl distances.pl

it says processing file 236...and than the system hangs, no more
blinking along the terminal... while when I run indivdual file for distance
calculation i am able to run the command

g_dist -s pull.tpr -f conf1.gro -n index.ndx -o dist1.xvg < groups.txt

i request you to kindly guide me to debug the error
-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer & Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha
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Re: [gmx-users] system explode when running in MD production

[Justin Lemkul]

On 4/21/13 8:09 PM, Nur Syafiqah Abdul Ghani wrote:

HI guys,

I got this problem when I running my protein and metal in mix solvent.
First of all,my question is can we use the original file of pdb and
dock it with metal and run it by simulation?



Maybe.  Dealing with metals is tricky and not all force fields are well suited 
to simulating them.


http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species


Second question, after the equilibration part where the pressure and
temperature is on.The pressure that I need is should be 1 bar but the
result that i had first is in negative value but after extend the time
steps the average of the pressure become positive with the value was
1.6 bar. Therefore I continue to MD production by using the equili.gro
file.



Instantaneous values of pressure mean very little.

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

Assessing whether or not your system has stabilized to the desired value (not 
just the pressure value in a given frame) is what is important.



Not so long after that the system said that my protein in this
simulation was explode and results shows it produce a lot of pdb file
at the certain step.Can you tell me why it is happened?



Without a complete description of what you're doing (the points that I posted in 
the last message), there is no way to know.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] system explode when running in MD production

[Nur Syafiqah Abdul Ghani]

HI guys,

I got this problem when I running my protein and metal in mix solvent.
First of all,my question is can we use the original file of pdb and
dock it with metal and run it by simulation?

Second question, after the equilibration part where the pressure and
temperature is on.The pressure that I need is should be 1 bar but the
result that i had first is in negative value but after extend the time
steps the average of the pressure become positive with the value was
1.6 bar. Therefore I continue to MD production by using the equili.gro
file.

Not so long after that the system said that my protein in this
simulation was explode and results shows it produce a lot of pdb file
at the certain step.Can you tell me why it is happened?

I have no idea with this situation.

--
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
alternative email : syafiqahabdulgh...@gmail.com
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Re: [gmx-users] system explode when running in MD production

[Justin Lemkul]

On 4/21/13 8:01 PM, Nur Syafiqah Abdul Ghani wrote:

HI guys,

I got this problem when I running my protein and metal in mix solvent condition.



Please see the standard advice:

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

Without significantly more detail (your preparation protocol, EM, equilibration, 
topology information, .mdp files, etc) then no one stands any chance of being 
able to help you.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] system explode when running in MD production

[Nur Syafiqah Abdul Ghani]

HI guys,

I got this problem when I running my protein and metal in mix solvent condition.


--
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
alternative email : syafiqahabdulgh...@gmail.com
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Re: [gmx-users] System size and minimum image convention

[Justin Lemkul]

On 2/21/13 6:30 PM, Elisabeth wrote:

Thanks Justin. Can you please elaborate on why for a binary
(solute+solvent) the size should be larger than 2 Rc? I thought minimum
image convention works for all atoms (solute ans solvent) and this makes
sure forces are not double-counted. What if the solute is a polymer, I mean
how can one calculate diameter of a long chain?



One can easily obtain an end-to-end distance in visualization software or with 
g_dist.  Caveat to my previous post: I am assuming that r_c is standard 
nomenclature, i.e. the longest nonbonded cutoff.  If, for instance, your force 
field requires a 1.0 nm cutoff for some term, and your solute is 5.0 nm across, 
it obviously wouldn't make sense that you can define a box that is 2.0 nm 
across.  The solute can potentially rotate in a spherically symmetric way, thus 
requiring that the minimum distance between any atoms in each periodic image is 
larger than r_c, thus for practical purposes, you would set a box with a size of 
5.0 + (2 * 1.0) = 7.0 nm.  Such a box is not strictly necessary, as you could 
theoretically avoid minimum image violations by adding 0.5 * r_c to each 
dimension, but there are potentially solvent layering effects and if using NPT, 
the box size will change and you can thus have sporadic violations.  In 
practice, the risk of junk data outweighs the relatively minor system size increase.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] System size and minimum image convention

[Elisabeth]

Thanks Justin. Can you please elaborate on why for a binary
(solute+solvent) the size should be larger than 2 Rc? I thought minimum
image convention works for all atoms (solute ans solvent) and this makes
sure forces are not double-counted. What if the solute is a polymer, I mean
how can one calculate diameter of a long chain?

Thanks in advance,


On 21 February 2013 18:16, Justin Lemkul  wrote:

>
>
> On 2/21/13 6:10 PM, Elisabeth wrote:
>
>> Hello everyone,
>>
>> Does anyone know if the minimum image convention has something to do with
>> the box size effect (independence of simulation results from system size)
>> ?
>> i.e. When the box size is larger than 2*r_c, does this ensure that the
>> results are independent of size pf the system (number of atoms in box)?
>>
>> Please guide me if I am confusing these two issues with each other,
>>
>>
> The finite size effect and minimum image convention are different.  The
> minimum image convention simply says that your molecules should not have
> their forces double-counted through interactions in the central unit cell
> and a neighboring one.  That leads to spurious dynamics.  A box of 2*r_c is
> an absolute minimum, but if there is a solute involved (i.e. not pure
> solvent) then your box must be larger (diameter of solute + 2*r_c).
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] System size and minimum image convention

[Justin Lemkul]

On 2/21/13 6:10 PM, Elisabeth wrote:

Hello everyone,

Does anyone know if the minimum image convention has something to do with
the box size effect (independence of simulation results from system size) ?
i.e. When the box size is larger than 2*r_c, does this ensure that the
results are independent of size pf the system (number of atoms in box)?

Please guide me if I am confusing these two issues with each other,



The finite size effect and minimum image convention are different.  The minimum 
image convention simply says that your molecules should not have their forces 
double-counted through interactions in the central unit cell and a neighboring 
one.  That leads to spurious dynamics.  A box of 2*r_c is an absolute minimum, 
but if there is a solute involved (i.e. not pure solvent) then your box must be 
larger (diameter of solute + 2*r_c).


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] system far from the equilibration state

[Justin Lemkul]

On 2/7/13 4:50 AM, Shima Arasteh wrote:


Thanks for your reply.
How would I know that when I get close to the equilibration state?  By 
Pressure, Temperature,or  RMSD plots?



There are no absolutes, and it also depends on what one means by "converged" or 
"equilibrated."  If we're talking about initial NVT/NPT equilibration steps 
where the solute of interest is restrained in some way, simple analysis of 
temperature and pressure is likely sufficient to demonstrate that the ensemble 
is stable.  If we're talking about trying to determine equilibrium sampling, 
that's something else entirely and likely will involve protein-specific and/or 
lipid-specific metrics.


-Justin



Thanks in advance for your suggestions.

Sincerely,
Shima



From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS users 

Sent: Monday, February 4, 2013 11:37 PM
Subject: Re: [gmx-users] system far from the equilibration state



On 2/4/13 2:04 PM, Shima Arasteh wrote:

Hi,

I am simulating a system of peptide/membrane/water. If my system is far from 
the equilibration, would that be correct if I use Berendsen pressure coupling 
for nano seconds to do NPT equilibration and then change it to 
Parrinello-Rahman to get the true pressure? Anybody may suggest me please?



Sounds reasonable.  Berendsen is a useful method in such cases.

-Justin



--


Justin A. Lemkul, Ph.D.
Research Scientist
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] system far from the equilibration state

[Shima Arasteh]

Thanks for your reply. 
How would I know that when I get close to the equilibration state?  By 
Pressure, Temperature,or  RMSD plots?


Thanks in advance for your suggestions.

Sincerely,
Shima



From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users  
Sent: Monday, February 4, 2013 11:37 PM
Subject: Re: [gmx-users] system far from the equilibration state



On 2/4/13 2:04 PM, Shima Arasteh wrote:
> Hi,
>
> I am simulating a system of peptide/membrane/water. If my system is far from 
> the equilibration, would that be correct if I use Berendsen pressure coupling 
> for nano seconds to do NPT equilibration and then change it to 
> Parrinello-Rahman to get the true pressure? Anybody may suggest me please?
>

Sounds reasonable.  Berendsen is a useful method in such cases.

-Justin

-- 


Justin A. Lemkul, Ph.D.
Research Scientist
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] system far from the equilibration state

[Justin Lemkul]

On 2/4/13 2:04 PM, Shima Arasteh wrote:

Hi,

I am simulating a system of peptide/membrane/water. If my system is far from 
the equilibration, would that be correct if I use Berendsen pressure coupling 
for nano seconds to do NPT equilibration and then change it to 
Parrinello-Rahman to get the true pressure? Anybody may suggest me please?



Sounds reasonable.  Berendsen is a useful method in such cases.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] system far from the equilibration state

[Shima Arasteh]

Hi,

I am simulating a system of peptide/membrane/water. If my system is far from 
the equilibration, would that be correct if I use Berendsen pressure coupling 
for nano seconds to do NPT equilibration and then change it to 
Parrinello-Rahman to get the true pressure? Anybody may suggest me please?


Thanks in advance.
Sincerely,
Shima 
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Re: [gmx-users] system not equilibrated

[Justin Lemkul]

On 1/9/13 3:41 AM, Gmx Niki wrote:



Hi all,
I ran energy minimization (em) step, (protein-CNT in water) by these conditions:
title= Minimization
integrator= steep
emtol= 1000.0
emstep  = 0.01
nsteps= 15
energygrps= Protein CNT
  nstlist= 1
ns_type= grid
rlist= 1.0
coulombtype= PME
rcoulomb= 1.0
rvdw= 1.0
pbc= xyz


but when it recieves to 4 step (nearly), it gives error:

Step=  125, Dmax= 7.8e-06 nm, Epot= -1.79432e+07 Fmax= 8.35837e+04, atom= 10656
Step=  129, Dmax= 1.2e-06 nm, Epot= -1.79432e+07 Fmax= 8.35979e+04, atom= 10656
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Back Off! I just backed up em2.gro to ./#em2.gro.1#

Steepest Descents converged to machine precision in 130 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -1.7943236e+07
Maximum force =  8.3583656e+04 on atom 10656
Norm of force =  2.1333945e+03

then I ran my system with emtol=10 , but the error repeated too. then I ran it 
by double-precision , but was not successful too.

1- I changed fmax value only in .mdp file, is it correct? or I should change 
any parameter in topology file?
2- is the nsteps too much ?and problem is long time?what is its problem?


You have a maximum force on the order of 10^4, which is an order of magnitude 
higher than what you initially requested.  mdrun is telling you that the problem 
is focused on atom 10656.  Open up your structure in your visualization software 
of choice and find that atom.  You likely have some unresolved clashes there 
that are causing this problem.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] system not equilibrated

[Gmx Niki]

Hi all,
I ran energy minimization (em) step, (protein-CNT in water) by these conditions:
title        = Minimization 
integrator    = steep     
emtol        = 1000.0   
emstep  = 0.01   
nsteps        = 15  
energygrps    = Protein CNT 
 nstlist        = 1         
ns_type        = grid  
rlist        = 1.0     
coulombtype    = PME     
rcoulomb    = 1.0     
rvdw        = 1.0     
pbc            = xyz  


but when it recieves to 4 step (nearly), it gives error:

Step=  125, Dmax= 7.8e-06 nm, Epot= -1.79432e+07 Fmax= 8.35837e+04, atom= 10656
Step=  129, Dmax= 1.2e-06 nm, Epot= -1.79432e+07 Fmax= 8.35979e+04, atom= 10656
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Back Off! I just backed up em2.gro to ./#em2.gro.1#

Steepest Descents converged to machine precision in 130 steps,
but did not reach the requested Fmax < 1000.
Potential Energy  = -1.7943236e+07
Maximum force =  8.3583656e+04 on atom 10656
Norm of force =  2.1333945e+03

then I ran my system with emtol=10 , but the error repeated too. then I ran it 
by double-precision , but was not successful too.

1- I changed fmax value only in .mdp file, is it correct? or I should change 
any parameter in topology file?
2- is the nsteps too much ?and problem is long time?what is its problem?
please guide me
tnx
Niki
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Re: [gmx-users] System killed after genbox

[Justin Lemkul]

On 12/18/12 9:47 PM, Nur Syafiqah Abdul Ghani wrote:

Dear Users,

Why I run the command genbox -cp protein_box.gro -ci hfi.gro -nmol
1534 -cs spc216.gro -p control.top -o protein_mixsol.gro.

And the result show like below.:


Grid: 15 x 15 x 11 cells
nri = 9466, nrj = 77062
Try 9579box_margin = 0.45overlap:
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
System total charge: 0.000
Killed


I already calculate the amount of no of molecule that I need to put
for the co-solvent.

Is there something wrong of my calculation?



You're doing too many things at once and running out of memory.  Add your 
co-solvent with -ci -nmol, then in a separate step add water with -cs.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] System killed after genbox

[Nur Syafiqah Abdul Ghani]

Dear Users,

Why I run the command genbox -cp protein_box.gro -ci hfi.gro -nmol
1534 -cs spc216.gro -p control.top -o protein_mixsol.gro.

And the result show like below.:


Grid: 15 x 15 x 11 cells
nri = 9466, nrj = 77062
Try 9579box_margin = 0.45overlap:
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
System total charge: 0.000
Killed


I already calculate the amount of no of molecule that I need to put
for the co-solvent.

Is there something wrong of my calculation?

the formula is

no.of molecule that need =( [ % need of hfi x density kg/m^3 x size of
box m^3] / molecular weight g/mol ) x avogadro number


--
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
013-7188131
alternative email : syafiqahabdulgh...@gmail.com
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Re: [gmx-users] system is not well equilibrated -Reg

[Justin Lemkul]

On 12/4/12 1:20 PM, venkatesh s wrote:

Respected Gromacs Peoples,
  i got following error in the step mdrun nvt

1 particles communicated to PME node 1 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 searched gmx user regarding the error but i cant get solution
i understand Blowing up concept (
http://www.gromacs.org/Documentation/Terminology/Blowing_Up) before nvt npt
itself error arise  what i want do ? rectifying the problem

(i followed protein&ligand tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/)


SYSTEM INFORMATIONS

ff :GROMOS96 43a1 force field
ligand -->prodrg ,antechamber (charge)
FOUR PROTEIN (USING :CHAINSEP -TER ) ONE LIGAND

TOTAL NUMBER OF ATOM & RESIDUE
chain  #res #atoms

   1 'A'   661   5352
   2 'B'   686   5550
   3 'Z' 4  4
   4 'C'   148   1236
   5 'D'   225   1706
   6 'E'   236   1817
   7 ligand45



With this level of complexity, you're searching for a needle in a haystack. 
Separate each component and attempt to simulate it, starting with the ligand to 
check the integrity of its topology.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] System neutralization in Thermodynamic Integration

[Leandro Bortot]

Dear All,

 In order to calculate the binding free energy of a ligand to a protein
I am using Thermodynamic Integration, i.e. making the ligand "disappear".

 Because this ligand is charged (-1), at lambdas different than zero
(when the ligand is already fading) the total system charge increases until
it is +1 when lambda=1.

 I am using 1 nm cutoff for the non-bonded interactions and PME. Should
I make something to account for this total system charge? Won't it induce
artifacts in my calculation?


thanks in advance,
Leandro Bortot
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Re: [gmx-users] system blowing up

[Shima Arasteh]

 I ran for the fourth time and got the error again. Now, I think the random 
output of such a system is not reliable!


Sincerely,
Shima


- Original Message -
From: Shima Arasteh 
To: Discussion list for GROMACS users 
Cc: 
Sent: Saturday, July 28, 2012 3:06 PM
Subject: Re: [gmx-users] system blowing up



Thanks for your reply.

I'm following the protocol of Diagnosing an unstable system. Corresponding the 
first step I changed th nstxout to 1 for 3 times.
The first and second time I got error the same as before ( some interactions 
seem to be assigned multiple times ) and it the warning as below was appeared:

Warning: 1-4 interaction between 5 and 18 at distance 2.017 which is larger 
than the 1-4 table size 2.000 nm

For the third time, I did'nt get any error and the output files were generated 
without any warning or error. 


Is it acceptable to go on with these outputs? Why such a thing happened? Is the 
system minimized sufficiently after 2 times?


Thanks 

Sincerely,
Shima



From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Saturday, July 28, 2012 6:12 AM
Subject: Re: [gmx-users] adding a new atom type

On 28/07/2012 4:34 AM, Shima Arasteh wrote:
>
> As I explained here before, I get an error ( some interactions seem to be 
> assigned multiple times).

And it's been suggested several times that your system may be 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up, and 
diagnostic and management strategies are described there. Since you 
haven't said whether it was immediately upon simulation start (so that 
the topology might be doubtful, and probably only if you are the first 
to find some new bug) or later on (when the topology is not directly to 
blame for blowing up). Messing around duplicating atom types to try to 
avoid the situation is presupposing the form of the solution to a 
problem that you have not yet identified.

>   I suspected the top file, so checked it  and visualized the output of 
>em.mdp; the output seems to be correct and I don't see any bonds behaves 
>strangely.

OK, but the "bonds" you see there do not relate to the ones in your 
topology. 
http://www.gromacs.org/About_Gromacs/Related_Software/Visualization_Software. 
So all you've seen is that nothing's gone wrong enough so far.

> As I studied in mailing lists it and you also mentioned , this may happen 
> because of the insufficient minimization. I'm wondering how a good and 
> sufficient minimization  is provided?

Often whatever comes out of a single-precision EM run is fine. You have 
not presented evidence that your minimization is insufficient, and there 
are many other possible causes for blowing up. In the absence of a 
description of your system, your .mdp file and how you've modified your 
forcefield and/or topology, it's impossible to get effective help.

Mark

>
>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc:
> Sent: Friday, July 27, 2012 10:51 PM
> Subject: Re: [gmx-users] adding a new atom type
>
>
>
> On 7/27/12 1:08 PM, Shima Arasteh wrote:
>>
>> Which parameter is supposed to be changed to get the sufficient minimized 
>> system? Would anyone guide me  please?
>>
> This question is very vague.  In principle, any system can be minimized but 
> the
> definition of "sufficient" depends on your goals.
>
> -Justin
>
>> Thanks in advance
>>
>> Cheers,
>> Shima
>>
>>
>> - Original Message -
>> From: Justin Lemkul 
>> To: Discussion list for GROMACS users 
>> Cc:
>> Sent: Wednesday, July 25, 2012 4:37 PM
>> Subject: Re: [gmx-users] adding a new atom type
>>
>>
>>
>> On 7/25/12 7:58 AM, Shima Arasteh wrote:
>>>
>>>       Some time ago I defined a new residue and after running grompp I got 
>>>an error as there are some interactions assigned multiple times. Then I 
>>>decided to duplicate the atoms involved in that residue to avoid this error.
>> That error usually indicates your system is crashing and the DD algorithm is 
>> failing.  That means either the coordinates are insufficiently minimized, 
>> the topology is incorrect, or the .mdp settings are leading to instability.
>>
>>> Next I renamed the atomtypes in atometypes.atp as below:
>>>       ZC    12.01100 ;    carbonyl C, peptide backbone
>>> ZCT1    12.01100 ;    aliphatic sp3 C for CH
>>> ZCT3    12.01100 ;    aliphatic sp3 C for CH3
>>> ZO    15.99900 ;    carbonyl oxygen
>>> ZHC    1.00800 ;    N-ter H
>>> ZNH1    14.00700 ;    peptide nitrogen
>>> ZH    1.008

Re: [gmx-users] system blowing up

[Shima Arasteh]

Thanks for your reply.

I'm following the protocol of Diagnosing an unstable system. Corresponding the 
first step I changed th nstxout to 1 for 3 times.
The first and second time I got error the same as before ( some interactions 
seem to be assigned multiple times ) and it the warning as below was appeared:

Warning: 1-4 interaction between 5 and 18 at distance 2.017 which is larger 
than the 1-4 table size 2.000 nm

For the third time, I did'nt get any error and the output files were generated 
without any warning or error. 


Is it acceptable to go on with these outputs? Why such a thing happened? Is the 
system minimized sufficiently after 2 times?


Thanks 

Sincerely,
Shima



From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Saturday, July 28, 2012 6:12 AM
Subject: Re: [gmx-users] adding a new atom type

On 28/07/2012 4:34 AM, Shima Arasteh wrote:
>
> As I explained here before, I get an error ( some interactions seem to be 
> assigned multiple times).

And it's been suggested several times that your system may be 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up, and 
diagnostic and management strategies are described there. Since you 
haven't said whether it was immediately upon simulation start (so that 
the topology might be doubtful, and probably only if you are the first 
to find some new bug) or later on (when the topology is not directly to 
blame for blowing up). Messing around duplicating atom types to try to 
avoid the situation is presupposing the form of the solution to a 
problem that you have not yet identified.

>   I suspected the top file, so checked it  and visualized the output of 
>em.mdp; the output seems to be correct and I don't see any bonds behaves 
>strangely.

OK, but the "bonds" you see there do not relate to the ones in your 
topology. 
http://www.gromacs.org/About_Gromacs/Related_Software/Visualization_Software. 
So all you've seen is that nothing's gone wrong enough so far.

> As I studied in mailing lists it and you also mentioned , this may happen 
> because of the insufficient minimization. I'm wondering how a good and 
> sufficient minimization  is provided?

Often whatever comes out of a single-precision EM run is fine. You have 
not presented evidence that your minimization is insufficient, and there 
are many other possible causes for blowing up. In the absence of a 
description of your system, your .mdp file and how you've modified your 
forcefield and/or topology, it's impossible to get effective help.

Mark

>
>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Justin Lemkul 
> To: Shima Arasteh ; Discussion list for GROMACS 
> users 
> Cc:
> Sent: Friday, July 27, 2012 10:51 PM
> Subject: Re: [gmx-users] adding a new atom type
>
>
>
> On 7/27/12 1:08 PM, Shima Arasteh wrote:
>>
>> Which parameter is supposed to be changed to get the sufficient minimized 
>> system? Would anyone guide me  please?
>>
> This question is very vague.  In principle, any system can be minimized but 
> the
> definition of "sufficient" depends on your goals.
>
> -Justin
>
>> Thanks in advance
>>
>> Cheers,
>> Shima
>>
>>
>> - Original Message -
>> From: Justin Lemkul 
>> To: Discussion list for GROMACS users 
>> Cc:
>> Sent: Wednesday, July 25, 2012 4:37 PM
>> Subject: Re: [gmx-users] adding a new atom type
>>
>>
>>
>> On 7/25/12 7:58 AM, Shima Arasteh wrote:
>>>
>>>       Some time ago I defined a new residue and after running grompp I got 
>>>an error as there are some interactions assigned multiple times. Then I 
>>>decided to duplicate the atoms involved in that residue to avoid this error.
>> That error usually indicates your system is crashing and the DD algorithm is 
>> failing.  That means either the coordinates are insufficiently minimized, 
>> the topology is incorrect, or the .mdp settings are leading to instability.
>>
>>> Next I renamed the atomtypes in atometypes.atp as below:
>>>       ZC    12.01100 ;    carbonyl C, peptide backbone
>>> ZCT1    12.01100 ;    aliphatic sp3 C for CH
>>> ZCT3    12.01100 ;    aliphatic sp3 C for CH3
>>> ZO    15.99900 ;    carbonyl oxygen
>>> ZHC    1.00800 ;    N-ter H
>>> ZNH1    14.00700 ;    peptide nitrogen
>>> ZH    1.00800 ;    polar H
>>> ZHB    1.00800 ;    backbone H
>>> ZHA    1.00800 ;    nonpolar H
>>>
>>> Then I wanted to modify the .itp file, got in to the trouble; I couldn't 
>>> find the C atomtype in nonbonded.itp file. Actually I don't know what to do 
>>> now!
>>>
>> Start over with a fresh set of force field files that you haven't 
>> experimented with and troubleshoot the stability of your system.  If you 
>> Google or search the mailing list archive for this error, tons of useful 
>> results show up.
>>
>> -Justin
>>
>> -- 
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www

Re: [gmx-users] system cooling down when runing NVE

[Erik Marklund]

In general, NVE is tricky business, since small integration errors build up and 
cause energy drift in the long run. Do you see energy drift too? In my 
experience one needs double precision and a shorter timestep than what you 
employ. But that is of course system dependent.

Erik


9 maj 2012 kl. 03.17 skrev Peter C. Lai:

> you have position restraints on, which I expect would damp collisions between 
> solvent and solute. temp drops towards some sort of equilibrium, which 
> doesn't necessarily match your starting temp even though energy of the system 
> is conserved ..sounds like expected behavior to me?
> -- 
> Sent from my Android phone with K-9 Mail. Please excuse my brevity.
> 
> Thanh Binh NGUYEN  wrote:
>Dear Gromacs experts,
> > I'm just a newbaby in Gromacs, and hence I have a lot of problem  
> > when  running this program. I try to run NVE simulation of a  
> > protein. First,  I run an NTP ensemble, follow by NVT and finally,  
> > NVE. In NPT and NVT, T remains as constant, however, in NVE   
> > simulation, the temperature drops gradually instead of maintain   
> > approximately constant. Could you give me any advice to solve this   
> > problem?
> > Thank you very much.
> > Regards,
> > Nguyen
> >
> > P.S: below is my mdp file for three simulations:
> > NPT ensemble:
> > title = DEN2pro_MD
> > define = -DFLEXIBLE
> > constraints = all-bonds
> > integrator = md
> > dt = 0.002 ; ps !
> > nsteps = 100 ; total 2000 ps.
> > nstcomm = 1
> > nstxout = 5000 ; output
> coordinates every 10 ps
> > nstvout = 5000 ; output velocities every 10 ps
> > nstfout = 0
> > nstlog = 10
> > nstenergy = 10
> > nstlist = 10
> > ns_type = grid
> > rlist = 0.9
> > coulombtype = PME
> > rcoulomb = 0.9
> > rvdw = 1.0
> > fourierspacing = 0.12
> > fourier_nx = 0
> > fourier_ny = 0
> > fourier_nz = 0
> > pme_order = 6
> > ewald_rtol = 1e-5
> > optimize_fft = yes
> > ; Berendsen temperature coupling is on in four groups
> > Tcoupl = berendsen
> > tau_t = 0.1 0.1
> > tc_grps = protein non-protein
> > ref_t = 300 300
> > ; Pressure coupling is on
> > Pcoupl = berendsen
> > pcoupltype = isotropic
> > tau_p = 1.0
> > compressibility = 4.5e-5
> > ref_p = 1.0
> > ; Generate velocites is on at 300 K.
> > gen_vel = yes
> > gen_temp = 300.0
> > gen_seed = 173529
> >
> ><
>  br
> />>
> > NVT ensemble
> > title   = DEN2pro_MD NVT equilibration
> > define  = -DPOSRES  ; position restrain the protein and ligand
> > ; Run parameters
> > integrator  = md; leap-frog integrator
> > nsteps  = 10 ; 2 * 10 = 200 ps
> > dt  = 0.002 ; 2 fs
> > ; Output control
> > nstxout = 5000   ; save coordinates every 10 ps
> > nstvout = 5000   ; save velocities every 10 ps
> > nstenergy   = 100   ; save energies every 0.2 ps
> > nstlog  = 100   ; update log file every 0.2 ps
> > energygrps  = Protein
> > ; Bond parameters
> > continuation= no; first dynamics run
> > constraint_algorithm = lincs; holonomic constraints
> > constraints = all-bonds ; all bonds (even heavy atom-H  
> > bonds)  constrained
> > lincs_iter  = 1 ; accuracy of LINCS
> &
>  gt;
> lincs_order = 4 ; also related to accuracy
> > ; Neighborsearching
> > ns_type = grid  ; search neighboring grid cells
> > nstlist = 5 ; 10 fs
> > rlist   = 0.9   ; short-range neighborlist cutoff (in nm)
> > rcoulomb= 0.9   ; short-range electrostatic cutoff (in nm)
> > rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
> > ; Electrostatics
> > coulombtype = PME   ; Particle Mesh Ewald for long-range   
> > electrostatics
> > pme_order   = 4 ; cubic interpolation
> > fourierspacing  = 0.12  ; grid spacing for FFT
> > ; Temperature coupling is on
> > tcoupl  = V-rescale ; modified Berendsen thermostat
> > tc-grps = Protein Non-protein   ; two coupling groups - more 
> > accurate
> > tau_t   = 0.1   0.1 ; time constant, in ps
> > ref_t   = 
>  300  
> 300 ; reference temperature,  
> >  one for each group, in K
> > ; Pressure coupling is off
> > pcoupl  = no; no pressure coupling in NVT
> > ; Periodic boundary conditions
> > pbc = xyz   ; 3-D PBC
> > ; Dispersion correction
> > DispCorr= EnerPres  ; account for cut-off vdW scheme
> > ; Velocity generation
> > gen_vel = yes   ; assign velocities from Maxwell distribution
> > gen_temp= 300   ; temperature for Maxwell distribution
> > gen_seed= -1; generate a random seed
> >
> >
> > NVE ensemble:
> > title   = DEN2pro_MD NVE equilibration
> > define  = -DPOSRES  ; position restrain the protein and ligand
> > ; Run parameters
> > integrator  = md-vv ; leap-frog integrator
> > nsteps  = 100   ; 2 * 100 = 2000 ps
> > dt  = 0.002 ; 2 fs
> > ; Out
>  put
> control
> > nstxout =

Re: [gmx-users] system cooling down when runing NVE

[Peter C. Lai]

you have position restraints on, which I expect would damp collisions between 
solvent and solute. temp drops towards some sort of equilibrium, which doesn't 
necessarily match your starting temp even though energy of the system is 
conserved ..sounds like expected behavior to me?
-- 
Sent from my Android phone with K-9 Mail. Please excuse my brevity.

Thanh Binh NGUYEN  wrote:

Dear Gromacs experts,
> I'm just a newbaby in Gromacs, and hence I have a lot of problem 
> when running this program. I try to run NVE simulation of a 
> protein. First, I run an NTP ensemble, follow by NVT and finally, 
> NVE. In NPT and NVT, T remains as constant, however, in NVE 
> simulation, the temperature drops gradually instead of maintain 
> approximately constant. Could you give me any advice to solve this 
> problem?
> Thank you very much.
> Regards,
> Nguyen
>
> P.S: below is my mdp file for three simulations:
> NPT ensemble:
> title = DEN2pro_MD
> define = -DFLEXIBLE
> constraints = all-bonds
> integrator = md
> dt = 0.002 ; ps !
> nsteps = 100 ; total 2000 ps.
> nstcomm = 1
> nstxout = 5000 ; output coordinates every 10 ps
> nstvout = 5000 ; output velocities every 10 ps
> nstfout = 0
> nstlog = 10
> nstenergy = 10
> nstlist = 10
> ns_type = grid
> rlist = 0.9
> coulombtype = PME
> rcoulomb = 0.9
> rvdw = 1.0
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 6
> ewald_rtol = 1e-5
> optimize_fft = yes
> ; Berendsen temperature coupling is on in four groups
> Tcoupl = berendsen
> tau_t = 0.1 0.1
> tc_grps = protein non-protein
> ref_t = 300 300
> ; Pressure coupling is on
> Pcoupl = berendsen
> pcoupltype = isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = yes
> gen_temp = 300.0
> gen_seed = 173529
>
>
>
> NVT ensemble
> title = DEN2pro_MD NVT equilibration
> define = -DPOSRES ; position restrain the protein and ligand
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 10 ; 2 * 10 = 200 ps
> dt = 0.002 ; 2 fs
> ; Output control
> nstxout = 5000 ; save coordinates every 10 ps
> nstvout = 5000 ; save velocities every 10 ps
> nstenergy = 100 ; save energies every 0.2 ps
> nstlog = 100 ; update log file every 0.2 ps
> energygrps = Protein
> ; Bond parameters
> continuation = no ; first dynamics run
> constraint_algorithm = lincs ; holonomic constraints
> constraints = all-bonds ; 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 = 5 ; 10 fs
> rlist = 0.9 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh Ewald for long-range 
> electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.12 ; grid spacing for FFT
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein Non-protein  ; two coupling groups - more accurate
> tau_t = 0.1 0.1 ; time constant, in ps
> ref_t = 300 300 ; reference temperature, 
> one for each group, in K
> ; Pressure coupling is off
> pcoupl = no ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes ; assign velocities from Maxwell distribution
> gen_temp = 300 ; temperature for Maxwell distribution
> gen_seed = -1 ; generate a random seed
>
>
> NVE ensemble:
> title = DEN2pro_MD NVE equilibration
> define = -DPOSRES ; position restrain the protein and ligand
> ; Run parameters
> integrator = md-vv ; leap-frog integrator
> nsteps = 100 ; 2 * 100 = 2000 ps
> dt = 0.002 ; 2 fs
> ; Output control
> nstxout = 5000 ; save coordinates every 10 ps
> nstvout = 5000 ; save velocities every 10 ps
> nstenergy = 100 ; save energies every 0.2 ps
> nstlog = 100 ; update log file every 0.2 ps
> energygrps = Protein
> ; Bond parameters
> continuation = no ; first dynamics run
> constraint_algorithm = lincs ; holonomic constraints
> constraints = all-bonds ; 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 = 5 ; 10 fs
> rlist = 1.6 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm)
> rlistlong = 1.6
> ;treatment of van der waals interactions
> vdwtype = Shift
> rvdw  = 0.95  ; short-range van der Waals cutoff (in nm)
> rvdw-switch = 0.9
> ; Electrostatics
> coulombtype = PME-Switch; Particle Mesh Ewald for long-range 
> electrostatics
> pme_order = 4 ; cubic interpolation
> fourierspacing = 0.12 ; grid spacing for FFT
> ; Tem

[gmx-users] system cooling down when runing NVE

[Thanh Binh NGUYEN]

  Dear Gromacs experts,
I'm just a newbaby in Gromacs, and hence I have a lot of problem  
when  running this program. I try to run NVE simulation of a  
protein. First,  I run an NTP ensemble, follow by NVT and finally,  
NVE. In NPT and NVT, T remains as constant, however, in NVE   
simulation, the temperature drops gradually instead of maintain   
approximately constant. Could you give me any advice to solve this   
problem?

Thank you very much.
Regards,
Nguyen

P.S: below is my mdp file for three simulations:
NPT ensemble:
title = DEN2pro_MD
define = -DFLEXIBLE
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 100 ; total 2000 ps.
nstcomm = 1
nstxout = 5000 ; output coordinates every 10 ps
nstvout = 5000 ; output velocities every 10 ps
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.0
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1
tc_grps = protein non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529



NVT ensemble
title   = DEN2pro_MD NVT equilibration
define  = -DPOSRES  ; position restrain the protein and ligand
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 10 ; 2 * 10 = 200 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 5000   ; save coordinates every 10 ps
nstvout = 5000   ; save velocities every 10 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
energygrps  = Protein
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; 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 = 5 ; 10 fs
rlist   = 0.9   ; short-range neighborlist cutoff (in nm)
rcoulomb= 0.9   ; short-range electrostatic cutoff (in nm)
rvdw= 1.4   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range   
electrostatics

pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-protein   ; two coupling groups - more 
accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature,  
 one for each group, in K

; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed


NVE ensemble:
title   = DEN2pro_MD NVE equilibration
define  = -DPOSRES  ; position restrain the protein and ligand
; Run parameters
integrator  = md-vv ; leap-frog integrator
nsteps  = 100   ; 2 * 100 = 2000 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 5000  ; save coordinates every 10 ps
nstvout = 5000  ; save velocities every 10 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
energygrps  = Protein
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; 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 = 5 ; 10 fs
rlist   = 1.6   ; short-range neighborlist cutoff (in nm)
rcoulomb= 0.9   ; short-range electrostatic cutoff (in nm)
rlistlong   = 1.6
;treatment of van der waals interactions
vdwtype = Shift
rvdw= 0.95  ; short-range van der Waals cutoff (in nm)
rvdw-switch = 0.9
; Electrostatics
coulombtype = PME-Switch; Particle Mesh Ewald for long-range   
electrostatics

pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.12  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = no  

Re: [gmx-users] System exploding

[Justin A. Lemkul]

Lara Bunte wrote:

Hello

If gromacs gives the warning that the system could explode, what could be the 
reason for that?


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

-Justin

--


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


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[gmx-users] System exploding

[Lara Bunte]

Hello

If gromacs gives the warning that the system could explode, what could be the 
reason for that?

Greetings

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Re: [gmx-users] System with 4 Hypericin Molecules in Water

[Justin A. Lemkul]

Hovakim Grabski wrote:

Dear GROMACS users,
I have been trying to set up a simulation system  containing  4 
Hypericin molecules in a box of water.
When I'm trying to run energy minimization,I get this error:  


WARNING 1 [file HYP1_GMX.itp, line 5]:
  Overriding atomtype CT


WARNING 2 [file HYP1_GMX.itp, line 6]:
  Overriding atomtype CA


WARNING 3 [file HYP1_GMX.itp, line 7]:
  Overriding atomtype C


WARNING 4 [file HYP1_GMX.itp, line 8]:
  Overriding atomtype O


WARNING 5 [file HYP1_GMX.itp, line 9]:
  Overriding atomtype OH


WARNING 6 [file HYP1_GMX.itp, line 10]:
  Overriding atomtype HA


WARNING 7 [file HYP1_GMX.itp, line 11]:
  Overriding atomtype HO


WARNING 8 [file HYP1_GMX.itp, line 12]:
  Overriding atomtype HC

Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'HYP1'
Excluding 2 bonded neighbours molecule type 'SOL'
Analysing residue names:
There are: 4Protein residues
There are:  5720  Water residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 52125.00
Largest charge group radii for Van der Waals: 0.039, 0.039 nm
Largest charge group radii for Coulomb:   0.084, 0.084 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 54x54x54, spacing 0.113 0.113 0.113
Estimate for the relative computational load of the PME mesh part: 0.32
This run will generate roughly 6 Mb of data

There were 8 warnings

I generated the topology file using acpype,after that with BallView 
copied the hypericin molecules 4 times and saved to a pdb file.
In the topology file I made changes so that in [molecules] part,HYP1 was 
4 (nmols) and  for forcefield I included 1. #include 
"amber99sb.ff/forcefield.itp" , 2.#include "HYP1_GMX.itp" and then 
#include "amber99sb.ff/tip3p.itp".
I didn't have any problems with setting up  the system with one molecule 
of Hypericin and water box.So what was my mistake?


You're re-defining atom types that are already present in the parent force 
field.  The error messages indicate precisely which ones.  This may or may not 
present a problem, but if you're introducing new atom types (such that they do 
not override global parameters for other species) then they need to have 
different names (case sensitivity applies).


-Justin

--


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


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[gmx-users] System with 4 Hypericin Molecules in Water

[Hovakim Grabski]

Dear GROMACS users,
I have been trying to set up a simulation system  containing  4 Hypericin 
molecules in a box of water.
When I'm trying to run energy minimization,I get this error:  

WARNING 1 [file HYP1_GMX.itp, line 5]:
  Overriding atomtype CT


WARNING 2 [file HYP1_GMX.itp, line 6]:
  Overriding atomtype CA


WARNING 3 [file HYP1_GMX.itp, line 7]:
  Overriding atomtype C


WARNING 4 [file HYP1_GMX.itp, line 8]:
  Overriding atomtype O


WARNING 5 [file HYP1_GMX.itp, line 9]:
  Overriding atomtype OH


WARNING 6 [file HYP1_GMX.itp, line 10]:
  Overriding atomtype HA


WARNING 7 [file HYP1_GMX.itp, line 11]:
  Overriding atomtype HO


WARNING 8 [file HYP1_GMX.itp, line 12]:
  Overriding atomtype HC

Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'HYP1'
Excluding 2 bonded neighbours molecule type 'SOL'
Analysing residue names:
There are: 4    Protein residues
There are:  5720  Water residues
Analysing Protein...
Number of degrees of freedom in T-Coupling group rest is 52125.00
Largest charge group radii for Van der Waals: 0.039, 0.039 nm
Largest charge group radii for Coulomb:   0.084, 0.084 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 54x54x54, spacing 0.113 0.113 0.113
Estimate for the relative computational load of the PME mesh part: 0.32
This run will generate roughly 6 Mb of data

There were 8 warnings

I generated the topology file using acpype,after that with BallView copied the 
hypericin molecules 4 times and saved to a pdb file.
In the topology file I made changes so that in [molecules] part,HYP1 was 4 
(nmols) and  for forcefield I included 1. #include 
"amber99sb.ff/forcefield.itp" , 2.#include "HYP1_GMX.itp" and then #include 
"amber99sb.ff/tip3p.itp".
I didn't have any problems with setting up  the system with one molecule of 
Hypericin and water box.So what was my mistake?
I need your help

Thanks in advance-- 
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] System Exploding

[Justin A. Lemkul]

Alex Seling wrote:
Given the unfavorable input, then, it seems odd then that the same .mdp 
and protein ran consistently on 4.0.7, and I can't seem to find anything 
in the changelog to indicate a relevant change.




There are numerous algorithmic changes in the 4.5.x series.  Many people have 
reported the same problem you have (something works in 4.0.x and not 4.5.x) and 
the solution is to set nsttcouple (and, if applicable, nstpcouple) to 1 for an 
initial equilibration phase.  The default is to have nsttcouple = nstlist, 
which, in your case, is very infrequent.


Then, once the system is relaxed, you can remove this (very) frequent updating. 
 The coupling algorithms in 4.0.x were more relaxed, such that a system that 
was not necessarily well-optimized might have had better odds of "working" (i.e. 
surviving), but as I understand it, the new algorithms are, overall, more robust.


-Justin

On Thu, Jan 26, 2012 at 1:26 AM, Mark Abraham > wrote:


On 26/01/2012 5:10 PM, Alex Seling wrote:

Hello,

After upgrading to gromacs 4.5.5, the old .mdp file that was
working is now giving me errors.


Marginally stable numerical integration can work out, or not. Here,
you are using a time step that is not suitable for a simulation
lacking bond constraints. See section 6.5 of manual, for example. If
you really want infinite cut-offs, read 7.3.9. Normal practice to
avoid problems is to use an equilibration regime whose integration
scheme is more gentle than your simulation regime.

Mark


Specifically, I'm getting 
"This usually means your system is exploding,

if not, you should increase table-extension in your mdp file
or with user tables increase the table size" 
for a few interactions, with each of them approaching inf.


This is with a good starting configuration. Any ideas as to the
error? My .mdp file is below.

Thanks,
Alex Seling


title = lea at 300K
cpp = /lib/cpp -traditional
integrator = md ;sd ;md ;bd
tinit = 0.0
dt = 0.001 ;time step of 1 fs
nsteps = 23800 ;1 us @ 1fs
nstxout = 20 ; frequency to write coordinates to output
trajectory file = 1ns
nstxtcout = 20 ; frequency to write coordinates to xtc
trajectory = 1 ns
nstvout = 0
nstfout = 0
nstlog = 20 ; frequency to write energies to log file = 1 ns
nstenergy = 20 ; frequency to write energies to energy file = 1ns
energygrps = system
comm_mode = angular
nstcomm = 40
nstlist = 100
nstype = simple
pbc = no
rlist = 100
rgbradii = 100
coulombtype = cut-off
epsilon_r = 1 ; double check this is what we want
rcoulomb = 100
vdwtype = cut-off
rvdw = 100
tc-grps = system
tau_t = 0.01099
ref_t = 300
gen_vel = yes
gen_temp = 273
constraints = none
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78






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--


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] System Exploding

[Alex Seling]

Given the unfavorable input, then, it seems odd then that the same .mdp and
protein ran consistently on 4.0.7, and I can't seem to find anything in the
changelog to indicate a relevant change.

On Thu, Jan 26, 2012 at 1:26 AM, Mark Abraham wrote:

>  On 26/01/2012 5:10 PM, Alex Seling wrote:
>
> Hello,
>
> After upgrading to gromacs 4.5.5, the old .mdp file that was working is
> now giving me errors.
>
>
> Marginally stable numerical integration can work out, or not. Here, you
> are using a time step that is not suitable for a simulation lacking bond
> constraints. See section 6.5 of manual, for example. If you really want
> infinite cut-offs, read 7.3.9. Normal practice to avoid problems is to use
> an equilibration regime whose integration scheme is more gentle than your
> simulation regime.
>
> Mark
>
>
>  Specifically, I'm getting
> "This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size"
> for a few interactions, with each of them approaching inf.
>
>  This is with a good starting configuration. Any ideas as to the error?
> My .mdp file is below.
>
>  Thanks,
> Alex Seling
>
>
>  title = lea at 300K
> cpp = /lib/cpp -traditional
> integrator = md ;sd ;md ;bd
> tinit = 0.0
> dt = 0.001 ;time step of 1 fs
> nsteps = 23800 ;1 us @ 1fs
> nstxout = 20 ; frequency to write coordinates to output trajectory
> file = 1ns
> nstxtcout = 20 ; frequency to write coordinates to xtc trajectory = 1
> ns
>  nstvout = 0
> nstfout = 0
> nstlog = 20 ; frequency to write energies to log file = 1 ns
> nstenergy = 20 ; frequency to write energies to energy file = 1ns
> energygrps = system
> comm_mode = angular
> nstcomm = 40
> nstlist = 100
> nstype = simple
> pbc = no
> rlist = 100
> rgbradii = 100
> coulombtype = cut-off
> epsilon_r = 1 ; double check this is what we want
> rcoulomb = 100
> vdwtype = cut-off
> rvdw = 100
> tc-grps = system
> tau_t = 0.01099
> ref_t = 300
> gen_vel = yes
> gen_temp = 273
> constraints = none
> implicit_solvent = GBSA
> gb_algorithm = OBC
> gb_epsilon_solvent = 78
>
>
>
>
>
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Re: [gmx-users] System Exploding

[Mark Abraham]

On 26/01/2012 5:10 PM, Alex Seling wrote:

Hello,

After upgrading to gromacs 4.5.5, the old .mdp file that was working 
is now giving me errors.


Marginally stable numerical integration can work out, or not. Here, you 
are using a time step that is not suitable for a simulation lacking bond 
constraints. See section 6.5 of manual, for example. If you really want 
infinite cut-offs, read 7.3.9. Normal practice to avoid problems is to 
use an equilibration regime whose integration scheme is more gentle than 
your simulation regime.


Mark


Specifically, I'm getting
"This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size"
for a few interactions, with each of them approaching inf.

This is with a good starting configuration. Any ideas as to the error? 
My .mdp file is below.


Thanks,
Alex Seling


title = lea at 300K
cpp = /lib/cpp -traditional
integrator = md ;sd ;md ;bd
tinit = 0.0
dt = 0.001 ;time step of 1 fs
nsteps = 23800 ;1 us @ 1fs
nstxout = 20 ; frequency to write coordinates to output trajectory 
file = 1ns
nstxtcout = 20 ; frequency to write coordinates to xtc trajectory 
= 1 ns

nstvout = 0
nstfout = 0
nstlog = 20 ; frequency to write energies to log file = 1 ns
nstenergy = 20 ; frequency to write energies to energy file = 1ns
energygrps = system
comm_mode = angular
nstcomm = 40
nstlist = 100
nstype = simple
pbc = no
rlist = 100
rgbradii = 100
coulombtype = cut-off
epsilon_r = 1 ; double check this is what we want
rcoulomb = 100
vdwtype = cut-off
rvdw = 100
tc-grps = system
tau_t = 0.01099
ref_t = 300
gen_vel = yes
gen_temp = 273
constraints = none
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78





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[gmx-users] System Exploding

[Alex Seling]

Hello,

After upgrading to gromacs 4.5.5, the old .mdp file that was working is now
giving me errors. Specifically, I'm getting
"This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size"
for a few interactions, with each of them approaching inf.

This is with a good starting configuration. Any ideas as to the error? My
.mdp file is below.

Thanks,
Alex Seling


title = lea at 300K
cpp = /lib/cpp -traditional
integrator = md ;sd ;md ;bd
tinit = 0.0
dt = 0.001 ;time step of 1 fs
nsteps = 23800 ;1 us @ 1fs
nstxout = 20 ; frequency to write coordinates to output trajectory file
= 1ns
nstxtcout = 20 ; frequency to write coordinates to xtc trajectory = 1 ns
nstvout = 0
nstfout = 0
nstlog = 20 ; frequency to write energies to log file = 1 ns
nstenergy = 20 ; frequency to write energies to energy file = 1ns
energygrps = system
comm_mode = angular
nstcomm = 40
nstlist = 100
nstype = simple
pbc = no
rlist = 100
rgbradii = 100
coulombtype = cut-off
epsilon_r = 1 ; double check this is what we want
rcoulomb = 100
vdwtype = cut-off
rvdw = 100
tc-grps = system
tau_t = 0.01099
ref_t = 300
gen_vel = yes
gen_temp = 273
constraints = none
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 78
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Re: [gmx-users] System blows up

[Guido Leoni]

Dear List and Mark
I followed your suggestions equilibrating the proteins of my complex
separately. In both cases i'm able to correctly equilibrate the system and
to perform a short md of 500ps. So I suppose that when i simulate both
protein together somewhere there is a clash. Now how could I highlight the
problem? In your opinion the clash could be more probably due to solvent
molecules or to my proteins perhaps too near each other?
Thank you very much
Guido

2012/1/11 Mark Abraham 

> On 11/01/2012 8:35 PM, Guido Leoni wrote:
>
>> Dear List
>> I'm newbie to gromacs (sigh). I'm simulating the interaction between two
>> proteins(chrystallographic structures) following the spider toxin tutorial.
>> I'm able to correctly minimize ( E<1000) and equilibrate (400 ps ) the
>> system. No error message appears to me and I'm quite sure that my starting
>> structures have no steric clashes.
>> My .mdp files are equal to the tutorial description excepted for the
>> choosen timesteps (400 ps in equilibration and 1000 ps in dynamics).
>> When I run the dynamic (launching gromacs with mpi) I retrieve after 7 ps
>> the following error message
>> "2 particles communicated to PME node 3 are more than a cell length out
>> of the domain decomposition cell of their charge group"
>> I suppose that this is due to the energy of some components that blow up.
>> Please how can i check which components are responsible for  the problem?
>> I'm also looking the instruction on the web site but they appear to me a
>> bit cryptic. For example
>>
>> If the crash is happening relatively early (within a few steps), set
>> nstxout (or nstxtcout) to 1, capturing all possible frames.  Watch the
>> resulting trajectory to see which atoms/residues/molecules become unstable
>> first.
>>
>> I looked the resulting trajectories of the 2 proteins with ngmx but they
>> seem to be always in the box and it is impossible to graphically check the
>> water molecules .
>>
>>
> The next piece of advice is to simplify your problem. If you can get each
> of your proteins to equilibrate on their own, then you probably have an
> atomic clash after all. If one doesn't equilibrate, then maybe your
> simulation conditions or topology is suspect.
>
> Mark
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-- 
Guido Leoni
National Research Institute on Food and Nutrition
(I.N.R.A.N.)
via Ardeatina 546
00178 Rome
Italy

tel + 39 06 51 49 41 (operator)
+ 39 06 51 49 4498 (direct)
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Re: [gmx-users] System blows up

[Mark Abraham]

On 11/01/2012 8:35 PM, Guido Leoni wrote:

Dear List
I'm newbie to gromacs (sigh). I'm simulating the interaction between 
two proteins(chrystallographic structures) following the spider toxin 
tutorial. I'm able to correctly minimize ( E<1000) and equilibrate 
(400 ps ) the system. No error message appears to me and I'm quite 
sure that my starting structures have no steric clashes.
My .mdp files are equal to the tutorial description excepted for the 
choosen timesteps (400 ps in equilibration and 1000 ps in dynamics).
When I run the dynamic (launching gromacs with mpi) I retrieve after 7 
ps the following error message
"2 particles communicated to PME node 3 are more than a cell length 
out of the domain decomposition cell of their charge group"

I suppose that this is due to the energy of some components that blow up.
Please how can i check which components are responsible for  the problem?
I'm also looking the instruction on the web site but they appear to me 
a bit cryptic. For example


If the crash is happening relatively early (within a few steps), set 
nstxout (or nstxtcout) to 1, capturing all possible frames.  Watch the 
resulting trajectory to see which atoms/residues/molecules become 
unstable first.


I looked the resulting trajectories of the 2 proteins with ngmx but 
they seem to be always in the box and it is impossible to graphically 
check the water molecules .




The next piece of advice is to simplify your problem. If you can get 
each of your proteins to equilibrate on their own, then you probably 
have an atomic clash after all. If one doesn't equilibrate, then maybe 
your simulation conditions or topology is suspect.


Mark
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[gmx-users] System blows up

[Guido Leoni]

Dear List
I'm newbie to gromacs (sigh). I'm simulating the interaction between two
proteins(chrystallographic structures) following the spider toxin tutorial.
I'm able to correctly minimize ( E<1000) and equilibrate (400 ps ) the
system. No error message appears to me and I'm quite sure that my starting
structures have no steric clashes.
My .mdp files are equal to the tutorial description excepted for the
choosen timesteps (400 ps in equilibration and 1000 ps in dynamics).
When I run the dynamic (launching gromacs with mpi) I retrieve after 7 ps
the following error message
"2 particles communicated to PME node 3 are more than a cell length out of
the domain decomposition cell of their charge group"
I suppose that this is due to the energy of some components that blow up.
Please how can i check which components are responsible for  the problem?
I'm also looking the instruction on the web site but they appear to me a
bit cryptic. For example

If the crash is happening relatively early (within a few steps), set
nstxout (or nstxtcout) to 1, capturing all possible frames.  Watch the
resulting trajectory to see which atoms/residues/molecules become unstable
first.

I looked the resulting trajectories of the 2 proteins with ngmx but they
seem to be always in the box and it is impossible to graphically check the
water molecules .
Many Thanks for any kind of suggestion
Best
Guido
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Re: [gmx-users] System heating up during MD run? (Implicit solvent)

[Justin A. Lemkul]

I would also add that the settings provided below probably produce severe cutoff 
artifacts.  In my experience, the only stable settings are those of the 
all-vs-all kernel (with infinite cutoffs).


-Justin

Per Larsson wrote:

Hi

There has been a number of reports lately about ill-behaving simulations using 
implicit solvent. I'm currently trying to investigate the cause of this, as 
such simulations used to work very nice in our hands.

In the meantime I would advice to use implicit solvent with caution.

Thanks
/Per

Skickat från min iPhone

30 okt 2011 kl. 02:10 skrev Matt Larson :


I've been having problems getting implicit solvent systems (which are
probably fairly experiment still in gromacs) to work correctly.  I've
been modelling a protein of about 11000 atoms with hydrogens in a 2 ns
simulation.  By the end of the simulation, the temperature has risen
from 300 K to 496 K - and the protein unfolds.  It was supposed to
maintain temp at 300 K.

I have an a non-zero total charge of -6.99.  With explicit
solvent, I would normally add the appropriate matching ions, but with
implicit solvent what should you do?   Could the non-zero total charge
result in heating?  Or is the thermostat not working well enough
(should I change tau-t or ref-t?)

Here is my md.mdp file:


constraints =  all-bonds ; trying..
integrator  =  md
dt  =  0.002; ps !
nsteps  =  100
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype =  cut-off
fourierspacing  =  0.16
vdwtype =  cut-off
rcoulomb=  1.0
rvdw=  1.0  ; important for neighbor searching
pbc =  no   ; no periodic boundary conditions
epsilon_rf  =  0
rgbradii=  1.0  ; must equal rlist, rcoulomb, rvdw
comm_mode   =  angular
optimize_fft= yes

implicit_solvent= GBSA
gb_algorithm= OBC
gb_epsilon_solvent  = 80
sa_surface_tension  = 2.25936

nstcomm = 10
nstxout = 1000
nstxtcout   = 1000
nstvout = 0
nstfout = 0

tcoupl  = andersen
tc-grps = system
tau-t   = 0.1
ref-t   = 300

gen_vel = yes
gen_temp= 300
gen_seed= -1

-
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--


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] System heating up during MD run? (Implicit solvent)

[Per Larsson]

Hi

There has been a number of reports lately about ill-behaving simulations using 
implicit solvent. I'm currently trying to investigate the cause of this, as 
such simulations used to work very nice in our hands.

In the meantime I would advice to use implicit solvent with caution.

Thanks
/Per

Skickat från min iPhone

30 okt 2011 kl. 02:10 skrev Matt Larson :

> I've been having problems getting implicit solvent systems (which are
> probably fairly experiment still in gromacs) to work correctly.  I've
> been modelling a protein of about 11000 atoms with hydrogens in a 2 ns
> simulation.  By the end of the simulation, the temperature has risen
> from 300 K to 496 K - and the protein unfolds.  It was supposed to
> maintain temp at 300 K.
> 
> I have an a non-zero total charge of -6.99.  With explicit
> solvent, I would normally add the appropriate matching ions, but with
> implicit solvent what should you do?   Could the non-zero total charge
> result in heating?  Or is the thermostat not working well enough
> (should I change tau-t or ref-t?)
> 
> Here is my md.mdp file:
> 
> 
> constraints =  all-bonds ; trying..
> integrator  =  md
> dt  =  0.002; ps !
> nsteps  =  100
> nstlist =  10
> ns_type =  grid
> rlist   =  1.0
> coulombtype =  cut-off
> fourierspacing  =  0.16
> vdwtype =  cut-off
> rcoulomb=  1.0
> rvdw=  1.0  ; important for neighbor searching
> pbc =  no   ; no periodic boundary conditions
> epsilon_rf  =  0
> rgbradii=  1.0  ; must equal rlist, rcoulomb, rvdw
> comm_mode   =  angular
> optimize_fft= yes
> 
> implicit_solvent= GBSA
> gb_algorithm= OBC
> gb_epsilon_solvent  = 80
> sa_surface_tension  = 2.25936
> 
> nstcomm = 10
> nstxout = 1000
> nstxtcout   = 1000
> nstvout = 0
> nstfout = 0
> 
> tcoupl  = andersen
> tc-grps = system
> tau-t   = 0.1
> ref-t   = 300
> 
> gen_vel = yes
> gen_temp= 300
> gen_seed= -1
> 
> -
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[gmx-users] System heating up during MD run? (Implicit solvent)

[Matt Larson]

I've been having problems getting implicit solvent systems (which are
probably fairly experiment still in gromacs) to work correctly.  I've
been modelling a protein of about 11000 atoms with hydrogens in a 2 ns
simulation.  By the end of the simulation, the temperature has risen
from 300 K to 496 K - and the protein unfolds.  It was supposed to
maintain temp at 300 K.

I have an a non-zero total charge of -6.99.  With explicit
solvent, I would normally add the appropriate matching ions, but with
implicit solvent what should you do?   Could the non-zero total charge
result in heating?  Or is the thermostat not working well enough
(should I change tau-t or ref-t?)

Here is my md.mdp file:


constraints =  all-bonds ; trying..
integrator  =  md
dt  =  0.002; ps !
nsteps  =  100
nstlist =  10
ns_type =  grid
rlist   =  1.0
coulombtype =  cut-off
fourierspacing  =  0.16
vdwtype =  cut-off
rcoulomb=  1.0
rvdw=  1.0  ; important for neighbor searching
pbc =  no   ; no periodic boundary conditions
epsilon_rf  =  0
rgbradii=  1.0  ; must equal rlist, rcoulomb, rvdw
comm_mode   =  angular
optimize_fft= yes

implicit_solvent= GBSA
gb_algorithm= OBC
gb_epsilon_solvent  = 80
sa_surface_tension  = 2.25936

nstcomm = 10
nstxout = 1000
nstxtcout   = 1000
nstvout = 0
nstfout = 0

tcoupl  = andersen
tc-grps = system
tau-t   = 0.1
ref-t   = 300

gen_vel = yes
gen_temp= 300
gen_seed= -1

-
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Re: [gmx-users] system is exploding

[Justin A. Lemkul]

Quoting Baofu Qiao :

>
> If you are really sure about the topology, the problem is the initial
> structure. Try to use PackMol to build it.
>

For simple molecules in water, there is no need for a complicated program like
packmol.  Such a configuration can easily be built in Gromacs.

I have yet to see any evidence of an error.  From the original post, it seems
that EM failed to start at all.

-Justin

> On 11/26/2010 11:42 AM, Olga Ivchenko wrote:
> > I tried today to run minimization in vacuum for my small molecules. This
> has
> > the same error.
> >
> > 2010/11/26 Baofu Qiao 
> >
> >
> >> Have you run the energy minimization (or further simulation to optimize
> >> the structure and test the FF) on the small molecule before you added it
> >> into water?
> >>
> >> On 11/26/2010 11:26 AM, Olga Ivchenko wrote:
> >>
> >>> Dear gromacs users,
> >>>
> >>> I am trying to run simulations for small molecules in water. Topology
> >>>
> >> files
> >>
> >>> I created by my self for charm ff. When I am trying to start energy
> >>> minimization I got an error:
> >>>
> >>>
> >>>  Steepest Descents:
> >>>
> >>> Tolerance (Fmax) = 1.0e+00
> >>>
> >>> Number of steps = 1000
> >>>
> >>>
> >>> That's means my system is exploding. Please can you advice me on this,
> >>>
> >> what
> >>
> >>> I need to check.
> >>>
> >>> best,
> >>>
> >>> Olga
> >>>
> >>>
> >>>
> >>
> >> --
> >> 
> >>  Dr. Baofu Qiao
> >>  Institute for Computational Physics
> >>  Universit�t Stuttgart
> >>  Pfaffenwaldring 27
> >>  70569 Stuttgart
> >>
> >>  Tel: +49(0)711 68563607
> >>  Fax: +49(0)711 68563658
> >>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >>
> >
>
>
> --
> 
>  Dr. Baofu Qiao
>  Institute for Computational Physics
>  Universit�t Stuttgart
>  Pfaffenwaldring 27
>  70569 Stuttgart
>
>  Tel: +49(0)711 68563607
>  Fax: +49(0)711 68563658
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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>




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] system is exploding

[T.M.D. Graen]

check your custom topology (this is where the error is 99% of the time), 
use qm minimized starting structures, make sure your structure matches 
your topology (atom names,numbers,ordering, etc.), test single molecules 
in vacuum first and/or reduce the step size of your SD minimizer.


On 11/26/2010 11:47 AM, Baofu Qiao wrote:


If you are really sure about the topology, the problem is the initial
structure. Try to use PackMol to build it.

On 11/26/2010 11:42 AM, Olga Ivchenko wrote:

I tried today to run minimization in vacuum for my small molecules. This has
the same error.

2010/11/26 Baofu Qiao



Have you run the energy minimization (or further simulation to optimize
the structure and test the FF) on the small molecule before you added it
into water?

On 11/26/2010 11:26 AM, Olga Ivchenko wrote:


Dear gromacs users,

I am trying to run simulations for small molecules in water. Topology


files


I created by my self for charm ff. When I am trying to start energy
minimization I got an error:


  Steepest Descents:

Tolerance (Fmax) = 1.0e+00

Number of steps = 1000


That's means my system is exploding. Please can you advice me on this,


what


I need to check.

best,

Olga





--

  Dr. Baofu Qiao
  Institute for Computational Physics
  Universität Stuttgart
  Pfaffenwaldring 27
  70569 Stuttgart

  Tel: +49(0)711 68563607
  Fax: +49(0)711 68563658

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Re: [gmx-users] system is exploding

[Baofu Qiao]

If you are really sure about the topology, the problem is the initial
structure. Try to use PackMol to build it.

On 11/26/2010 11:42 AM, Olga Ivchenko wrote:
> I tried today to run minimization in vacuum for my small molecules. This has
> the same error.
>
> 2010/11/26 Baofu Qiao 
>
>   
>> Have you run the energy minimization (or further simulation to optimize
>> the structure and test the FF) on the small molecule before you added it
>> into water?
>>
>> On 11/26/2010 11:26 AM, Olga Ivchenko wrote:
>> 
>>> Dear gromacs users,
>>>
>>> I am trying to run simulations for small molecules in water. Topology
>>>   
>> files
>> 
>>> I created by my self for charm ff. When I am trying to start energy
>>> minimization I got an error:
>>>
>>>
>>>  Steepest Descents:
>>>
>>> Tolerance (Fmax) = 1.0e+00
>>>
>>> Number of steps = 1000
>>>
>>>
>>> That's means my system is exploding. Please can you advice me on this,
>>>   
>> what
>> 
>>> I need to check.
>>>
>>> best,
>>>
>>> Olga
>>>
>>>
>>>   
>>
>> --
>> 
>>  Dr. Baofu Qiao
>>  Institute for Computational Physics
>>  Universität Stuttgart
>>  Pfaffenwaldring 27
>>  70569 Stuttgart
>>
>>  Tel: +49(0)711 68563607
>>  Fax: +49(0)711 68563658
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> 
>   


-- 

 Dr. Baofu Qiao
 Institute for Computational Physics
 Universität Stuttgart
 Pfaffenwaldring 27
 70569 Stuttgart

 Tel: +49(0)711 68563607
 Fax: +49(0)711 68563658

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Re: [gmx-users] system is exploding

[Olga Ivchenko]

I tried today to run minimization in vacuum for my small molecules. This has
the same error.

2010/11/26 Baofu Qiao 

>
> Have you run the energy minimization (or further simulation to optimize
> the structure and test the FF) on the small molecule before you added it
> into water?
>
> On 11/26/2010 11:26 AM, Olga Ivchenko wrote:
> > Dear gromacs users,
> >
> > I am trying to run simulations for small molecules in water. Topology
> files
> > I created by my self for charm ff. When I am trying to start energy
> > minimization I got an error:
> >
> >
> >  Steepest Descents:
> >
> > Tolerance (Fmax) = 1.0e+00
> >
> > Number of steps = 1000
> >
> >
> > That's means my system is exploding. Please can you advice me on this,
> what
> > I need to check.
> >
> > best,
> >
> > Olga
> >
> >
>
>
> --
> 
>  Dr. Baofu Qiao
>  Institute for Computational Physics
>  Universität Stuttgart
>  Pfaffenwaldring 27
>  70569 Stuttgart
>
>  Tel: +49(0)711 68563607
>  Fax: +49(0)711 68563658
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] system is exploding

[Baofu Qiao]

Have you run the energy minimization (or further simulation to optimize
the structure and test the FF) on the small molecule before you added it
into water?

On 11/26/2010 11:26 AM, Olga Ivchenko wrote:
> Dear gromacs users,
>
> I am trying to run simulations for small molecules in water. Topology files
> I created by my self for charm ff. When I am trying to start energy
> minimization I got an error:
>
>
>  Steepest Descents:
>
> Tolerance (Fmax) = 1.0e+00
>
> Number of steps = 1000
>
>
> That's means my system is exploding. Please can you advice me on this, what
> I need to check.
>
> best,
>
> Olga
>
>   


-- 

 Dr. Baofu Qiao
 Institute for Computational Physics
 Universität Stuttgart
 Pfaffenwaldring 27
 70569 Stuttgart

 Tel: +49(0)711 68563607
 Fax: +49(0)711 68563658

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[gmx-users] system is exploding

[Olga Ivchenko]

Dear gromacs users,

I am trying to run simulations for small molecules in water. Topology files
I created by my self for charm ff. When I am trying to start energy
minimization I got an error:


 Steepest Descents:

Tolerance (Fmax) = 1.0e+00

Number of steps = 1000


That's means my system is exploding. Please can you advice me on this, what
I need to check.

best,

Olga
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Re: [gmx-users] System net charge

[Justin A. Lemkul]

Rabab Toubar wrote:

I have noticed that you get the overall charge WHILE you are setting up the 
system - when using grompp I think. Now if after the mdrun and I want to check 
the overall charge, how can I possibly do that?
I tried the mailing list but didn't find an answer to my question


The net charge of any molecule (if processed by pdb2gmx) is printed in the 
topology at the end of the [atoms] directive.  Otherwise, take note of what 
grompp tells you and/or log all your output.


-Justin



Thanks
Rabab Toubar



  



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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] System net charge

[Rabab Toubar]

I have noticed that you get the overall charge WHILE you are setting up the 
system - when using grompp I think. Now if after the mdrun and I want to check 
the overall charge, how can I possibly do that?
I tried the mailing list but didn't find an answer to my question

Thanks
Rabab Toubar



  

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Re: [gmx-users] System has non-zero total charge: -8.000001e+00

[Tamas Horvath]

You should always neutralise your sysem.

On Thu, Feb 25, 2010 at 1:42 PM, Maurício Menegatti Rigo <
mauriciomr1...@gmail.com> wrote:

> IS this a problem?
>
> *System has non-zero total charge: -8.01e+00*
>
> If yes, can I fix that changing COulomb cutt-off to PME electrostatics?
>
> THanks!!
>
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Re: [gmx-users] System has non-zero total charge: -8.000001e+00

[Justin A. Lemkul]

Maurício Menegatti Rigo wrote:

IS this a problem?

/System has non-zero total charge: -8.01e+00/

If yes, can I fix that changing COulomb cutt-off to PME electrostatics?


You need to add counterions to your system.  Consult some basic tutorial 
material, as well as the manual entry for genion.


-Justin



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
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[gmx-users] System has non-zero total charge: -8.000001e+00

[Maurício Menegatti Rigo]

IS this a problem?

*System has non-zero total charge: -8.01e+00*

If yes, can I fix that changing COulomb cutt-off to PME electrostatics?

THanks!!
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Re: [gmx-users] system blowing

[Mark Abraham]

Ramachandran G wrote:

Dear all,
  I am trying to minimize a protein structure but i noticed 
initially before it starts minimization, it gives warning

-
Warning: 1-4 interaction between 1434 and 1490 at distance 1.783 which 
is larger than the 1-4 table size 1.000 nm

These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
Using 10 BFGS correction steps.

   F-max =  7.89523e+03 on atom 1185
   F-Norm=  4.87025e+04
 --
finally it converged to machine precision but not to the requested 
precision Fmax < 1000. When i view final structure, it
looks the residues are sprayed out. The mdp file which i used for 
minimization is


This .mdp does not match the above output.



Title   =   protien test
cpp =  /lib/cpp
;include =  -I../top
define  = -DFLEXIBLE
constraints = none
integrator  =  steep
nstcomm =  1
dt  =  0.002; ps !
nsteps  =  5
nstlist =  10
ns_type =  grid
rlist   =  1.4
coulombtype =  shift
rcoulomb=  1.2
vdwtype =  shift
rvdw=  1.2
;
;   Energy minimizing stuff
;
emtol   =  1000.0
emstep  =  0.01




This protein structure has been minimized using Charmm but in gromacs i 
am having problem. Can anyone help me. Thank you.


There's so many things you might have done to it since leaving CHARMM 
that it's scarcely material that it was minimized there. Check your 
termini and the locations of your solvent molecules. It's impossible to 
help you further without more detail of your preparation.


Mark
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[gmx-users] system blowing

[Ramachandran G]

Dear all,
  I am trying to minimize a protein structure but i noticed initially
before it starts minimization, it gives warning
-
Warning: 1-4 interaction between 1434 and 1490 at distance 1.783 which is
larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
Using 10 BFGS correction steps.

   F-max =  7.89523e+03 on atom 1185
   F-Norm=  4.87025e+04
 --
finally it converged to machine precision but not to the requested precision
Fmax < 1000. When i view final structure, it
looks the residues are sprayed out. The mdp file which i used for
minimization is

Title   =   protien test
cpp =  /lib/cpp
;include =  -I../top
define  = -DFLEXIBLE
constraints = none
integrator  =  steep
nstcomm =  1
dt  =  0.002; ps !
nsteps  =  5
nstlist =  10
ns_type =  grid
rlist   =  1.4
coulombtype =  shift
rcoulomb=  1.2
vdwtype =  shift
rvdw=  1.2
;
;   Energy minimizing stuff
;
emtol   =  1000.0
emstep  =  0.01




This protein structure has been minimized using Charmm but in gromacs i am
having problem. Can anyone help me. Thank you.
Rama
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Re: [gmx-users] System has non-zero total charge: 2.570000e+00

[Justin A. Lemkul]

Itamar Kass wrote:




Hi,

If you have non water molecule in the box (eg protein) their charge 
might differ from 0. SO you might add ions in order to neutralize it.




In general, that is a correct solution.  But in the case of a +2.57 net charge, 
something is certainly wrong with the species in the simulation.  This charge 
represents a non-negligible rounding error that occasionally arises, and it is 
doubtful that ions alone can solve it.


-Justin


Best,
Itamar



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ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] System has non-zero total charge: 2.570000e+00

[Itamar Kass]

Justin A. Lemkul wrote:



najwa drici wrote:

hello Gromacs users,
I have some problems about the total charge of system using Gromacs.
I wanted to perform molecular dynamic simulation in box of SPC water.  
before energy minimization step , I performed the preprosessing step 
using grompp  . However, there’s a note that : System has non-zero 
total charge: 2.57e+00 “.

why the total charge of system is not an integer?


Something is broken.  Check the topology to see what is causing the 
non-integral charge.  If you want any other help, you'll have to 
describe what you're doing in much greater detail.


-Justin


thank you
nejoua DRICI


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Hi,

If you have non water molecule in the box (eg protein) their charge 
might differ from 0. SO you might add ions in order to neutralize it.


Best,
Itamar
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Re: [gmx-users] System has non-zero total charge: 2.570000e+00

[Justin A. Lemkul]

najwa drici wrote:

hello Gromacs users,
I have some problems about the total charge of system using Gromacs.
I wanted to perform molecular dynamic simulation in box of SPC water. 
 
before energy minimization step , I performed the preprosessing 
step using grompp  . However, there’s a note that : System has non-zero 
total charge: 2.57e+00 “.

why the total charge of system is not an integer?


Something is broken.  Check the topology to see what is causing the non-integral 
charge.  If you want any other help, you'll have to describe what you're doing 
in much greater detail.


-Justin


thank you
nejoua DRICI 




Messenger débarque dans Hotmail ! Essayez-le ! 






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--


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


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[gmx-users] System has non-zero total charge: 2.570000e+00

[najwa drici]

hello Gromacs users,
I have some problems about the total charge of system using Gromacs.
I wanted to perform molecular dynamic simulation in box of SPC water. 

 

before energy minimization step , I performed the preprosessing step using 
grompp  . However, there’s a note that : System has non-zero total charge: 
2.57e+00 “.
why the total charge of system is not an integer?

thank you

nejoua DRICI 


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Re: [gmx-users] System has non-zero total charge: 1.999878e+00

[Mark Abraham]

zakiya wrote:
> Hi Gromacs users,
> I have some problems about the total charge of system using Gromacs.
> I wanted to perform a protein denaturation simulation induced by urea. At 
> first, I added urea molecules into the box including one CI2 protein. Then I 
> performed the energy minimization step. However, there’s a note that “NOTE 1 
> [file ci2.top, line 3998]:  System has non-zero total charge: 1.999878e+00 “.
> My question is that why the total charge of system is not an integer. The 
> whole charge of CI2 protein is 2.000e+00. 

Arithmetic on computers is subject to rounding errors after each
operation. There are a number of threads on this list that have
discussed this in the past. So long as the total charge is still close
to an integer, you don't have evidence of a serious problem. See also
http://oldwiki.gromacs.org/index.php/Errors#System_has_non-zero_total_charge

Mark

I got the ITP file of urea molecule from the “share” file in the Gromacs
library directory. The total charge is zero. So this phenomena puzzled me.
> The [atoms] field in the ITP file of urea molecule is as follows:
> [ atoms ]
> ;   nrtype   resnr  residuatomcgnr  charge   mass
> #ifdef Boek
>  1   C   1UREA  C1   1   0.38  12.0110
>  2   O   1UREA  O2   1   -0.3815.9994
>  3  NT   1UREA  N3   2   -0.8314.0067
>  4   H   1UREA  H4   2   0.4151.0080
>  5   H   1UREA  H5   2   0.4151.0080
>  6  NT   1UREA  N6   3   -0.83 14.0067
>  7   H   1UREA  H7   3 0.4151.0080
>  8   H   1UREA  H8   3   0.4151.0080
> #else
>  1   C   1UREA  C1   1   0.68312.0110
>  2   O   1UREA  O2   1   -0.683   15.9994
>  3  NT   1UREA  N3   2   -0.622   14.0067
>  4   H   1UREA  H4   2   0.346   1.0080
>  5   H   1UREA  H5   2   0.276   1.0080
>  6  NT   1UREA  N6   3   -0.622   14.0067
>  7   H   1UREA  H7   3 0.346   1.0080
>  8   H   1UREA  H8   3   0.276   1.0080
> #endif
>  
> Any help/suggestions will be greatly appreciated!
>  
> Thank you!!
> Na  Zhang
>  
> 
> 
> 
> 
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[gmx-users] System has non-zero total charge: 1.999878e+00

[zakiya]

Hi Gromacs users,
I have some problems about the total charge of system using Gromacs.
I wanted to perform a protein denaturation simulation induced by urea. At 
first, I added urea molecules into the box including one CI2 protein. Then I 
performed the energy minimization step. However, there’s a note that “NOTE 1 
[file ci2.top, line 3998]:  System has non-zero total charge: 1.999878e+00 “.
My question is that why the total charge of system is not an integer. The whole 
charge of CI2 protein is 2.000e+00. I got the ITP file of urea molecule from 
the “share” file in the Gromacs library directory. The total charge is zero. So 
this phenomena puzzled me.
The [atoms] field in the ITP file of urea molecule is as follows:
[ atoms ]
;   nrtype   resnr  residuatomcgnr  charge   mass
#ifdef Boek
 1   C   1UREA  C1   1   0.38  12.0110
 2   O   1UREA  O2   1   -0.3815.9994
 3  NT   1UREA  N3   2   -0.8314.0067
 4   H   1UREA  H4   2   0.4151.0080
 5   H   1UREA  H5   2   0.4151.0080
 6  NT   1UREA  N6   3   -0.83 14.0067
 7   H   1UREA  H7   3 0.4151.0080
 8   H   1UREA  H8   3   0.4151.0080
#else
 1   C   1UREA  C1   1   0.68312.0110
 2   O   1UREA  O2   1   -0.683   15.9994
 3  NT   1UREA  N3   2   -0.622   14.0067
 4   H   1UREA  H4   2   0.346   1.0080
 5   H   1UREA  H5   2   0.276   1.0080
 6  NT   1UREA  N6   3   -0.622   14.0067
 7   H   1UREA  H7   3 0.346   1.0080
 8   H   1UREA  H8   3   0.276   1.0080
#endif
 
Any help/suggestions will be greatly appreciated!
 
Thank you!!
Na  Zhang
 
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RE: [gmx-users] System instability with switched cut-off

[Berk Hess]

Hi,

Never ever use switched cut-off's!
Switched cut-off's can give extremely strong artifacts.
In 4.1 grompp will warn you about this.

Switch gives you correct energies at short range, but incorrect forces
in the switching region.
What you want is correct forces up to (nearly) the cut-off.
Shift does this.
But reaction-field does this smoother and it even has a physical interpretation.
So use RF if you can not use PME.

But why can't you use PME, you have pbc, right?

Berk


From: matteus.lindg...@chem.umu.se
To: gmx-users@gromacs.org
Date: Fri, 7 Aug 2009 13:13:24 +0200
Subject: [gmx-users] System instability with switched cut-off
















Dear all

 

Im trying to extract the interaction
energies between protein and solvent. Since PME cant be used for this, plain
cutoffs causes problems and shifted cut-offs gives incorrect energies I want to
use switched cutoff but with rather long cutoffs to get the correct energy. 

 

Unfortunately my system is unstable and
within a few ps the total energy and kinetic energy fluctuates several hundred
per cent. I´ve tried different options but can´t get it to stabilize except if
I´m using any other coulomb type. Any ideas?

 

title=
Dyna

cpp  =
/usr/bin/cpp

constraints  =
hbonds

integrator   =
md

dt   =
0.002

nsteps   =
2000

nstxout  =
2000

nstvout  =
2000

nstfout  =
5000

nstlog   =
250

nstenergy=
500

nstxtcout=
500

xtc_grps = 

energygrps   =
polar hydrophobic peptide  SOL 

nstlist  = 1

ns_type  =
grid

coulombtype  =
switch

rcoulomb_switch  =
1.4

rcoulomb =
1.7

rlist=
2.0

vdwtype  =
switch

rvdw_switch  =
1.4

rvdw =
1.7

tcoupl   =
nose-hoover

tc-grps  = Protein   
Non-Protein

tau_t=
0.5  0.5

ref_t=
298298

Pcoupl   =
parrinello-rahman

tau_p=
1.0

compressibility  =
4.5e-5

ref_p=
1.0

 

;disre_fc =
30

 

gen_vel  = yes

gen_temp = 298

gen_seed = 173529

unconstrained_start 
= no

 

Thanks

Matteus 

 

- 

Matteus
Lindgren, graduate student

Department of Chemistry, Umeå University 

SE-901 87 Umeå, Sweden

Phone:  +46 (0)90-7865368  

 

 


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[gmx-users] System instability with switched cut-off

[Matteus Lindgren]

Dear all

 

Im trying to extract the interaction energies between protein and solvent.
Since PME cant be used for this, plain cutoffs causes problems and shifted
cut-offs gives incorrect energies I want to use switched cutoff but with
rather long cutoffs to get the correct energy. 

 

Unfortunately my system is unstable and within a few ps the total energy and
kinetic energy fluctuates several hundred per cent. I´ve tried different
options but can´t get it to stabilize except if I´m using any other coulomb
type. Any ideas?

 

title= Dyna

cpp  = /usr/bin/cpp

constraints  = hbonds

integrator   = md

dt   = 0.002

nsteps   = 2000

nstxout  = 2000

nstvout  = 2000

nstfout  = 5000

nstlog   = 250

nstenergy= 500

nstxtcout= 500

xtc_grps = 

energygrps   = polar hydrophobic peptide  SOL 

nstlist  = 1

ns_type  = grid

coulombtype  = switch

rcoulomb_switch  = 1.4

rcoulomb = 1.7

rlist= 2.0

vdwtype  = switch

rvdw_switch  = 1.4

rvdw = 1.7

tcoupl   = nose-hoover

tc-grps  = ProteinNon-Protein

tau_t= 0.5  0.5

ref_t= 298298

Pcoupl   = parrinello-rahman

tau_p= 1.0

compressibility  = 4.5e-5

ref_p= 1.0

 

;disre_fc = 30

 

gen_vel  = yes

gen_temp = 298

gen_seed = 173529

unconstrained_start  = no

 

Thanks

Matteus 

 

- 

Matteus Lindgren, graduate student
Department of Chemistry, Umeå University 
SE-901 87 Umeå, Sweden
Phone:  +46 (0)90-7865368  

 

 

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Re: [gmx-users] system explodes

[Andrea Muntean]

Thank you. I will do so.

kind regards,
Andrea

2008/11/11 Justin A. Lemkul <[EMAIL PROTECTED]>:
>
>
> Andrea Muntean wrote:
>>
>> I am simulating one chain of PS. The box is produced by pdb2gmx. If I
>> run simulations with timestep 0.1 fs up to 0.4 fs everything seem to
>> be ok. With 1 fs (which should be a normal time for my system) I would
>> get the following warning:
>>
>> Warning: 1-4 interaction between 290 and 299 at distance 108.224 which
>> is larger than the 1-4 table size 1.000 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>>
>> The parameters I use are the following:
>>
>> title= PS
>> cpp  = /lib/cpp
>> integrator   = md
>> dt   = 0.0001; ps !
>> nsteps   = 1 ; total 10 ps
>> nstlist  = 10
>> nstxout  = 100
>> nstvout  = 100
>> nstenergy= 100
>> unconstrained-start  = yes
>> nstxtcout= 50
>> nstlog   = 50
>> constraints  = none
>> ns_type  = grid
>> vdwtype  = Cut-off
>> fourierspacing   = 0.055 ; Lbox/0.055 ~ 50
>> rlist= 0.9
>> rvdw = 1.2
>> tc_grps  = system
>> tcoupl   = berendsen
>> tau_t= 0.1
>> ref_t= 540
>> Pcoupl   = no
>> optimize_fft = yes
>>
>> the rest is set default
>>
>> Did I miss something? What goes wrong?
>>
>
> You are running a very high temperature with no bond constraints.  I would
> expect you would need a very small timestep (like 0.1 fs) to get reasonable
> dynamics.  Try using constraints.
>
> -Justin
>
>> Any help and/or comments are really appreciated.
>>
>> Thank you!
>>
>> Andrea
>> ___
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>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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] system explodes

[Justin A. Lemkul]

Andrea Muntean wrote:

I am simulating one chain of PS. The box is produced by pdb2gmx. If I
run simulations with timestep 0.1 fs up to 0.4 fs everything seem to
be ok. With 1 fs (which should be a normal time for my system) I would
get the following warning:

Warning: 1-4 interaction between 290 and 299 at distance 108.224 which
is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

The parameters I use are the following:

title= PS
cpp  = /lib/cpp
integrator   = md
dt   = 0.0001; ps !
nsteps   = 1 ; total 10 ps
nstlist  = 10
nstxout  = 100
nstvout  = 100
nstenergy= 100
unconstrained-start  = yes
nstxtcout= 50
nstlog   = 50
constraints  = none
ns_type  = grid
vdwtype  = Cut-off
fourierspacing   = 0.055 ; Lbox/0.055 ~ 50
rlist= 0.9
rvdw = 1.2
tc_grps  = system
tcoupl   = berendsen
tau_t= 0.1
ref_t= 540
Pcoupl   = no
optimize_fft = yes

the rest is set default

Did I miss something? What goes wrong?



You are running a very high temperature with no bond constraints.  I would 
expect you would need a very small timestep (like 0.1 fs) to get reasonable 
dynamics.  Try using constraints.


-Justin


Any help and/or comments are really appreciated.

Thank you!

Andrea
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--


Justin A. Lemkul
Graduate Research Assistant
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] system explodes

[Andrea Muntean]

I am simulating one chain of PS. The box is produced by pdb2gmx. If I
run simulations with timestep 0.1 fs up to 0.4 fs everything seem to
be ok. With 1 fs (which should be a normal time for my system) I would
get the following warning:

Warning: 1-4 interaction between 290 and 299 at distance 108.224 which
is larger than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

The parameters I use are the following:

title= PS
cpp  = /lib/cpp
integrator   = md
dt   = 0.0001; ps !
nsteps   = 1 ; total 10 ps
nstlist  = 10
nstxout  = 100
nstvout  = 100
nstenergy= 100
unconstrained-start  = yes
nstxtcout= 50
nstlog   = 50
constraints  = none
ns_type  = grid
vdwtype  = Cut-off
fourierspacing   = 0.055 ; Lbox/0.055 ~ 50
rlist= 0.9
rvdw = 1.2
tc_grps  = system
tcoupl   = berendsen
tau_t= 0.1
ref_t= 540
Pcoupl   = no
optimize_fft = yes

the rest is set default

Did I miss something? What goes wrong?

Any help and/or comments are really appreciated.

Thank you!

Andrea
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[gmx-users] system exploid during running

[Morteza Khabiri]

Dear gmxuser

Thanks for your advices. Because of your help I could run my solution and
protein together.
but during the run I faced with this warning which cause the run again be
crashed, The message is:

relative constraint deviation after LINCS:
max 0.000615 (between atoms 1731 and 1732) rms 0.23
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1731   1732   30.70.1000   0.0999  0.1000

do anybody knows what should I do now?

Thanks

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Re: [gmx-users] system couldn't be run

[Justin A. Lemkul]

Morteza Khabiri wrote:

Dear

I make the solution box of organic solvent. It is homeogen and mixed
properly.
It also has a minimum energy. I put one protein in this solution. Before
put the protein in the solution I minimimized it also. Now I mixed 2
system which each of them are minimized. After put the protein in the
solution I try first to minimized it then run it but unfortunately it
crashed. I did not work at all. I also tried to run the system without
minimization but it also did not work at all. I changed mdp file (


If the system crashes during minimization, I certainly wouldn't expect it to do 
anything but crash if you don't run EM!



eg,remove center of mass motion or decrease the temprature,..) but non of
them did work.



Usually it is better to show the .mdp file than to make us guess at what you've 
got...



Thats very nice of you if you guid me what should i do?


Dealing with mixed solvents can be difficult.  You probably have some severe 
overlap that cannot be resolved by energy minimization.  Usually if you set 
nstxout = 1 in the .mdp file you can get a glimpse of where the system begins to 
explode.  That will provide some clues.


-Justin



Thanks

Morteza

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--


Justin A. Lemkul
Graduate Research Assistant
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] system couldn't be run

[Morteza Khabiri]

Dear

I make the solution box of organic solvent. It is homeogen and mixed
properly.
It also has a minimum energy. I put one protein in this solution. Before
put the protein in the solution I minimimized it also. Now I mixed 2
system which each of them are minimized. After put the protein in the
solution I try first to minimized it then run it but unfortunately it
crashed. I did not work at all. I also tried to run the system without
minimization but it also did not work at all. I changed mdp file (
eg,remove center of mass motion or decrease the temprature,..) but non of
them did work.

Thats very nice of you if you guid me what should i do?

Thanks

Morteza

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[gmx-users] system contains proteins and DNAs with ffamber99

[servaas michielssens]

If you have amber, you can make your topology in amber and convert them to 
gromacs with the script on this website:


http://chemistry.csulb.edu/ffamber/tools.html


kind regards,

servaas



Dear all,

   Sometimes,the PDB file contains water molecules which only have the 
oxygen atom. Can

Gromacs add the hydrogen atoms of the water molecules?

   Additionly, when use Gromacs with the force field ffamber99, Can it add 
the hydrogen
atoms of the DNA? Can I use the force field ffamber99 to simulate the 
system which contains

proteins and DNAs?



Best regards, 


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Re: [gmx-users] system contains proteins and DNAs with ffamber99

[Balazs Jojart]

Dear Dechang,
in ff03 forcfield the nucleic acid parameters are the same as in the
ff99. But ff99 forcefield for proteins is not the best choice due to
it's 'helix friendly'nature. A better choice is to choose the ff03
forcfield for protein and dna, as well.
hoe this helps.
Balazs

Mark Abraham írta:
> Dechang Li wrote:
>   
>> Dear all, 
>>
>> Sometimes,the PDB file contains water molecules which only have the 
>> oxygen atom. Can 
>> Gromacs add the hydrogen atoms of the water molecules?
>> 
>
> No - you'll be better off deleting them all, re-solvating using genbox
> and then doing a normal minimization & equilibration process. An
> exception might be waters in an enzyme active site or such, in which
> case you're best off building the hydrogens by hand.
>
>   
>> Additionly, when use Gromacs with the force field ffamber99, Can it add 
>> the hydrogen 
>> atoms of the DNA? 
>> 
>
> Yes, if there are suitable hydrogen database entries in the relevant
> .hdb file. See chapter 5 of the manual for background here.
>
>   
>> Can I use the force field ffamber99 to simulate the system which contains
>> proteins and DNAs?  
>> 
>
> Check the contents of the .rtp file to see what "residues" are defined.
>
> Mark
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Re: [gmx-users] system contains proteins and DNAs with ffamber99

[Vigneshwar Ramakrishnan]

hi,

I think the answer to both of your questions is YES!
Though, I have used ffamber03 for simulating protein+DNA. But I guess it
shouldn't matter.

Regards,
Vignesh

On Wed, Jun 11, 2008 at 3:50 PM, Dechang Li <[EMAIL PROTECTED]> wrote:

> Dear all,
>
>Sometimes,the PDB file contains water molecules which only have the
> oxygen atom. Can
> Gromacs add the hydrogen atoms of the water molecules?
>
>Additionly, when use Gromacs with the force field ffamber99, Can it add
> the hydrogen
> atoms of the DNA? Can I use the force field ffamber99 to simulate the
> system which contains
> proteins and DNAs?
>
>
>
> Best regards,
>
>
>
> =
> Dechang Li, PhD Candidate
> Department of Engineering Mechanics
> Tsinghua University
> Beijing 100084
> PR China
>
> Tel:   +86-10-62773779(O)
> Email: [EMAIL PROTECTED]
> =
>
>
>
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-- 
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Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

"The rewards of sincere resolves are highs money can never buy!"
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Re: [gmx-users] system contains proteins and DNAs with ffamber99

[Mark Abraham]

Dechang Li wrote:
> Dear all, 
> 
> Sometimes,the PDB file contains water molecules which only have the 
> oxygen atom. Can 
> Gromacs add the hydrogen atoms of the water molecules?

No - you'll be better off deleting them all, re-solvating using genbox
and then doing a normal minimization & equilibration process. An
exception might be waters in an enzyme active site or such, in which
case you're best off building the hydrogens by hand.

> Additionly, when use Gromacs with the force field ffamber99, Can it add 
> the hydrogen 
> atoms of the DNA? 

Yes, if there are suitable hydrogen database entries in the relevant
.hdb file. See chapter 5 of the manual for background here.

> Can I use the force field ffamber99 to simulate the system which contains
> proteins and DNAs?  

Check the contents of the .rtp file to see what "residues" are defined.

Mark
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[gmx-users] system contains proteins and DNAs with ffamber99

[Dechang Li]

Dear all, 

Sometimes,the PDB file contains water molecules which only have the oxygen 
atom. Can 
Gromacs add the hydrogen atoms of the water molecules?
  
Additionly, when use Gromacs with the force field ffamber99, Can it add the 
hydrogen 
atoms of the DNA? Can I use the force field ffamber99 to simulate the system 
which contains
proteins and DNAs?  



Best regards,



= 
Dechang Li, PhD Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
PR China 

Tel:   +86-10-62773779(O) 
Email: [EMAIL PROTECTED]
=

  

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Re: [gmx-users] system collapsed

[Mark Abraham]

Gitanjali tandon wrote:

helo
i have a prolblem whenever we carry out simulation in gromacs it gives 
the error message that number of grid cells is zero and the system is 
collapsed..


Your simulation system is non-physical.

In order to get effective help on problems on mailing lists like this 
one, you need to give a much more detailed description of what you are 
doing and what the outputs are. If it's too hard for people to help you, 
 they won't.


See http://www.catb.org/~esr/faqs/smart-questions.html and/or 
http://wiki.gromacs.org/index.php/Support


Mark
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[gmx-users] system collapsed

[Gitanjali tandon]

helo
i have a prolblem whenever we carry out simulation in gromacs it gives the
error message that number of grid cells is zero and the system is
collapsed..
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[gmx-users] System

[s lal badshah]

Dear Justin,
Hi,
I want to do MD simulation of cholera toxin A-subunit.I took PDB file and 
remove other complexes from the protein so it comes to 185 amino acid 
residues.Through Whatif server I added the missing atoms. I uses oplsaa force 
field.Added about 11700 water molecules, closed it in cubic box, added 5 sodium 
ions.Run the energy minimization but it didn't reached the full and output 
says:Converged to machine precision, but not to the requested precision.The EM 
value was in negative.Then I do the equilibration and the mentioned errors 
occured.My EM file is:
title  = cholera.mdp
cpp= /usr/bin/cpp ; the c preprocessor
include= -I/usr/share/gromacs/top
define = -DFLEXIBLE
constraints= none
integrator = steep
dt = 0.002
nsteps = 1
nstlist= 10
ns_type= grid
rlist  = 1.0
coulombtype= PME
rcoulomb   = 1.0
vdwtype= cut-off
rvdw   = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order  = 4
ewald_rtol = 1es
optimize_fft   = yes
;
;  Energy minimization stuff
emtol = 1000.0
emstep = 0.01
--
Wile pr.mdp file istitle   = pr.mdp
cpp = /usr/bin/cpp
define  = -DPOSRES
constraints = all-bonds
integrator  = md
dt  = 0.002
nsteps  = 10
nstcomm = 1
nstxout = 250
nstvout = 1000
nstlog  = 10
nstenergy   = 10
nstlist = 10
ns_type = grid
rlist   = 1.0
coulombtype = PME
rcoulomb= 1.0
vdwtype = cut-off
rvdw= 1.4
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e5
optimize_fft= yes
;Berendsen temperature coupling is on
Tcoupl  = berendsen
tau_t   = 0.1   0.1 
tc-grps  = protein  non-protein
ref_t   = 298   298 
;Pressure coupling is on
Pcoupl  = berendsen
tau_p   = 20 20
compressibility = 4.5e-5 4.5e-5
ref_p   = 1.01.0
;Generate velocities is on at 298 K
gen_vel = yes
gen_temp= 298
gen_seed= 173529
#
Waiting for your reply.
Regards,
Lal badshah.

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RE: [gmx-users] system goes out of the water box

[Dallas B. Warren]

Belquis,

> everything seems fine and the MD run went smooth. However 
> when I look at the trajectory, I see that the drug goes of 
> the water box and the simulation ends up with the drug 
> attached to the outside of the box.
> 
> Does this mean that I should increase the size of my box? 
> before running the md, the drug was centered into the box of 
> water molecules.

Three letters or three words explain that and means everything is fine,
and recommend you read up on it either in the manual or any textbook
dealing with MD ...

PBC

Periodic Boundary Condition

Catch ya,

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

[Justin Lemkul]

> Hello all,
>
> I am new to using Gromacs and MD simulation. I am simulating a 9-residue
> drug with a box of water. I generated the box using this:
> editconf -f xx.gro -o xx.gro -d 0.5 -bt cubic
>
> everything seems fine and the MD run went smooth. However when I look at
> the trajectory, I see that the drug goes of the water box and the
> simulation ends up with the drug attached to the outside of the box.
>
> Does this mean that I should increase the size of my box?
> before running the md, the drug was centered into the box of water molecules.
>
> I appreciate any help.
> Thank you
>
> Belquis Mothana

There are a number of threads in the mailing list archive about this.  A fairly
recent one can be found at:

http://www.gromacs.org/pipermail/gmx-users/2007-February/025797.html

I believe that deals with a similar problem, based on what you've described.  If
you're applying periodic boundary conditions (pbc = xyz) in your .mdp file, then
there shouldn't be anything wrong with the simulation.  Search the archives for
more information.

Best of luck,
Justin
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[gmx-users] system goes out of the water box

[bmmothan]

Hello all,

I am new to using Gromacs and MD simulation. I am simulating a 9-residue
drug with a box of water. I generated the box using this:
editconf -f xx.gro -o xx.gro -d 0.5 -bt cubic

everything seems fine and the MD run went smooth. However when I look at
the trajectory, I see that the drug goes of the water box and the
simulation ends up with the drug attached to the outside of the box.

Does this mean that I should increase the size of my box?
before running the md, the drug was centered into the box of water molecules.

I appreciate any help.
Thank you

Belquis Mothana

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Re: [gmx-users] System is exploding

[David van der Spoel]

abhigna polavarapu wrote:
I am running a 10ns simulation on a 42 mer peptide. I am doing this for 
predicting the stability of the beta sheet. So I deleted a bond called 
the lactame bond between two amino acids Lys and Asp. So if I just 
create mutation  at any other position in the beta sheet the mdrun 
crashes with an error saying that 1-4 interaction between the residues 
in Lys is greater than the size of the box. Increase the table 
extension. This seems like system is exploding. But if I mutate those 
two amino acids to Ala I am not getting that error. So please help me 
with this. As I need to analyse lots of mutations othen than mutation 
those two amino acids
 
Thank you

abhigna




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search the archives.
your structure is bad.

--
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] System is exploding

[abhigna polavarapu]

I am running a 10ns simulation on a 42 mer peptide. I am doing this for
predicting the stability of the beta sheet. So I deleted a bond called the
lactame bond between two amino acids Lys and Asp. So if I just create
mutation  at any other position in the beta sheet the mdrun crashes with an
error saying that 1-4 interaction between the residues in Lys is greater
than the size of the box. Increase the table extension. This seems like
system is exploding. But if I mutate those two amino acids to Ala I am not
getting that error. So please help me with this. As I need to analyse lots
of mutations othen than mutation those two amino acids

Thank you
abhigna
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Re: [gmx-users] system and box collapsed

[Mark Abraham]

Qiang Zhong wrote:

Dear users:
 I have a protein complex,which is docking result that from cluspr 
server,The
complex maybe not perfect,So when I simulate it on gromacs ,many linus warning 
was
reported.
 Could somebody tell me how to handle this problem,how to pre-optimize the
complex,Thank you very much!


Have you tried following the methodologies in the tutorials?

Mark
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[gmx-users] system and box collapsed

[Qiang Zhong]

Dear users:
 I have a protein complex,which is docking result that from cluspr 
server,The
complex maybe not perfect,So when I simulate it on gromacs ,many linus warning 
was
reported.
 Could somebody tell me how to handle this problem,how to pre-optimize the
complex,Thank you very much!



Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.002631 (between atoms 2524 and 2525) rms 0.76
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   63.20.1090   0.1092  0.1090
   2524   2525   44.40.1090   0.1093  0.1090
   3162   3163   76.00.1090   0.1092  0.1090
step 0
Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.003897 (between atoms 1658 and 1659) rms 0.89
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   52.80.1092   0.1086  0.1090
   2524   2525   37.30.1093   0.1088  0.1090
   3162   3163   58.60.1092   0.1086  0.1090

Step 2, time 0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.003313 (between atoms 1658 and 1659) rms 0.85
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   41.00.1086   0.1086  0.1090
   2524   2525   31.40.1089   0.1088  0.1090
   3162   3163   43.90.1087   0.1088  0.1090

Step 3, time 0.006 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.608712 (between atoms 1658 and 1659) rms 0.008897
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   90.00.1087   0.1753  0.1090
   3162   3163   35.50.1088   0.1092  0.1090

Step 4, time 0.008 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.007990 (between atoms 1656 and 1658) rms 0.000219
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   82.20.1754   0.1099  0.1090
   3162   3163   44.10.1092   0.1095  0.1090

Step 5, time 0.01 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.429637 (between atoms 1658 and 1659) rms 0.006280
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   1658   1659   90.00.1099   0.1558  0.1090
   3162   3163   49.40.1095   0.1094  0.1090





--
Qiang Zhong
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry 
of Education  
College of Animal Sciences and Technology 
Huazhong Agricultural University
Wuhan,Hubei, 430070
PR China
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Re: [gmx-users] system net charge 0f -1.6

[David van der Spoel]

Tsjerk Wassenaar wrote:

Hi,

Actually, the decision between HISA and HISB is made based upon some
criteria, which use the environment of the histidine residue. As
mentioned, you can manually set the type using the -his flag

Best,

Tsjerk


Hydrogen bonding to be exact.

--
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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Re: [gmx-users] system net charge 0f -1.6

[Tsjerk Wassenaar]

Hi,

Actually, the decision between HISA and HISB is made based upon some
criteria, which use the environment of the histidine residue. As
mentioned, you can manually set the type using the -his flag

Best,

Tsjerk

On 10/20/06, Florian Haberl <[EMAIL PROTECTED]> wrote:

Hi,

On Friday 20 October 2006 03:30, Stefan Schöbel wrote:
> I am using only a protein and the GROMOS96 43a1 force field.
> After pdb2gmx I got:
> Back Off! I just backed up test.top to ./#test.top.3#
> Processing chain 1 (1594 atoms, 214 residues)
> There are 288 donors and 315 acceptors
> There are 479 hydrogen bonds
> Will use HISB for residue 45
> Will use HISB for residue 79
> Will use HISB for residue 177
> Will use HISB for residue 202
> Checking for duplicate atoms
> Now there are 1593 atoms. Deleted 1 duplicates.
> Opening library file /home/mpaetzel/programs/share/gromacs/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> Special Atom Distance matrix:
>   CYS102
>SG760
>   CYS167  SG1251   2.930
> N-terminus: NH3+
> C-terminus: COO-
> Now there are 214 residues with 1957 atoms
> Making bonds...
> Opening library file
> /home/mpaetzel/programs/share/gromacs/top/aminoacids.dat Number of bonds
> was 1996, now 1991
> Generating angles, dihedrals and pairs...
> Before cleaning: 3360 pairs
> Before cleaning: 3782 dihedrals
> There are 1101 dihedrals,  946 impropers, 2896 angles
>   3360 pairs, 1991 bonds and 0 virtual sites
> Total mass 22620.601 a.m.u.
> Total charge -18.000 e
> Writing topology
>
>
> --> why are the HIS residues changed into HISB?

you can change this interactivly with pdb2gmx. Option is -his (and others)

>
> after editconf:
>
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Excluding 2 bonded neighbours for SOL 7683
> Excluding 2 bonded neighbours for SOL 2730
> NOTE:
>   System has non-zero total charge: -1.80e+01
>
>
> I tried adding C term Oxygen with spdbv as well, but it still the same
> uneven charge.
>
> What happened?
>
> thanks in advance
>
> Stefan

Florian

--
---
 Florian Haberl
 Computer-Chemie-Centrum
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone: +49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
---
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--
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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Re: [gmx-users] system net charge 0f -1.6

[Florian Haberl]

Hi,

On Friday 20 October 2006 03:30, Stefan Schöbel wrote:
> I am using only a protein and the GROMOS96 43a1 force field.
> After pdb2gmx I got:
> Back Off! I just backed up test.top to ./#test.top.3#
> Processing chain 1 (1594 atoms, 214 residues)
> There are 288 donors and 315 acceptors
> There are 479 hydrogen bonds
> Will use HISB for residue 45
> Will use HISB for residue 79
> Will use HISB for residue 177
> Will use HISB for residue 202
> Checking for duplicate atoms
> Now there are 1593 atoms. Deleted 1 duplicates.
> Opening library file /home/mpaetzel/programs/share/gromacs/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> Special Atom Distance matrix:
>   CYS102
>SG760
>   CYS167  SG1251   2.930
> N-terminus: NH3+
> C-terminus: COO-
> Now there are 214 residues with 1957 atoms
> Making bonds...
> Opening library file
> /home/mpaetzel/programs/share/gromacs/top/aminoacids.dat Number of bonds
> was 1996, now 1991
> Generating angles, dihedrals and pairs...
> Before cleaning: 3360 pairs
> Before cleaning: 3782 dihedrals
> There are 1101 dihedrals,  946 impropers, 2896 angles
>   3360 pairs, 1991 bonds and 0 virtual sites
> Total mass 22620.601 a.m.u.
> Total charge -18.000 e
> Writing topology
>
>
> --> why are the HIS residues changed into HISB?

you can change this interactivly with pdb2gmx. Option is -his (and others) 

>
> after editconf:
>
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Excluding 2 bonded neighbours for SOL 7683
> Excluding 2 bonded neighbours for SOL 2730
> NOTE:
>   System has non-zero total charge: -1.80e+01
>
>
> I tried adding C term Oxygen with spdbv as well, but it still the same
> uneven charge.
>
> What happened?
>
> thanks in advance
>
> Stefan

Florian

-- 
---
 Florian Haberl
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone: +49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
---
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Re: [gmx-users] system net charge 0f -1.6

[Mark Abraham]

Stefan Schöbel wrote:


--> why are the HIS residues changed into HISB?


Histidine has different protonation states. You need to choose one of 
them. Apparently, this one is the default. You should apply some 
chemical judgement to ensure you've made a reasonable choice.



after editconf:

Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 7683
Excluding 2 bonded neighbours for SOL 2730
NOTE:
  System has non-zero total charge: -1.80e+01


I tried adding C term Oxygen with spdbv as well, but it still the same uneven 
charge.


1.8e+01 = 18


What happened?


You didn't read the computer version of scientific notation properly!

Mark
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Re: [gmx-users] system net charge 0f -1.6

[Viswanadham Sridhara]

Looks fine to me.
you can add 18 positive (Na) ions to neutralise. 
On 10/19/06, "Stefan Schöbel" <[EMAIL PROTECTED]> wrote:
I am using only a protein and the GROMOS96 43a1 force field.After pdb2gmx I got:Back Off! I just backed up 
test.top to ./#test.top.3#Processing chain 1 (1594 atoms, 214 residues)There are 288 donors and 315 acceptorsThere are 479 hydrogen bondsWill use HISB for residue 45Will use HISB for residue 79Will use HISB for residue 177
Will use HISB for residue 202Checking for duplicate atomsNow there are 1593 atoms. Deleted 1 duplicates.Opening library file /home/mpaetzel/programs/share/gromacs/top/specbond.dat5 out of 5 lines of 
specbond.dat converted succesfullySpecial Atom Distance matrix: CYS102  SG760CYS167  SG1251   2.930N-terminus: NH3+C-terminus: COO-Now there are 214 residues with 1957 atoms
Making bonds...Opening library file /home/mpaetzel/programs/share/gromacs/top/aminoacids.datNumber of bonds was 1996, now 1991Generating angles, dihedrals and pairs...Before cleaning: 3360 pairsBefore cleaning: 3782 dihedrals
There are 1101 dihedrals,  946 impropers, 2896 angles 3360 pairs, 1991 bonds and 0 virtual sitesTotal mass 22620.601 a.m.u.Total charge -18.000 eWriting topology--> why are the HIS residues changed into HISB?
after editconf:Generated 279 of the 1225 non-bonded parameter combinationsExcluding 3 bonded neighbours for Protein 1Excluding 2 bonded neighbours for SOL 7683Excluding 2 bonded neighbours for SOL 2730
NOTE:System has non-zero total charge: -1.80e+01I tried adding C term Oxygen with spdbv as well, but it still the same uneven charge.What happened?thanks in advanceStefan
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-- Viswanadham Sridhara,Research Assistant,Old Dominion University,Norfolk, Va-23529. 
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[gmx-users] system net charge 0f -1.6

[Stefan Schöbel]

I am using only a protein and the GROMOS96 43a1 force field. 
After pdb2gmx I got:
Back Off! I just backed up test.top to ./#test.top.3#
Processing chain 1 (1594 atoms, 214 residues)
There are 288 donors and 315 acceptors
There are 479 hydrogen bonds
Will use HISB for residue 45
Will use HISB for residue 79
Will use HISB for residue 177
Will use HISB for residue 202
Checking for duplicate atoms
Now there are 1593 atoms. Deleted 1 duplicates.
Opening library file /home/mpaetzel/programs/share/gromacs/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
  CYS102
   SG760
  CYS167  SG1251   2.930
N-terminus: NH3+
C-terminus: COO-
Now there are 214 residues with 1957 atoms
Making bonds...
Opening library file /home/mpaetzel/programs/share/gromacs/top/aminoacids.dat
Number of bonds was 1996, now 1991
Generating angles, dihedrals and pairs...
Before cleaning: 3360 pairs
Before cleaning: 3782 dihedrals
There are 1101 dihedrals,  946 impropers, 2896 angles
  3360 pairs, 1991 bonds and 0 virtual sites
Total mass 22620.601 a.m.u.
Total charge -18.000 e
Writing topology


--> why are the HIS residues changed into HISB?

after editconf:

Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 7683
Excluding 2 bonded neighbours for SOL 2730
NOTE:
  System has non-zero total charge: -1.80e+01


I tried adding C term Oxygen with spdbv as well, but it still the same uneven 
charge.

What happened?

thanks in advance 

Stefan
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Re: [gmx-users] system net charge 0f -1.6

[Mark Abraham]

Stefan Schöbel wrote:

Hi,

I am new to Gromacs and got an uneven system charge when I run grompp the first 
time. After setting the box with editconf I the system had a charge of 16. Does 
anybody know what happend?


We'd have a better chance if you'd told us the kind of system you were 
running on, and the command lines you used.



How do I have to handle uneven charges, can I added 1.6 counterions? I don't 
think so.


Probably, the termini are being treated wrongly. Have a look at the 
resulting structures.


Mark
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[gmx-users] system net charge 0f -1.6

[chris . neale]

After setting the box with editconf I the system had a charge of 16.  
Does anybody
know what happend? How do I have to handle uneven charges, can I  
added 1.6 counterions? I don't think so.


I assume that you meant to put 1.6 both times, not 16?
What is your system?
What is your forcefield?
If you have many different parts, which part has the non-integer  
charge? (You could remake your system one piece at a time and look at  
the charge)

If you have a protein, how have you handled the N- and C-termini?


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