Re: [gmx-users] UREA + Protein Simulation error.

[karan syal]

Dear David, Thanks for the reply, guess i will do some literature survey and
see if i can find some validated urea parameters.

karan

On Mon, Sep 21, 2009 at 8:51 PM, David van der Spoel
wrote:

> karan syal wrote:
>
>> Dear Justin,
>>
>> Thanks for the reply!
>>
>> I will surely try minimize the protein in Vacuum and then try adding Urea
>> again.
>>
>> Just that i was wondering how will that effect my artifact bonds which are
>> between Urea and Water, and not at all between any Protein atom and
>> Urea/Sol?? As i mentioned earlier, these bonds are formed only after
>> minimization, they are not present before adding 10M urea+water box (No such
>> bonds in its individual 10M urea+water .gro either ) to protein, they are
>> neither there in the before minimized protein+10M urea+water system.
>>
>>  Don't use the Urea topology that is in the gromacs distribution. It is
> not based on any force field known to man.
>
>>
>> Thanks again,
>>
>> cherrz
>> karan
>>
>>
>> On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>karan syal wrote:
>>
>>Dear Gromacs users,
>>
>>I am trying to run a urea+protein simulation and encountering a
>>few problems at various stages.
>>
>>I have taken an equilibrated 10M urea box of size
>>2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea +
>>398 SOL, ran NPT @ 1 bar and 300K)
>>
>>I am using this equilibrated box to add to a globular protein of
>>about 250 residues using following commands :
>>
>>
>>editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron
>> (Giving me a dodecahedron with Vol = 407.98nm^3, so for this
>>volume, for 10M urea the number of urea above box should add is
>>2448.)
>>
>>genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro
>>  (*This adds 2064 Urea only, shouldnt it be adding 2448 urea
>>molecules, corresponding to 10M urea box i have solvated with??)*
>>
>>
>>No, it shouldn't.  The protein occupies space within that volume, as
>>well.
>>
>>
>>
>>When i try to minimize this using the following em.mdp
>>
>>
>>cpp =  /usr/bin/cpp
>>constraints =  none
>>integrator  =  steep
>>nsteps  =  5000
>>coulombtype = PME
>>pme_order = 4
>>nstlist = 5
>>ns_type = grid
>>rlist   =  1.0
>>rcoulomb=  1.0
>>rvdw=  1.0
>>Tcoupl  =  no
>>Pcoupl  =  no
>>fourierspacing = 0.12
>>fourier_nx = 0
>>fourier_ny = 0
>>fourier_nz = 0
>>;   Energy minimizing stuff
>>;
>>emtol   =  100
>>emstep  =  0.01
>>
>>
>>*It gives me the following output*
>>
>>
>>Steepest Descents:
>>  Tolerance (Fmax)   =  1.0e+02
>>  Number of steps= 5000
>>Warning: 1-4 interaction between 2796 and 2801 at distance 2.727
>>which is larger than the 1-4 table size 2.000 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
>>or with user tables increase the table size
>>
>>t = 0.015 ps: Water molecule starting at atom 34477 can not be
>>settled.
>>Check for bad contacts and/or reduce the timestep.
>>Wrote pdb files with previous and current coordinates
>>
>>Stepsize too small, or no change in energy.
>>Converged to machine precision,
>>but not to the requested precision Fmax < 100
>>
>>Double precision normally gives you higher accuracy.
>>You might need to increase your constraint accuracy, or turn
>>off constraints alltogether (set constraints = none in mdp file)
>>
>>writing lowest energy coordinates.
>>
>>Steepest Descents converged to machine precision in 34 steps,
>>but did not reach the requested Fmax < 100.
>>Potential Energy  = -1.3092671e+22
>>Maximum force =inf on atom 12598
>>Norm of force =inf
>>
>>gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)
>>
>>
>>
>>/When i look at the file in VMD, the protein is completely out
>>of the box + There are unusual bonds between a lot of UREA and
>>SOL molecules/. ( The unusual bonds are artifcats after
>>minimization which are not there when i initially look at my
>>P48_10Mrea.gro, that is the gro generated after genbox wth -cs
>>as 10M urea)
>>
>>
>>"Out of the box" doesn't exist for a periodic system.  The "bonds"
>>you see are also *not* generated by Gromacs, but are also just an
>>artefact of visualization.  Bonds are not created or bro

Re: [gmx-users] UREA + Protein Simulation error.

[David van der Spoel]

karan syal wrote:

Dear Justin,

Thanks for the reply!

I will surely try minimize the protein in Vacuum and then try adding 
Urea again.


Just that i was wondering how will that effect my artifact bonds which 
are between Urea and Water, and not at all between any Protein atom and 
Urea/Sol?? As i mentioned earlier, these bonds are formed only after 
minimization, they are not present before adding 10M urea+water box (No 
such bonds in its individual 10M urea+water .gro either ) to protein, 
they are neither there in the before minimized protein+10M urea+water 
system.


Don't use the Urea topology that is in the gromacs distribution. It is 
not based on any force field known to man.


Thanks again,

cherrz
karan

On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul > wrote:




karan syal wrote:

Dear Gromacs users,

I am trying to run a urea+protein simulation and encountering a
few problems at various stages.

I have taken an equilibrated 10M urea box of size
2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea +
398 SOL, ran NPT @ 1 bar and 300K)

I am using this equilibrated box to add to a globular protein of
about 250 residues using following commands :


editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron  
 (Giving me a dodecahedron with Vol = 407.98nm^3, so for this

volume, for 10M urea the number of urea above box should add is
2448.)

genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro  
(*This adds 2064 Urea only, shouldnt it be adding 2448 urea

molecules, corresponding to 10M urea box i have solvated with??)*


No, it shouldn't.  The protein occupies space within that volume, as
well.



When i try to minimize this using the following em.mdp


cpp =  /usr/bin/cpp
constraints =  none
integrator  =  steep
nsteps  =  5000
coulombtype = PME
pme_order = 4
nstlist = 5
ns_type = grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
Tcoupl  =  no
Pcoupl  =  no
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
;   Energy minimizing stuff
;
emtol   =  100
emstep  =  0.01


*It gives me the following output*


Steepest Descents:
  Tolerance (Fmax)   =  1.0e+02
  Number of steps= 5000
Warning: 1-4 interaction between 2796 and 2801 at distance 2.727
which is larger than the 1-4 table size 2.000 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
or with user tables increase the table size

t = 0.015 ps: Water molecule starting at atom 34477 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 34 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -1.3092671e+22
Maximum force =inf on atom 12598
Norm of force =inf

gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)



/When i look at the file in VMD, the protein is completely out
of the box + There are unusual bonds between a lot of UREA and
SOL molecules/. ( The unusual bonds are artifcats after
minimization which are not there when i initially look at my
P48_10Mrea.gro, that is the gro generated after genbox wth -cs
as 10M urea)


"Out of the box" doesn't exist for a periodic system.  The "bonds"
you see are also *not* generated by Gromacs, but are also just an
artefact of visualization.  Bonds are not created or broken in
molecular mechanics.


I tried constraining hbonds as well in em.mdp bit to no effect.


I used the above em.gro to run a production run, with following
pr.mdp


Don't, it's a waste of time.  Never just plow ahead when something
isn't working.  There is something unreasonable about the starting
structure.  Try minimizing the protein in vacuo first, then add your
urea and try EM again.

-Ju

Re: [gmx-users] UREA + Protein Simulation error.

[Justin A. Lemkul]

karan syal wrote:

Dear Justin,

Thanks for the reply!

I will surely try minimize the protein in Vacuum and then try adding 
Urea again.


Just that i was wondering how will that effect my artifact bonds which 
are between Urea and Water, and not at all between any Protein atom and 
Urea/Sol?? As i mentioned earlier, these bonds are formed only after 
minimization, they are not present before adding 10M urea+water box (No 
such bonds in its individual 10M urea+water .gro either ) to protein, 
they are neither there in the before minimized protein+10M urea+water 
system.




There are no bonds.  Visualization software attempts to guess where bonds should 
be based on distances between atoms.  The only bonds that are actually present 
are defined in the topology.  It is impossible for bonds to break and form in a 
standard MD or EM protocol - it defies the physics!


-Justin



Thanks again,

cherrz
karan

On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul > wrote:




karan syal wrote:

Dear Gromacs users,

I am trying to run a urea+protein simulation and encountering a
few problems at various stages.

I have taken an equilibrated 10M urea box of size
2.84nmx2.84nmx2.84nm (I started with 3x3x3 containing 160 urea +
398 SOL, ran NPT @ 1 bar and 300K)

I am using this equilibrated box to add to a globular protein of
about 250 residues using following commands :


editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron  
 (Giving me a dodecahedron with Vol = 407.98nm^3, so for this

volume, for 10M urea the number of urea above box should add is
2448.)

genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro  
(*This adds 2064 Urea only, shouldnt it be adding 2448 urea

molecules, corresponding to 10M urea box i have solvated with??)*


No, it shouldn't.  The protein occupies space within that volume, as
well.



When i try to minimize this using the following em.mdp


cpp =  /usr/bin/cpp
constraints =  none
integrator  =  steep
nsteps  =  5000
coulombtype = PME
pme_order = 4
nstlist = 5
ns_type = grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
Tcoupl  =  no
Pcoupl  =  no
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
;   Energy minimizing stuff
;
emtol   =  100
emstep  =  0.01


*It gives me the following output*


Steepest Descents:
  Tolerance (Fmax)   =  1.0e+02
  Number of steps= 5000
Warning: 1-4 interaction between 2796 and 2801 at distance 2.727
which is larger than the 1-4 table size 2.000 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
or with user tables increase the table size

t = 0.015 ps: Water molecule starting at atom 34477 can not be
settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 34 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -1.3092671e+22
Maximum force =inf on atom 12598
Norm of force =inf

gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)



/When i look at the file in VMD, the protein is completely out
of the box + There are unusual bonds between a lot of UREA and
SOL molecules/. ( The unusual bonds are artifcats after
minimization which are not there when i initially look at my
P48_10Mrea.gro, that is the gro generated after genbox wth -cs
as 10M urea)


"Out of the box" doesn't exist for a periodic system.  The "bonds"
you see are also *not* generated by Gromacs, but are also just an
artefact of visualization.  Bonds are not created or broken in
molecular mechanics.


I tried constraining hbonds as well in em.mdp bit to no effect.


I used the above em.gro to run a production run, with following
pr.mdp


Don't, it's a waste of time.  Never just plow ahead

Re: [gmx-users] UREA + Protein Simulation error.

[karan syal]

Dear Justin,

Thanks for the reply!

I will surely try minimize the protein in Vacuum and then try adding Urea
again.

Just that i was wondering how will that effect my artifact bonds which are
between Urea and Water, and not at all between any Protein atom and
Urea/Sol?? As i mentioned earlier, these bonds are formed only after
minimization, they are not present before adding 10M urea+water box (No such
bonds in its individual 10M urea+water .gro either ) to protein, they are
neither there in the before minimized protein+10M urea+water system.


Thanks again,

cherrz
karan

On Mon, Sep 21, 2009 at 4:11 PM, Justin A. Lemkul  wrote:

>
>
> karan syal wrote:
>
>> Dear Gromacs users,
>>
>> I am trying to run a urea+protein simulation and encountering a few
>> problems at various stages.
>>
>> I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I
>> started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K)
>>
>> I am using this equilibrated box to add to a globular protein of about 250
>> residues using following commands :
>>
>>
>> editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron(Giving
>> me a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M urea
>> the number of urea above box should add is 2448.)
>>
>> genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro   (*This adds
>> 2064 Urea only, shouldnt it be adding 2448 urea molecules, corresponding to
>> 10M urea box i have solvated with??)*
>>
>>
> No, it shouldn't.  The protein occupies space within that volume, as well.
>
>
>
>> When i try to minimize this using the following em.mdp
>>
>>
>> cpp =  /usr/bin/cpp
>> constraints =  none
>> integrator  =  steep
>> nsteps  =  5000
>> coulombtype = PME
>> pme_order = 4
>> nstlist = 5
>> ns_type = grid
>> rlist   =  1.0
>> rcoulomb=  1.0
>> rvdw=  1.0
>> Tcoupl  =  no
>> Pcoupl  =  no
>> fourierspacing = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> ;   Energy minimizing stuff
>> ;
>> emtol   =  100
>> emstep  =  0.01
>>
>>
>> *It gives me the following output*
>>
>>
>> Steepest Descents:
>>   Tolerance (Fmax)   =  1.0e+02
>>   Number of steps= 5000
>> Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which is
>> larger than the 1-4 table size 2.000 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
>> or with user tables increase the table size
>>
>> t = 0.015 ps: Water molecule starting at atom 34477 can not be settled.
>> Check for bad contacts and/or reduce the timestep.
>> Wrote pdb files with previous and current coordinates
>>
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 100
>>
>> Double precision normally gives you higher accuracy.
>> You might need to increase your constraint accuracy, or turn
>> off constraints alltogether (set constraints = none in mdp file)
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to machine precision in 34 steps,
>> but did not reach the requested Fmax < 100.
>> Potential Energy  = -1.3092671e+22
>> Maximum force =inf on atom 12598
>> Norm of force =inf
>>
>> gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)
>>
>>
>>
>> /When i look at the file in VMD, the protein is completely out of the box
>> + There are unusual bonds between a lot of UREA and SOL molecules/. ( The
>> unusual bonds are artifcats after minimization which are not there when i
>> initially look at my P48_10Mrea.gro, that is the gro generated after genbox
>> wth -cs as 10M urea)
>>
>>
> "Out of the box" doesn't exist for a periodic system.  The "bonds" you see
> are also *not* generated by Gromacs, but are also just an artefact of
> visualization.  Bonds are not created or broken in molecular mechanics.
>
>  I tried constraining hbonds as well in em.mdp bit to no effect.
>>
>>
>> I used the above em.gro to run a production run, with following pr.mdp
>>
>>
> Don't, it's a waste of time.  Never just plow ahead when something isn't
> working.  There is something unreasonable about the starting structure.  Try
> minimizing the protein in vacuo first, then add your urea and try EM again.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www

Re: [gmx-users] UREA + Protein Simulation error.

[Justin A. Lemkul]

karan syal wrote:

Dear Gromacs users,

I am trying to run a urea+protein simulation and encountering a few 
problems at various stages.


I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm 
(I started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 
300K)


I am using this equilibrated box to add to a globular protein of about 
250 residues using following commands :



editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron(Giving 
me a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M 
urea the number of urea above box should add is 2448.)


genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro   (*This adds 
2064 Urea only, shouldnt it be adding 2448 urea molecules, corresponding 
to 10M urea box i have solvated with??)*




No, it shouldn't.  The protein occupies space within that volume, as well.



When i try to minimize this using the following em.mdp


cpp =  /usr/bin/cpp
constraints =  none
integrator  =  steep
nsteps  =  5000
coulombtype = PME
pme_order = 4
nstlist = 5
ns_type = grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
Tcoupl  =  no
Pcoupl  =  no
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
;   Energy minimizing stuff
;
emtol   =  100
emstep  =  0.01


*It gives me the following output*


Steepest Descents:
   Tolerance (Fmax)   =  1.0e+02
   Number of steps= 5000
Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which 
is larger than the 1-4 table size 2.000 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
or with user tables increase the table size

t = 0.015 ps: Water molecule starting at atom 34477 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 34 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -1.3092671e+22
Maximum force =inf on atom 12598
Norm of force =inf

gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)



/When i look at the file in VMD, the protein is completely out of the 
box + There are unusual bonds between a lot of UREA and SOL molecules/. 
( The unusual bonds are artifcats after minimization which are not there 
when i initially look at my P48_10Mrea.gro, that is the gro generated 
after genbox wth -cs as 10M urea)




"Out of the box" doesn't exist for a periodic system.  The "bonds" you see are 
also *not* generated by Gromacs, but are also just an artefact of visualization. 
 Bonds are not created or broken in molecular mechanics.



I tried constraining hbonds as well in em.mdp bit to no effect.


I used the above em.gro to run a production run, with following pr.mdp



Don't, it's a waste of time.  Never just plow ahead when something isn't 
working.  There is something unreasonable about the starting structure.  Try 
minimizing the protein in vacuo first, then add your urea and try EM again.


-Justin

--


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


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[gmx-users] UREA + Protein Simulation error.

[karan syal]

Dear Gromacs users,

I am trying to run a urea+protein simulation and encountering a few problems
at various stages.

I have taken an equilibrated 10M urea box of size 2.84nmx2.84nmx2.84nm (I
started with 3x3x3 containing 160 urea + 398 SOL, ran NPT @ 1 bar and 300K)

I am using this equilibrated box to add to a globular protein of about 250
residues using following commands :


editconf -f P48.gro -o P48_box.gro -c -d 0.6 -bt dodecahedron(Giving me
a dodecahedron with Vol = 407.98nm^3, so for this volume, for 10M urea the
number of urea above box should add is 2448.)

genbox -cp P48_box.gro -cs 10Murea.gro -o P48_10MUrea.gro   (*This adds 2064
Urea only, shouldnt it be adding 2448 urea molecules, corresponding to 10M
urea box i have solvated with??)*


When i try to minimize this using the following em.mdp


cpp =  /usr/bin/cpp
constraints =  none
integrator  =  steep
nsteps  =  5000
coulombtype = PME
pme_order = 4
nstlist = 5
ns_type = grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
Tcoupl  =  no
Pcoupl  =  no
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
;   Energy minimizing stuff
;
emtol   =  100
emstep  =  0.01


*It gives me the following output*


Steepest Descents:
   Tolerance (Fmax)   =  1.0e+02
   Number of steps= 5000
Warning: 1-4 interaction between 2796 and 2801 at distance 2.727 which is
larger than the 1-4 table size 2.000 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
or with user tables increase the table size

t = 0.015 ps: Water molecule starting at atom 34477 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100

Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 34 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -1.3092671e+22
Maximum force =inf on atom 12598
Norm of force =inf

gcq#160: "The Microsecond is Within Reach" (P.J. Van Maaren)



*When i look at the file in VMD, the protein is completely out of the box +
There are unusual bonds between a lot of UREA and SOL molecules*. ( The
unusual bonds are artifcats after minimization which are not there when i
initially look at my P48_10Mrea.gro, that is the gro generated after genbox
wth -cs as 10M urea)

I tried constraining hbonds as well in em.mdp bit to no effect.


I used the above em.gro to run a production run, with following pr.mdp


cpp = /usr/bin/cpp
define = -DPOSRES
constraints = hbonds
integrator = md
dt = 0.002 ; ps !
nsteps = 10 ; total 200 ps
nstcomm = 1
nstxtcout = 50 ; collect data every 1 ps
nstxout = 100
nstvout = 100
nstfout = 100
nstlog = 100
nstenergy = 100
nstlist = 5
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
Tcoupl = V-rescale
tau_t = 0.1 0.1 ; use items in bold if you have Cl ions
tcgrps = Protein Non-protein
ref_t = 300 300
; Pressure coupling is on
Pcoupl = berendsen
tau_p = 1
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




*the simulation stops after following error*

t = 0.002 ps: Water molecule starting at atom 36943 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates




Can anyone pls suggest what should i modify to effectively simulate my
system?



Any suggestions regarding how i can run a urea+protein simulation with the
exact desired concentration will be highly appreciated.




Thanks for all the time and pateince,
Regards
Karan
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