Re: [gmx-users] Domain decomposition configuration

[Justin A. Lemkul]

Mark Abraham wrote:

On 10/02/2011 12:45 PM, Justin A. Lemkul wrote:



Mark Abraham wrote:

On 10/02/2011 8:10 AM, Justin A. Lemkul wrote:



Denny Frost wrote:
Is tpbconv with the "pbc" option the best way to make the molecules 
whole again?




The only way, as far as I'm aware (aside from editconf's crude 
approach).  Do this before you concatenate your systems.


And you will then have potential issues with clashing atoms, so need 
to re-equilibrate. Unfortunately, in general there is no box 
definition where all molecules are whole and inside the box, and it's 
certainly not worthwhile looking for one.




Not worthwhile?  In the case of the OP's problem, there's no way out 
unless you make the molecules whole. 


Sure, whole molecules are necessary for the OP's approach, but my point 
is that it is not worthwhile looking for a box with all of the molecules 
whole *and* inside the (pre-concatenation) box (e.g. by trying new box 
centers), because in general there need not be one.




Ah, now I understand what you were saying.  Good point, and certainly more 
generally true than the specific case I was thinking of.


-Justin


Mark

You certainly can't have it both ways (both whole and in the box, but 
take, for instance, atoms A and B in the same molecule, which are 
bonded.  The normal situation across PBC:


 |  |
 -BA-
 |  |

is fine.  DD can re-establish the proper bond across PBC.  But if this 
system is concatenated to one with water (*):


 |  |**|
 -BA
 |  |**|

the bond is physically unrealistic and DD fails.  Even if you *could* 
get the simulation to run (i.e. in serial or mdrun -pd), it would 
instantly crash due either to LINCS failure or some such problem.  So 
making the molecules whole prior to concatenation gives:


 |  |**|
 | A-B*|
 |  |**|

which works.  Of course, you do have to worry about clashes, so maybe 
concatenation is not the best approach, but rather a run through 
genbox would be more suitable.


-Justin


Mark



-Justin

On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul > wrote:




Denny Frost wrote:

This run is actually a combination of two 5x5x5 nm boxes, 
one if

which was previously run in DD, and the other is water.  Since
the length of that bond is almost 5 nm, is it possible that 
the

pbc's are not being recognized?  There is no way I have a bond
that long from my previous run.


I'll venture a guess that there were broken molecules in the 
system
you concatenated?  That would gel with a bond that stretches 
across

a 5-nm box.  You have to deal with whole molecules in the input
configuration.

-Justin

On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Denny Frost wrote:

   I'm using version 4.5.3

   Here's the output from the log file from DD 
initiation to

the error:

   Initializing Domain Decomposition on 8 nodes
   Dynamic load balancing: auto
   Will sort the charge groups at every domain 
(re)decomposition

   Initial maximum inter charge-group distances:
  two-body bonded interactions: 4.893 nm, Bond, atoms
8994 8996
multi-body bonded interactions: 4.893 nm, Angle, atoms
8994 8997
   Minimum cell size due to bonded interactions: 5.382 nm


   Bonded interactions should normally not occur over such 
a length.
The information printed here points to the culprits.  
What are
   these atoms, and why are they bonded if they are so far 
away?


   -Justin

   Using 0 separate PME nodes
   Scaling the initial minimum size with 1/0.8 (option 
-dds)

= 1.25
   Optimizing the DD grid for 8 cells with a minimum 
initial

size
   of 6.728 nm
   The maximum allowed number of cells is: X 0 Y 0 Z 1

   ---
   Program mdrun_mpi, VERSION 4.5.3
   Source code file: domdec.c, line: 6428

   Fatal error:
   There is no domain decomposition for 8 nodes that is
compatible
   with the given box and a minimum cell size of 
6.72787 nm

   Change the number of nodes or mdrun option -rdd or -dds
   Look in the log file for details on the domain 
decomposition
   For more information and tips for troubleshooting, 
please

check
   the GROMACS
   website at http://www.gromacs.org/Documentation/Errors

   And here is my mdp file

   title   =  BMIM+PF6
   cpp =  /lib/cpp
   constraints =  hbonds

Re: [gmx-users] Domain decomposition configuration

[Mark Abraham]

On 10/02/2011 12:45 PM, Justin A. Lemkul wrote:



Mark Abraham wrote:

On 10/02/2011 8:10 AM, Justin A. Lemkul wrote:



Denny Frost wrote:
Is tpbconv with the "pbc" option the best way to make the molecules 
whole again?




The only way, as far as I'm aware (aside from editconf's crude 
approach).  Do this before you concatenate your systems.


And you will then have potential issues with clashing atoms, so need 
to re-equilibrate. Unfortunately, in general there is no box 
definition where all molecules are whole and inside the box, and it's 
certainly not worthwhile looking for one.




Not worthwhile?  In the case of the OP's problem, there's no way out 
unless you make the molecules whole. 


Sure, whole molecules are necessary for the OP's approach, but my point 
is that it is not worthwhile looking for a box with all of the molecules 
whole *and* inside the (pre-concatenation) box (e.g. by trying new box 
centers), because in general there need not be one.


Mark

You certainly can't have it both ways (both whole and in the box, but 
take, for instance, atoms A and B in the same molecule, which are 
bonded.  The normal situation across PBC:


 |  |
 -BA-
 |  |

is fine.  DD can re-establish the proper bond across PBC.  But if this 
system is concatenated to one with water (*):


 |  |**|
 -BA
 |  |**|

the bond is physically unrealistic and DD fails.  Even if you *could* 
get the simulation to run (i.e. in serial or mdrun -pd), it would 
instantly crash due either to LINCS failure or some such problem.  So 
making the molecules whole prior to concatenation gives:


 |  |**|
 | A-B*|
 |  |**|

which works.  Of course, you do have to worry about clashes, so maybe 
concatenation is not the best approach, but rather a run through 
genbox would be more suitable.


-Justin


Mark



-Justin

On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul > wrote:




Denny Frost wrote:

This run is actually a combination of two 5x5x5 nm boxes, 
one if

which was previously run in DD, and the other is water.  Since
the length of that bond is almost 5 nm, is it possible that 
the

pbc's are not being recognized?  There is no way I have a bond
that long from my previous run.


I'll venture a guess that there were broken molecules in the 
system
you concatenated?  That would gel with a bond that stretches 
across

a 5-nm box.  You have to deal with whole molecules in the input
configuration.

-Justin

On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Denny Frost wrote:

   I'm using version 4.5.3

   Here's the output from the log file from DD 
initiation to

the error:

   Initializing Domain Decomposition on 8 nodes
   Dynamic load balancing: auto
   Will sort the charge groups at every domain 
(re)decomposition

   Initial maximum inter charge-group distances:
  two-body bonded interactions: 4.893 nm, Bond, atoms
8994 8996
multi-body bonded interactions: 4.893 nm, Angle, atoms
8994 8997
   Minimum cell size due to bonded interactions: 5.382 nm


   Bonded interactions should normally not occur over such 
a length.
The information printed here points to the culprits.  
What are
   these atoms, and why are they bonded if they are so far 
away?


   -Justin

   Using 0 separate PME nodes
   Scaling the initial minimum size with 1/0.8 (option 
-dds)

= 1.25
   Optimizing the DD grid for 8 cells with a minimum 
initial

size
   of 6.728 nm
   The maximum allowed number of cells is: X 0 Y 0 Z 1

   ---
   Program mdrun_mpi, VERSION 4.5.3
   Source code file: domdec.c, line: 6428

   Fatal error:
   There is no domain decomposition for 8 nodes that is
compatible
   with the given box and a minimum cell size of 
6.72787 nm

   Change the number of nodes or mdrun option -rdd or -dds
   Look in the log file for details on the domain 
decomposition
   For more information and tips for troubleshooting, 
please

check
   the GROMACS
   website at http://www.gromacs.org/Documentation/Errors

   And here is my mdp file

   title   =  BMIM+PF6
   cpp =  /lib/cpp
   constraints =  hbonds
   integrator  =  md
   dt  =  0.002   ; ps !
   nsteps  =  75000   ; total 150 ps
   nstc

Re: [gmx-users] Domain decomposition configuration

[Justin A. Lemkul]

Mark Abraham wrote:

On 10/02/2011 8:10 AM, Justin A. Lemkul wrote:



Denny Frost wrote:
Is tpbconv with the "pbc" option the best way to make the molecules 
whole again?




The only way, as far as I'm aware (aside from editconf's crude 
approach).  Do this before you concatenate your systems.


And you will then have potential issues with clashing atoms, so need to 
re-equilibrate. Unfortunately, in general there is no box definition 
where all molecules are whole and inside the box, and it's certainly not 
worthwhile looking for one.




Not worthwhile?  In the case of the OP's problem, there's no way out unless you 
make the molecules whole.  You certainly can't have it both ways (both whole and 
in the box, but take, for instance, atoms A and B in the same molecule, which 
are bonded.  The normal situation across PBC:


 |  |
 -BA-
 |  |

is fine.  DD can re-establish the proper bond across PBC.  But if this system is 
concatenated to one with water (*):


 |  |**|
 -BA
 |  |**|

the bond is physically unrealistic and DD fails.  Even if you *could* get the 
simulation to run (i.e. in serial or mdrun -pd), it would instantly crash due 
either to LINCS failure or some such problem.  So making the molecules whole 
prior to concatenation gives:


 |  |**|
 | A-B*|
 |  |**|

which works.  Of course, you do have to worry about clashes, so maybe 
concatenation is not the best approach, but rather a run through genbox would be 
more suitable.


-Justin


Mark



-Justin

On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul > wrote:




Denny Frost wrote:

This run is actually a combination of two 5x5x5 nm boxes, one if
which was previously run in DD, and the other is water.  Since
the length of that bond is almost 5 nm, is it possible that the
pbc's are not being recognized?  There is no way I have a bond
that long from my previous run.


I'll venture a guess that there were broken molecules in the system
you concatenated?  That would gel with a bond that stretches across
a 5-nm box.  You have to deal with whole molecules in the input
configuration.

-Justin

On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Denny Frost wrote:

   I'm using version 4.5.3

   Here's the output from the log file from DD initiation to
the error:

   Initializing Domain Decomposition on 8 nodes
   Dynamic load balancing: auto
   Will sort the charge groups at every domain 
(re)decomposition

   Initial maximum inter charge-group distances:
  two-body bonded interactions: 4.893 nm, Bond, atoms
8994 8996
multi-body bonded interactions: 4.893 nm, Angle, atoms
8994 8997
   Minimum cell size due to bonded interactions: 5.382 nm


   Bonded interactions should normally not occur over such a 
length.
The information printed here points to the culprits.  
What are

   these atoms, and why are they bonded if they are so far away?

   -Justin

   Using 0 separate PME nodes
   Scaling the initial minimum size with 1/0.8 (option -dds)
= 1.25
   Optimizing the DD grid for 8 cells with a minimum initial
size
   of 6.728 nm
   The maximum allowed number of cells is: X 0 Y 0 Z 1

   ---
   Program mdrun_mpi, VERSION 4.5.3
   Source code file: domdec.c, line: 6428

   Fatal error:
   There is no domain decomposition for 8 nodes that is
compatible
   with the given box and a minimum cell size of 6.72787 nm
   Change the number of nodes or mdrun option -rdd or -dds
   Look in the log file for details on the domain 
decomposition

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

   And here is my mdp file

   title   =  BMIM+PF6
   cpp =  /lib/cpp
   constraints =  hbonds
   integrator  =  md
   dt  =  0.002   ; ps !
   nsteps  =  75000   ; total 150 ps
   nstcomm =  10
   nstxout =  5
   nstvout =  5
   nstfout =  0
   nstlog  =  5000
   nstenergy   =  5000
   nstxtcout   =  25000
   nstlist =  10
   ns_type

Re: [gmx-users] localpressure.dat file not created

[Mark Abraham]

On 10/02/2011 11:48 AM, ma...@physics.ucsb.edu wrote:

I successfully ran version 4.5.3 to simulate a small DPPC bilayer patch
using the files from Marrink's website by typing:

/usr/bin/grompp -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr -maxwarn 100

mdrun

In the .mdp file I then added the line "userreal1=0.1" and typed

/usr/bin/grompp_d -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr
-maxwarn 100

mdrun_d -rerun traj.xtc -v

Everything ran smoothly, but I don't see any localpressure.dat file
sitting in my directory. How can I get it?


AFAIK there's no port of the "local pressure" variant of GROMACS to 
4.5.3. You haven't told us whether you think you have one.


Mark
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[gmx-users] localpressure.dat file not created

[maxcw]

I successfully ran version 4.5.3 to simulate a small DPPC bilayer patch
using the files from Marrink's website by typing:

/usr/bin/grompp -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr -maxwarn 100

mdrun

In the .mdp file I then added the line "userreal1=0.1" and typed

/usr/bin/grompp_d -v -f mem.mdp -c mem.gro -p mem.top -o topol.tpr
-maxwarn 100

mdrun_d -rerun traj.xtc -v

Everything ran smoothly, but I don't see any localpressure.dat file
sitting in my directory. How can I get it?

Thank you!

--Max



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Re: [gmx-users] Domain decomposition configuration

[Mark Abraham]

On 10/02/2011 8:10 AM, Justin A. Lemkul wrote:



Denny Frost wrote:
Is tpbconv with the "pbc" option the best way to make the molecules 
whole again?




The only way, as far as I'm aware (aside from editconf's crude 
approach).  Do this before you concatenate your systems.


And you will then have potential issues with clashing atoms, so need to 
re-equilibrate. Unfortunately, in general there is no box definition 
where all molecules are whole and inside the box, and it's certainly not 
worthwhile looking for one.


Mark



-Justin

On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul > wrote:




Denny Frost wrote:

This run is actually a combination of two 5x5x5 nm boxes, one if
which was previously run in DD, and the other is water.  Since
the length of that bond is almost 5 nm, is it possible that the
pbc's are not being recognized?  There is no way I have a bond
that long from my previous run.


I'll venture a guess that there were broken molecules in the system
you concatenated?  That would gel with a bond that stretches across
a 5-nm box.  You have to deal with whole molecules in the input
configuration.

-Justin

On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Denny Frost wrote:

   I'm using version 4.5.3

   Here's the output from the log file from DD initiation to
the error:

   Initializing Domain Decomposition on 8 nodes
   Dynamic load balancing: auto
   Will sort the charge groups at every domain 
(re)decomposition

   Initial maximum inter charge-group distances:
  two-body bonded interactions: 4.893 nm, Bond, atoms
8994 8996
multi-body bonded interactions: 4.893 nm, Angle, atoms
8994 8997
   Minimum cell size due to bonded interactions: 5.382 nm


   Bonded interactions should normally not occur over such a 
length.
The information printed here points to the culprits.  
What are

   these atoms, and why are they bonded if they are so far away?

   -Justin

   Using 0 separate PME nodes
   Scaling the initial minimum size with 1/0.8 (option -dds)
= 1.25
   Optimizing the DD grid for 8 cells with a minimum initial
size
   of 6.728 nm
   The maximum allowed number of cells is: X 0 Y 0 Z 1

   ---
   Program mdrun_mpi, VERSION 4.5.3
   Source code file: domdec.c, line: 6428

   Fatal error:
   There is no domain decomposition for 8 nodes that is
compatible
   with the given box and a minimum cell size of 6.72787 nm
   Change the number of nodes or mdrun option -rdd or -dds
   Look in the log file for details on the domain 
decomposition

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

   And here is my mdp file

   title   =  BMIM+PF6
   cpp =  /lib/cpp
   constraints =  hbonds
   integrator  =  md
   dt  =  0.002   ; ps !
   nsteps  =  75000   ; total 150 ps
   nstcomm =  10
   nstxout =  5
   nstvout =  5
   nstfout =  0
   nstlog  =  5000
   nstenergy   =  5000
   nstxtcout   =  25000
   nstlist =  10
   ns_type =  grid
   pbc =  xyz
   coulombtype =  PME
   vdwtype =  Cut-off
   rlist   =  1.2
   rcoulomb=  1.2
   rvdw=  1.2
   fourierspacing  =  0.12
   pme_order   =  4
   ewald_rtol  =  1e-5
   ; Berendsen temperature coupling is on in two groups
   Tcoupl  =  berendsen
   tc_grps =  BMI  PF6 SOL 
tau_t =  0.2  0.2  0.2

   ref_t   =  300  300  300
   nsttcouple  =  1
   ; Energy monitoring
   energygrps  =  BMI  PF6 SOL
   ; Isotropic pressure coupling is now on
   Pcoupl  =  berendsen
   pcoupltype  =  isotropic
   ;pc-grps =  BMI  PFF
  

Re: [gmx-users] how to switch from NPT to NVT ensemble during equilibration

[Mark Abraham]

On 10/02/2011 10:54 AM, Rini Gupta wrote:

Dear gmx users,

I am using gromacs (version 4.0.7) first time
to setup a 2-butoxyethanol-water simulation.
I created topology and coordinate file for BE using AUTOMATED TOPOLOGY 
BUILDER server.
It created a topology file (for united atom) compatible with GROMOS 
ffG53a6 forcefield.

Then a generated a box containing 20 BE and 480 water molecules using
genbox.

When I performed energy minimization followed by mdrun using NPT ensemble.
I get

Potential Energy = -1.56616474544600e+04
Maximum force = 9.72854664927673e+02 on atom 910


Then, I run for 200ps equlibration using NPT ensemble with Berendsen
thermostat and P coupling
I want to use NVT ensemble for my calculations, so it is ok to switch 
from NPT to NVT ensemble during equilibration?


Sure. See 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation



First, I did equilibation for 200ps using NPT ensemble
I get
Total Energy Temperature Pressure (bar) Cons. rmsd ()
-1.81617e+04 3.00167e+02 -4.32808e+00 0.0e+00
and,
My box length changes from 2.7 nm to 2.6503 nm

Then using state.cpt with mdrun I run for another 200ps using NVT 
settings in .mpd file ( I turn off the P-coupling).


I use the following commands:
I regenerated new .tpr file
grompp_d_mpi -f grompp.mdp -c confout.gro -p topol.top -o topol.tpr

mdrun_d_mpi -s topol.tpr -cpi state.cpt

Simulation is completed with warning

WARNING: The checkpoint state entries do not match the simulation,
see the log file for details


OK and what did you learn from the .log file about this? (Probably, it 
restarted from the coordinates of the confout.gro, which loses precision 
and some of the value of your initial equilibration)



and Pressure again increases up to 60 bar


No, it probably doesn't. See 
http://www.gromacs.org/Documentation/Terminology/Pressure




Total Energy Temperature Pressure (bar) Cons. rmsd ()
-1.82304e+04 2.2e+02 6.20706e+01 0.0e+00


I want to know if this is a right procedure for switching ensemble.
do i need to generate new velocities during second run using NVT ensemble?
If this is correct, how can i reach the target of Pressure 1 bar using 
this approach?


See 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Version_4



I am using following topology file:
Can anyone please tell me if this topology is o.k to use


It's syntactically correct because grompp doesn't complain. Whether its 
a sensible model physics can sometimes be rejected off-the-cuff, but 
can't really be confirmed without actually testing against some other data.


Mark


; Include forcefield parameters
#include "ffG53a6.itp"

[ moleculetype ]
; Name nrexcl
G269 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass total_charge
1 OE 1 G269 O 1 -0.345 15.9994
2 CH2 1 G269 C 1 0.151 14.0270
3 CH2 1 G269 C 1 0.194 14.0270 ; 0.000
4 CH2 1 G269 C 2 0.231 14.0270
5 OA 1 G269 O 2 -0.617 15.9994
6 H 1 G269 H 2 0.386 1.0080 ; 0.000
7 CH2 1 G269 C 3 -0.035 14.0270
8 CH2 1 G269 C 3 0.143 14.0270
9 CH3 1 G269 C 3 -0.108 15.0350 ; -0.000
; total charge of the molecule: 0.000
[ bonds ]
; ai aj funct c0 c1
1 2 2 0.1430 8.1800e+06
1 3 2 0.1430 8.1800e+06
2 4 2 0.1520 5.4300e+06
3 7 2 0.1520 5.4300e+06
4 5 2 0.1430 8.1800e+06
5 6 2 0.1000 2.3200e+07
7 8 2 0.1530 7.1500e+06
8 9 2 0.1530 7.1500e+06
[ pairs ]
; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp
1 5 1
1 8 1
2 6 1
2 7 1
3 4 1
3 9 1
[ angles ]
; ai aj ak funct angle fc
2 1 3 2 109.50 380.00
1 2 4 2 109.50 320.00
1 3 7 2 109.50 320.00
2 4 5 2 111.00 530.00
4 5 6 2 108.53 443.00
3 7 8 2 111.00 530.00
7 8 9 2 111.00 530.00
[ dihedrals ]
; GROMOS improper dihedrals
; ai aj ak al funct angle fc
[ dihedrals ]
; ai aj ak al funct ph0 cp mult
3 1 2 4 1 0.00 1.26 3
2 1 3 7 1 0.00 1.26 3
1 2 4 5 1 0.00 2.53 3
1 3 7 8 1 0.00 3.77 3
2 4 5 6 1 0.00 1.26 3
3 7 8 9 1 0.00 3.77 3
[ exclusions ]
; ai aj funct ; GROMOS 1-4 exclusions




; Include water topology
#include "spce.itp"
[ system ]
; Name
BE in Water

[ molecules ]
; Compound #mols
G269 20
SOL 480

Please help me in this regard.

Thanks and Regards,
Rini


Dr. Rini Gupta
Postdoctoral Fellow
University of British Columbia
Vancouver



 





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[gmx-users] how to switch from NPT to NVT ensemble during equilibration

[Rini Gupta]

Dear gmx users,

 I am using gromacs (version 4.0.7) first time
 to setup a 2-butoxyethanol-water simulation.
 I created topology and coordinate file for BE using AUTOMATED TOPOLOGY BUILDER 
server.
It created a topology file (for united atom) compatible with GROMOS ffG53a6 
forcefield.
 Then a generated a box containing 20 BE and 480 water molecules using
 genbox.

 When I performed energy minimization followed by mdrun using NPT ensemble.
I get

Potential Energy  = -1.56616474544600e+04 
Maximum force =  9.72854664927673e+02 on atom 910


Then, I run for 200ps equlibration using NPT ensemble with Berendsen 
thermostat and P coupling
I want to use NVT ensemble for my calculations, so it is ok to switch from NPT 
to NVT ensemble during equilibration?
First, I did equilibation for 200ps using NPT ensemble
I get 
 Total EnergyTemperature Pressure (bar)  Cons. rmsd ()
   -1.81617e+043.00167e+02   -4.32808e+000.0e+00
and,
My box length changes from 2.7 nm to 2.6503 nm

Then using state.cpt with mdrun I run for another 200ps using NVT settings in 
.mpd file ( I turn off the P-coupling).

I use the following commands:
I regenerated new .tpr file 
grompp_d_mpi -f grompp.mdp -c confout.gro -p topol.top -o topol.tpr

mdrun_d_mpi -s topol.tpr -cpi state.cpt

 Simulation is completed with warning

WARNING: The checkpoint state entries do not match the simulation,
 see the log file for details

and Pressure again increases up to 60 bar

 Total EnergyTemperature Pressure (bar)  Cons. rmsd ()
   -1.82304e+042.2e+026.20706e+010.0e+00


I want to know if this is a right procedure for switching ensemble.
do i need to generate new velocities during second run using NVT ensemble?
If this is correct, how can i reach the target of Pressure 1 bar using this 
approach?

I am using following topology file:
Can anyone please tell me if this topology is o.k to use


; Include forcefield parameters
#include "ffG53a6.itp"

[ moleculetype ]
; Name   nrexcl
G269 3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
1OE1G269  O1   -0.345  15.9994
2   CH21G269  C10.151  14.0270
3   CH21G269  C10.194  14.0270  ;  0.000
4   CH21G269  C20.231  14.0270
5OA1G269  O2   -0.617  15.9994
6 H1G269  H20.386   1.0080  ;  0.000
7   CH21G269  C3   -0.035  14.0270
8   CH21G269  C30.143  14.0270
9   CH31G269  C3   -0.108  15.0350  ; -0.000
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0 c1
122   0.1430   8.1800e+06
132   0.1430   8.1800e+06
242   0.1520   5.4300e+06
372   0.1520   5.4300e+06
452   0.1430   8.1800e+06
562   0.1000   2.3200e+07
782   0.1530   7.1500e+06
892   0.1530   7.1500e+06
[ pairs ]
;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
151
181
261
271
341
391
[ angles ]
;  ai   aj   ak  funct   angle fc
2132109.50   380.00
1242109.50   320.00
1372109.50   320.00
2452111.00   530.00
4562108.53   443.00
3782111.00   530.00
7892111.00   530.00
[ dihedrals ]
; GROMOS improper dihedrals
;  ai   aj   ak   al  funct   angle fc
[ dihedrals ]
;  ai   aj   ak   al  functph0  cp mult
31241  0.00 1.263
21371  0.00 1.263
12451  0.00 2.533
13781  0.00 3.773
24561  0.00 1.263
37891  0.00 3.773
[ exclusions ]
;  ai   aj  funct  ;  GROMOS 1-4 exclusions




; Include water topology
#include "spce.itp"
[ system ]
; Name
BE in Water

[ molecules ]
; Compound  #mols
G269  20
SOL   480

Please help me in this regard.

Thanks and Regards,
Rini


Dr. Rini Gupta
Postdoctoral Fellow
University of British Columbia
Vancouver


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Re: [gmx-users] g_hbond and 4.5.2 version

[Justin A. Lemkul]

Zuzana Benkova wrote:

Dear GROMACS users,

I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds 
in water. I got the average  number per time frame and number of water 
oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 
1.677, which is twice the former value. TIP3P model predicts over 3 
hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply 
the digit from version 4.0.7. by 2 I get the expected number. That is 
why I supposed that the number of 1.677 means per one water oxygen and  
per one water molecule means 2x1.677 since two water molecules 
participate at one hydrogen bond.
However, I do not know yet if my interpretation is correct and how to 
interpret the number obtained by version 4.5.2.

I would appreciate any help. Thank you in advance.



Try pulling the latest stable development version.  This issue was reported in 
4.5.1:


http://lists.gromacs.org/pipermail/gmx-users/2010-October/054905.html

but not fixed until after 4.5.3 was released:

http://lists.gromacs.org/pipermail/gmx-users/2010-December/056406.html

-Justin


Greetings
Zuzana



--


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] g_hbond and 4.5.2 version

[Zuzana Benkova]

Dear GROMACS users,I have used g_hbond of version 4.5.2 to analyze number of hydrogen bonds in water. I got the average  number per time frame and number of water oxygen atoms equal to 0.839. When I used g_hbond of version 4.0.7 I got 1.677, which is twice the former value. TIP3P model predicts over 3 hydrogen bonds per one water molecule. I am a bit puzzled. If I multiply the digit from version 4.0.7. by 2 I get the expected number. That is why I supposed that the number of 1.677 means per one water oxygen and  per one water molecule means 2x1.677 since two water molecules participate at one hydrogen bond. However, I do not know yet if my interpretation is correct and how to interpret the number obtained by version 4.5.2. I would appreciate any help. Thank you in advance.GreetingsZuzana
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Re: [gmx-users] Domain decomposition configuration

[Justin A. Lemkul]

Denny Frost wrote:
Is tpbconv with the "pbc" option the best way to make the molecules 
whole again?




The only way, as far as I'm aware (aside from editconf's crude approach).  Do 
this before you concatenate your systems.


-Justin

On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul > wrote:




Denny Frost wrote:

This run is actually a combination of two 5x5x5 nm boxes, one if
which was previously run in DD, and the other is water.  Since
the length of that bond is almost 5 nm, is it possible that the
pbc's are not being recognized?  There is no way I have a bond
that long from my previous run.


I'll venture a guess that there were broken molecules in the system
you concatenated?  That would gel with a bond that stretches across
a 5-nm box.  You have to deal with whole molecules in the input
configuration.

-Justin

On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Denny Frost wrote:

   I'm using version 4.5.3

   Here's the output from the log file from DD initiation to
the error:

   Initializing Domain Decomposition on 8 nodes
   Dynamic load balancing: auto
   Will sort the charge groups at every domain (re)decomposition
   Initial maximum inter charge-group distances:
  two-body bonded interactions: 4.893 nm, Bond, atoms
8994 8996
multi-body bonded interactions: 4.893 nm, Angle, atoms
8994 8997
   Minimum cell size due to bonded interactions: 5.382 nm


   Bonded interactions should normally not occur over such a length.
The information printed here points to the culprits.  What are
   these atoms, and why are they bonded if they are so far away?

   -Justin

   Using 0 separate PME nodes
   Scaling the initial minimum size with 1/0.8 (option -dds)
= 1.25
   Optimizing the DD grid for 8 cells with a minimum initial
size
   of 6.728 nm
   The maximum allowed number of cells is: X 0 Y 0 Z 1

   ---
   Program mdrun_mpi, VERSION 4.5.3
   Source code file: domdec.c, line: 6428

   Fatal error:
   There is no domain decomposition for 8 nodes that is
compatible
   with the given box and a minimum cell size of 6.72787 nm
   Change the number of nodes or mdrun option -rdd or -dds
   Look in the log file for details on the domain decomposition
   For more information and tips for troubleshooting, please
check
   the GROMACS
   website at http://www.gromacs.org/Documentation/Errors

   And here is my mdp file

   title   =  BMIM+PF6
   cpp =  /lib/cpp
   constraints =  hbonds
   integrator  =  md
   dt  =  0.002   ; ps !
   nsteps  =  75000   ; total 150 ps
   nstcomm =  10
   nstxout =  5
   nstvout =  5
   nstfout =  0
   nstlog  =  5000
   nstenergy   =  5000
   nstxtcout   =  25000
   nstlist =  10
   ns_type =  grid
   pbc =  xyz
   coulombtype =  PME
   vdwtype =  Cut-off
   rlist   =  1.2
   rcoulomb=  1.2
   rvdw=  1.2
   fourierspacing  =  0.12
   pme_order   =  4
   ewald_rtol  =  1e-5
   ; Berendsen temperature coupling is on in two groups
   Tcoupl  =  berendsen
   tc_grps =  BMI  PF6 SOL tau_t
 =  0.2  0.2  0.2

   ref_t   =  300  300  300
   nsttcouple  =  1
   ; Energy monitoring
   energygrps  =  BMI  PF6 SOL
   ; Isotropic pressure coupling is now on
   Pcoupl  =  berendsen
   pcoupltype  =  isotropic
   ;pc-grps =  BMI  PFF
   tau_p   =  2.0
   ref_p   =  1.0
   compressibility =  4.5e-5

   ; Generate velocites is off at 300 K.
   gen_vel =  yes
   gen_temp=  300.0
   gen_seed

Re: [gmx-users] Domain decomposition configuration

[Denny Frost]

Is tpbconv with the "pbc" option the best way to make the molecules whole
again?

On Wed, Feb 9, 2011 at 2:06 PM, Justin A. Lemkul  wrote:

>
>
> Denny Frost wrote:
>
>> This run is actually a combination of two 5x5x5 nm boxes, one if which was
>> previously run in DD, and the other is water.  Since the length of that bond
>> is almost 5 nm, is it possible that the pbc's are not being recognized?
>>  There is no way I have a bond that long from my previous run.
>>
>>
> I'll venture a guess that there were broken molecules in the system you
> concatenated?  That would gel with a bond that stretches across a 5-nm box.
>  You have to deal with whole molecules in the input configuration.
>
> -Justin
>
>  On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Denny Frost wrote:
>>
>>I'm using version 4.5.3
>>
>>Here's the output from the log file from DD initiation to the
>> error:
>>
>>Initializing Domain Decomposition on 8 nodes
>>Dynamic load balancing: auto
>>Will sort the charge groups at every domain (re)decomposition
>>Initial maximum inter charge-group distances:
>>   two-body bonded interactions: 4.893 nm, Bond, atoms 8994 8996
>> multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997
>>Minimum cell size due to bonded interactions: 5.382 nm
>>
>>
>>Bonded interactions should normally not occur over such a length.
>> The information printed here points to the culprits.  What are
>>these atoms, and why are they bonded if they are so far away?
>>
>>-Justin
>>
>>Using 0 separate PME nodes
>>Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>>Optimizing the DD grid for 8 cells with a minimum initial size
>>of 6.728 nm
>>The maximum allowed number of cells is: X 0 Y 0 Z 1
>>
>>---
>>Program mdrun_mpi, VERSION 4.5.3
>>Source code file: domdec.c, line: 6428
>>
>>Fatal error:
>>There is no domain decomposition for 8 nodes that is compatible
>>with the given box and a minimum cell size of 6.72787 nm
>>Change the number of nodes or mdrun option -rdd or -dds
>>Look in the log file for details on the domain decomposition
>>For more information and tips for troubleshooting, please check
>>the GROMACS
>>website at http://www.gromacs.org/Documentation/Errors
>>
>>And here is my mdp file
>>
>>title   =  BMIM+PF6
>>cpp =  /lib/cpp
>>constraints =  hbonds
>>integrator  =  md
>>dt  =  0.002   ; ps !
>>nsteps  =  75000   ; total 150 ps
>>nstcomm =  10
>>nstxout =  5
>>nstvout =  5
>>nstfout =  0
>>nstlog  =  5000
>>nstenergy   =  5000
>>nstxtcout   =  25000
>>nstlist =  10
>>ns_type =  grid
>>pbc =  xyz
>>coulombtype =  PME
>>vdwtype =  Cut-off
>>rlist   =  1.2
>>rcoulomb=  1.2
>>rvdw=  1.2
>>fourierspacing  =  0.12
>>pme_order   =  4
>>ewald_rtol  =  1e-5
>>; Berendsen temperature coupling is on in two groups
>>Tcoupl  =  berendsen
>>tc_grps =  BMI  PF6 SOL tau_t
>>=  0.2  0.2  0.2
>>ref_t   =  300  300  300
>>nsttcouple  =  1
>>; Energy monitoring
>>energygrps  =  BMI  PF6 SOL
>>; Isotropic pressure coupling is now on
>>Pcoupl  =  berendsen
>>pcoupltype  =  isotropic
>>;pc-grps =  BMI  PFF
>>tau_p   =  2.0
>>ref_p   =  1.0
>>compressibility =  4.5e-5
>>
>>; Generate velocites is off at 300 K.
>>gen_vel =  yes
>>gen_temp=  300.0
>>gen_seed=  10
>>
>>
>>On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   Denny Frost wrote:
>>
>>   I am trying to start a run using domain decomposition on a
>>   5x5x10 nm box with about 26,000 atoms in it.  I've tried
>>running
>>   8-16 pp nodes, but gromacs always throws an error saying
>> that
>>   there is no domain decomposition compatible with this box
>>and a
>>   minimum cell size of 6.728 nm.  I've tried many values
>>for -dds
>>   and a few dd vectors, but w

Re: [gmx-users] Domain decomposition configuration

[Justin A. Lemkul]

Denny Frost wrote:
This run is actually a combination of two 5x5x5 nm boxes, one if which 
was previously run in DD, and the other is water.  Since the length of 
that bond is almost 5 nm, is it possible that the pbc's are not being 
recognized?  There is no way I have a bond that long from my previous run.




I'll venture a guess that there were broken molecules in the system you 
concatenated?  That would gel with a bond that stretches across a 5-nm box.  You 
have to deal with whole molecules in the input configuration.


-Justin

On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul > wrote:




Denny Frost wrote:

I'm using version 4.5.3

Here's the output from the log file from DD initiation to the error:

Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
   two-body bonded interactions: 4.893 nm, Bond, atoms 8994 8996
 multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997
Minimum cell size due to bonded interactions: 5.382 nm


Bonded interactions should normally not occur over such a length.
 The information printed here points to the culprits.  What are
these atoms, and why are they bonded if they are so far away?

-Justin

Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size
of 6.728 nm
The maximum allowed number of cells is: X 0 Y 0 Z 1

---
Program mdrun_mpi, VERSION 4.5.3
Source code file: domdec.c, line: 6428

Fatal error:
There is no domain decomposition for 8 nodes that is compatible
with the given box and a minimum cell size of 6.72787 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/Documentation/Errors

And here is my mdp file

title   =  BMIM+PF6
cpp =  /lib/cpp
constraints =  hbonds
integrator  =  md
dt  =  0.002   ; ps !
nsteps  =  75000   ; total 150 ps
nstcomm =  10
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
vdwtype =  Cut-off
rlist   =  1.2
rcoulomb=  1.2
rvdw=  1.2
fourierspacing  =  0.12
pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc_grps =  BMI  PF6 SOL tau_t  
=  0.2  0.2  0.2

ref_t   =  300  300  300
nsttcouple  =  1
; Energy monitoring
energygrps  =  BMI  PF6 SOL
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps =  BMI  PFF
tau_p   =  2.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10


On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Denny Frost wrote:

   I am trying to start a run using domain decomposition on a
   5x5x10 nm box with about 26,000 atoms in it.  I've tried
running
   8-16 pp nodes, but gromacs always throws an error saying that
   there is no domain decomposition compatible with this box
and a
   minimum cell size of 6.728 nm.  I've tried many values
for -dds
   and a few dd vectors, but with no luck.  Does anyone know
to get
   domain decomposition working on a rectangular system like
this?


   Not without significantly more information.  Please post:

   1. Your Gromacs version
   2. Any DD-related information that is printed to either the
log file
   or stdout
   3.

Re: [gmx-users] Domain decomposition configuration

[Denny Frost]

This run is actually a combination of two 5x5x5 nm boxes, one if which was
previously run in DD, and the other is water.  Since the length of that bond
is almost 5 nm, is it possible that the pbc's are not being recognized?
 There is no way I have a bond that long from my previous run.

On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul  wrote:

>
>
> Denny Frost wrote:
>
>> I'm using version 4.5.3
>>
>> Here's the output from the log file from DD initiation to the error:
>>
>> Initializing Domain Decomposition on 8 nodes
>> Dynamic load balancing: auto
>> Will sort the charge groups at every domain (re)decomposition
>> Initial maximum inter charge-group distances:
>>two-body bonded interactions: 4.893 nm, Bond, atoms 8994 8996
>>  multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997
>> Minimum cell size due to bonded interactions: 5.382 nm
>>
>
> Bonded interactions should normally not occur over such a length.  The
> information printed here points to the culprits.  What are these atoms, and
> why are they bonded if they are so far away?
>
> -Justin
>
>  Using 0 separate PME nodes
>> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
>> Optimizing the DD grid for 8 cells with a minimum initial size of 6.728 nm
>> The maximum allowed number of cells is: X 0 Y 0 Z 1
>>
>> ---
>> Program mdrun_mpi, VERSION 4.5.3
>> Source code file: domdec.c, line: 6428
>>
>> Fatal error:
>> There is no domain decomposition for 8 nodes that is compatible with the
>> given box and a minimum cell size of 6.72787 nm
>> Change the number of nodes or mdrun option -rdd or -dds
>> Look in the log file for details on the domain decomposition
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> And here is my mdp file
>>
>> title   =  BMIM+PF6
>> cpp =  /lib/cpp
>> constraints =  hbonds
>> integrator  =  md
>> dt  =  0.002   ; ps !
>> nsteps  =  75000   ; total 150 ps
>> nstcomm =  10
>> nstxout =  5
>> nstvout =  5
>> nstfout =  0
>> nstlog  =  5000
>> nstenergy   =  5000
>> nstxtcout   =  25000
>> nstlist =  10
>> ns_type =  grid
>> pbc =  xyz
>> coulombtype =  PME
>> vdwtype =  Cut-off
>> rlist   =  1.2
>> rcoulomb=  1.2
>> rvdw=  1.2
>> fourierspacing  =  0.12
>> pme_order   =  4
>> ewald_rtol  =  1e-5
>> ; Berendsen temperature coupling is on in two groups
>> Tcoupl  =  berendsen
>> tc_grps =  BMI  PF6 SOL tau_t   =  0.2
>>  0.2  0.2
>> ref_t   =  300  300  300
>> nsttcouple  =  1
>> ; Energy monitoring
>> energygrps  =  BMI  PF6 SOL
>> ; Isotropic pressure coupling is now on
>> Pcoupl  =  berendsen
>> pcoupltype  =  isotropic
>> ;pc-grps =  BMI  PFF
>> tau_p   =  2.0
>> ref_p   =  1.0
>> compressibility =  4.5e-5
>>
>> ; Generate velocites is off at 300 K.
>> gen_vel =  yes
>> gen_temp=  300.0
>> gen_seed=  10
>>
>>
>> On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Denny Frost wrote:
>>
>>I am trying to start a run using domain decomposition on a
>>5x5x10 nm box with about 26,000 atoms in it.  I've tried running
>>8-16 pp nodes, but gromacs always throws an error saying that
>>there is no domain decomposition compatible with this box and a
>>minimum cell size of 6.728 nm.  I've tried many values for -dds
>>and a few dd vectors, but with no luck.  Does anyone know to get
>>domain decomposition working on a rectangular system like this?
>>
>>
>>Not without significantly more information.  Please post:
>>
>>1. Your Gromacs version
>>2. Any DD-related information that is printed to either the log file
>>or stdout
>>3. Your .mdp file
>>
>>-Justin
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu  | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>int

Re: [gmx-users] Domain decomposition configuration

[Justin A. Lemkul]

Denny Frost wrote:

I'm using version 4.5.3

Here's the output from the log file from DD initiation to the error:

Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 4.893 nm, Bond, atoms 8994 8996
  multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997
Minimum cell size due to bonded interactions: 5.382 nm


Bonded interactions should normally not occur over such a length.  The 
information printed here points to the culprits.  What are these atoms, and why 
are they bonded if they are so far away?


-Justin


Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 6.728 nm
The maximum allowed number of cells is: X 0 Y 0 Z 1

---
Program mdrun_mpi, VERSION 4.5.3
Source code file: domdec.c, line: 6428

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the 
given box and a minimum cell size of 6.72787 nm

Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

And here is my mdp file

title   =  BMIM+PF6
cpp =  /lib/cpp
constraints =  hbonds
integrator  =  md
dt  =  0.002   ; ps !
nsteps  =  75000   ; total 150 ps
nstcomm =  10
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
vdwtype =  Cut-off
rlist   =  1.2
rcoulomb=  1.2
rvdw=  1.2
fourierspacing  =  0.12
pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc_grps =  BMI  PF6 SOL 
tau_t   =  0.2  0.2  0.2

ref_t   =  300  300  300
nsttcouple  =  1
; Energy monitoring
energygrps  =  BMI  PF6 SOL
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps =  BMI  PFF
tau_p   =  2.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10


On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul > wrote:




Denny Frost wrote:

I am trying to start a run using domain decomposition on a
5x5x10 nm box with about 26,000 atoms in it.  I've tried running
8-16 pp nodes, but gromacs always throws an error saying that
there is no domain decomposition compatible with this box and a
minimum cell size of 6.728 nm.  I've tried many values for -dds
and a few dd vectors, but with no luck.  Does anyone know to get
domain decomposition working on a rectangular system like this?


Not without significantly more information.  Please post:

1. Your Gromacs version
2. Any DD-related information that is printed to either the log file
or stdout
3. Your .mdp file

-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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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] Domain decomposition configuration

[Denny Frost]

I'm using version 4.5.3

Here's the output from the log file from DD initiation to the error:

Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 4.893 nm, Bond, atoms 8994 8996
  multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997
Minimum cell size due to bonded interactions: 5.382 nm
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 6.728 nm
The maximum allowed number of cells is: X 0 Y 0 Z 1

---
Program mdrun_mpi, VERSION 4.5.3
Source code file: domdec.c, line: 6428

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the
given box and a minimum cell size of 6.72787 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

And here is my mdp file

title   =  BMIM+PF6
cpp =  /lib/cpp
constraints =  hbonds
integrator  =  md
dt  =  0.002   ; ps !
nsteps  =  75000   ; total 150 ps
nstcomm =  10
nstxout =  5
nstvout =  5
nstfout =  0
nstlog  =  5000
nstenergy   =  5000
nstxtcout   =  25000
nstlist =  10
ns_type =  grid
pbc =  xyz
coulombtype =  PME
vdwtype =  Cut-off
rlist   =  1.2
rcoulomb=  1.2
rvdw=  1.2
fourierspacing  =  0.12
pme_order   =  4
ewald_rtol  =  1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl  =  berendsen
tc_grps =  BMI  PF6 SOL
tau_t   =  0.2  0.2  0.2
ref_t   =  300  300  300
nsttcouple  =  1
; Energy monitoring
energygrps  =  BMI  PF6 SOL
; Isotropic pressure coupling is now on
Pcoupl  =  berendsen
pcoupltype  =  isotropic
;pc-grps =  BMI  PFF
tau_p   =  2.0
ref_p   =  1.0
compressibility =  4.5e-5

; Generate velocites is off at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  10


On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul  wrote:

>
>
> Denny Frost wrote:
>
>> I am trying to start a run using domain decomposition on a 5x5x10 nm box
>> with about 26,000 atoms in it.  I've tried running 8-16 pp nodes, but
>> gromacs always throws an error saying that there is no domain decomposition
>> compatible with this box and a minimum cell size of 6.728 nm.  I've tried
>> many values for -dds and a few dd vectors, but with no luck.  Does anyone
>> know to get domain decomposition working on a rectangular system like this?
>>
>>
> Not without significantly more information.  Please post:
>
> 1. Your Gromacs version
> 2. Any DD-related information that is printed to either the log file or
> stdout
> 3. Your .mdp file
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] Domain decomposition configuration

[Justin A. Lemkul]

Denny Frost wrote:
I am trying to start a run using domain decomposition on a 5x5x10 nm box 
with about 26,000 atoms in it.  I've tried running 8-16 pp nodes, but 
gromacs always throws an error saying that there is no domain 
decomposition compatible with this box and a minimum cell size of 6.728 
nm.  I've tried many values for -dds and a few dd vectors, but with no 
luck.  Does anyone know to get domain decomposition working on a 
rectangular system like this?




Not without significantly more information.  Please post:

1. Your Gromacs version
2. Any DD-related information that is printed to either the log file or stdout
3. Your .mdp file

-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] Domain decomposition configuration

[Denny Frost]

I am trying to start a run using domain decomposition on a 5x5x10 nm box
with about 26,000 atoms in it.  I've tried running 8-16 pp nodes, but
gromacs always throws an error saying that there is no domain decomposition
compatible with this box and a minimum cell size of 6.728 nm.  I've tried
many values for -dds and a few dd vectors, but with no luck.  Does anyone
know to get domain decomposition working on a rectangular system like this?
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Re: [gmx-users] PRODRG

[jorge_quintero]

I'm completely in agreement with that advice.  To use antechamber tool, I
recommend use force field for all the system.

>
> The OP's question is easily answered by referring to the PRODRG FAQ in
> dealing
> with proper protonation.
>
> As for Antechamber and the like, these are good tools, but do not produce
> GROMOS-compatible topologies, if that is indeed the underlying goal.
> We've done
> thorough analysis of various QM calculation methods for GROMOS charges,
> and none
> of them produce completely satisfactory topologies.  Antechamber, Spartan,
> Gaussian, etc are good for initial charge calculations, but IMHO do not
> qualify
> as an "end result" for GROMOS parameterization due to the empirical
> refinement
> used in the force field derivation.  All of that makes GROMOS
> parameterization
> somewhat tricky, and hence why force field choice is so incredibly
> important
> when designing projects... ;)
>
> -Justin
>
> TJ Mustard wrote:
>>
>>
>> Yes I would recommend acpype.
>>
>> On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote:
>>
>>  > I think that is better to use antechamber tools.
>>  >
>>  >
>>  > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
>>  > >> Dear Users
>>  > >>
>>  > >> I am using PRODRG to make topology for my drug
>>  > >> It addes Hydrogenes but in wrong way.
>>  > >> My Nitrogen atom is bonded to 2 Carbos,
>>  > >> and PRODRG addes 2 Hydrogenes to it .
>>  > >> Please let me know how can I do.
>>  > >> Thanks in advance
>>  > >
>>  > > This is not really the forum to get help about that. You need to
>> read
>>  > > how to PRODRG needs input, and supply something it can deal with.
>> Then
>>  > > do a whole bunch more work testing what it produced.
>>  > >
>>  > > Mark
>>  > > --
>>  > > 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!
>>  > > Please don't post (un)subscribe requests to the list. Use the
>>  > > www interface or send it to gmx-users-requ...@gromacs.org.
>>  > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>  > >
>>  >
>>  >
>>  > --
>>  > Jorge R. Quintero
>>  > Químico
>>  > Universidad Industrial de Santander
>>  > Bucaramanga, Santander - Colombia
>>  >
>>  > --
>>  > 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!
>>  > Please don't post (un)subscribe requests to the list. Use the
>>  > www interface or send it to gmx-users-requ...@gromacs.org.
>>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>  >
>>
>>
>>
>> TJ Mustard
>> Email: musta...@onid.orst.edu
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>


-- 
Jorge R. Quintero
Químico
Universidad Industrial de Santander
Bucaramanga, Santander - Colombia

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Re: [gmx-users] Comparing ff in Topology file by PRODRG and gromos G45a3

[Justin A. Lemkul]

XUEMING TANG wrote:

Hi there

This is maybe an old question. I want to ask a general procedure of 
generate topology file with gromo96 force field by Dundee Prodrg. 
Take SDS for an example, I want to use gromos96 G45a3 forcefield. After 
the file is generated by dundee, I compare the forcefield parameter of 
G45a3 with what Dundee output for(bond length, angle, dihedral, imp, 
potential). There are some differences (see below). While from papers 
author usually just mentioned that the file is generated by Prodrg 
without detailed information. According to Dundee website, the 


An unfortunate practice.  PRODRG topologies are questionable, at best, and often 
the time is not taken to properly refine them, or at least describe what changes 
were made when writing methodology.


forcefield is gromos which is outdated. Should I change all the 
forcefield parameter by hand for any molecule I want to use with gromos 
ff. Or there is any shortcut I can try. I understand that charge 


All of this depends on what you mean by "GROMOS" force field.  There are many 
such parameter sets.  The original PRODRG was based on GROMOS87, which is indeed 
extremely outdated.  The PRODRG 2.5 (beta) server supports GROMOS96 43A1, but 
the same caveat applies as far as accuracy.  At least it's based on a newer 
force field.


Unfortunately, "shortcuts" taken during parameterization usually leave you with 
junk in the topology.  Parameterizing new species is very time-consuming, if 
done properly.



calculated by prodrg is inaccurate.
Additional question, would G53a6 is basically better than G45a3 for SDS?



There are a number of papers that have done simulations with SDS.  You should 
probably base your force field choice on what you find in the literature.




 DundeePRo ff45a3
 Length  Potential  Length Potential
CHn-CHn 0.153   3.35E+050.153   7.15E+06   
C-SO1   0.143   2.51E+05   0.143   8.18E+06
SO1-S   0.143   3.35E+05
S-SO2   0.143   3.35E+05
S=SO3   0.153.77E+05   0.158.37E+06

S=SO4   0.153.77E+05   0.158.37E+06

 anglePotentialanglePotential
C-C-C111460.2111530

C-C-SO1  109.5  460.2  109.5520
C-SO1-S  120397.5   
SO1-S-SOn109.5  460.2



dihedralPotentialdihedralPotential
S-SO1-SO3-SO2   35.3836.8   35.3334.8
C-C-C-C 0   5.93
SO1-C-C-C   0   5.93
S-SO1-C1-C2 0   3.830   1.33

C1-SO1-S-SO40   1.33
~  
Mainly the potential is different. And I didnot find the exact value on 
the blank parts in ff45a3 categories. 



You're comparing different force fields, so yes, there will be differences.  If 
you're planning to constrain all bonds, then the force constants there are not 
significant and aren't used (they apply to a quartic potential).  Otherwise, use 
parameters that consistently originate from one force field parameter set.  If 
you can't find certain parameters, then you should consider your force field 
choice more thoroughly.


-Justin


File generated by Dundee:

[ bonds ]
; ai  aj  fuc0, c1, ...
   1   2   20.153334720.00.153334720.0 ;   C12  C11
   2   3   20.153334720.00.153334720.0 ;   C11  C10
   3   4   20.153334720.00.153334720.0 ;   C10  C9
   4   5   20.153334720.00.153334720.0 ;   C9  C8
   5   6   20.153334720.00.153334720.0 ;   C8  C7
   6   7   20.153334720.00.153334720.0 ;   C7  C6
   7   8   20.153334720.00.153334720.0 ;   C6  C5
   8   9   20.153334720.00.153334720.0 ;   C5  C4
   9  10   20.153334720.00.153334720.0 ;   C4  C3
  10  11   20.153334720.00.153334720.0 ;   C3  C2
  11  12   20.153334720.00.153334720.0 ;   C2  C1
  12  13   20.143251040.00.143251040.0 ;   C1  SO1
  13  14   20.143334720.00.143334720.0 ;   SO1  S
  14  15   20.143334720.00.143334720.0 ;   S  SO2
  14  16   20.150376560.00.150376560.0 ;   S  SO3
  14  17   20.150376560.00.150376560.0 ;   S  SO4

[ pairs ]
; ai  aj  fuc0, c1, ...
   1   4   1   ;   C12  C9
   2   5   1   ;   C11  C8
   3   6   1   ;   C10  C7
   4   7   1   ;   C9  C6
   5   8   1   ;   C8  C5
   6   9   1   ;   C7  C4
   7  10   1   ;   C6  C3
   8  11   1  

[gmx-users] Comparing ff in Topology file by PRODRG and gromos G45a3

[XUEMING TANG]

Hi there

This is maybe an old question. I want to ask a general procedure of generate
topology file with gromo96 force field by Dundee Prodrg. Take SDS for an
example, I want to use gromos96 G45a3 forcefield. After the file is
generated by dundee, I compare the forcefield parameter of G45a3 with what
Dundee output for(bond length, angle, dihedral, imp, potential). There are
some differences (see below). While from papers author usually just
mentioned that the file is generated by Prodrg without detailed information.
According to Dundee website, the forcefield is gromos which is outdated.
Should I change all the forcefield parameter by hand for any molecule I want
to use with gromos ff. Or there is any shortcut I can try. I understand that
charge calculated by prodrg is inaccurate.
Additional question, would G53a6 is basically better than G45a3 for SDS?


 DundeePRo ff45a3
 Length  Potential  Length Potential
CHn-CHn 0.153   3.35E+050.153   7.15E+06
C-SO1   0.143   2.51E+05   0.143   8.18E+06
SO1-S   0.143   3.35E+05
S-SO2   0.143   3.35E+05
S=SO3   0.153.77E+05   0.158.37E+06
S=SO4   0.153.77E+05   0.158.37E+06

 anglePotentialanglePotential
C-C-C111460.2111530
C-C-SO1  109.5  460.2  109.5520
C-SO1-S  120397.5
SO1-S-SOn109.5  460.2


dihedralPotentialdihedralPotential
S-SO1-SO3-SO2   35.3836.8   35.3334.8
C-C-C-C 0   5.93
SO1-C-C-C   0   5.93
S-SO1-C1-C2 0   3.830   1.33
C1-SO1-S-SO40   1.33
~
Mainly the potential is different. And I didnot find the exact value on the
blank parts in ff45a3 categories.

File generated by Dundee:

[ bonds ]
; ai  aj  fuc0, c1, ...
   1   2   20.153334720.00.153334720.0 ;   C12  C11
   2   3   20.153334720.00.153334720.0 ;   C11  C10
   3   4   20.153334720.00.153334720.0 ;   C10  C9
   4   5   20.153334720.00.153334720.0 ;   C9  C8
   5   6   20.153334720.00.153334720.0 ;   C8  C7
   6   7   20.153334720.00.153334720.0 ;   C7  C6
   7   8   20.153334720.00.153334720.0 ;   C6  C5
   8   9   20.153334720.00.153334720.0 ;   C5  C4
   9  10   20.153334720.00.153334720.0 ;   C4  C3
  10  11   20.153334720.00.153334720.0 ;   C3  C2
  11  12   20.153334720.00.153334720.0 ;   C2  C1
  12  13   20.143251040.00.143251040.0 ;   C1  SO1
  13  14   20.143334720.00.143334720.0 ;   SO1  S
  14  15   20.143334720.00.143334720.0 ;   S  SO2
  14  16   20.150376560.00.150376560.0 ;   S  SO3
  14  17   20.150376560.00.150376560.0 ;   S  SO4

[ pairs ]
; ai  aj  fuc0, c1, ...
   1   4   1   ;   C12  C9
   2   5   1   ;   C11  C8
   3   6   1   ;   C10  C7
   4   7   1   ;   C9  C6
   5   8   1   ;   C8  C5
   6   9   1   ;   C7  C4
   7  10   1   ;   C6  C3
   8  11   1   ;   C5  C2
   9  12   1   ;   C4  C1
  10  13   1   ;   C3  SO1
  11  14   1   ;   C2  S
  12  15   1   ;   C1  SO2
  12  16   1   ;   C1  SO3
  12  17   1   ;   C1  SO4

[ angles ]
; ai  aj  ak  fuc0, c1, ...
   1   2   3   1111.0   460.2111.0   460.2 ;   C12  C11  C10
   2   3   4   1111.0   460.2111.0   460.2 ;   C11  C10  C9
   3   4   5   1111.0   460.2111.0   460.2 ;   C10  C9  C8
   4   5   6   1111.0   460.2111.0   460.2 ;   C9  C8  C7
   5   6   7   1111.0   460.2111.0   460.2 ;   C8  C7  C6
   6   7   8   1111.0   460.2111.0   460.2 ;   C7  C6  C5
   7   8   9   1111.0   460.2111.0   460.2 ;   C6  C5  C4
   8   9  10   1111.0   460.2111.0   460.2 ;   C5  C4  C3
   9  10  11   1111.0   460.2111.0   460.2 ;   C4  C3  C2
  10  11  12   1111.0   460.2111.0   460.2 ;   C3  C2  C1
  11  12  13   1109.5   460.2109.5   460.2 ;   C2  C1  SO1
  12  13  14   1120.0   397.5120.0   397.5 ;   C1  SO1  S
  13  14  15   1109.5   460.2109.5   460.2 ;   SO1  S  SO2
  13  14  16   1109.5   460.2109.5  

Re: [gmx-users] Annealing--Fatal Error message can't be right.

[Justin A. Lemkul]

William Welch wrote:

Dear kind helpers,
I am using GROMACS 4.0.5.  I cannot find an answer to my exact problem 
in the archives.  I am getting the error message "not enough annealing 
values 2 for 1 group"  but I do not have 2 values specified for 
annealing--not for any of the variables. I tried reading the source code 
in the file specified in the error message, but I don't know what all 
the variables are.  I can't figure out where it thinks I have 2 values 
specified. My annealing section follows what is given in the manual.   I 
am using a simple mdp file adapted from the the tutorial files which is 
as follows:



title   =  Yo
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.001 ; ps !
nsteps  =  48 ; total 500 ps.
nstcomm =  1
nstxout =  50
nstvout =  100
nstfout =  0
nstlog  =  100
nstenergy   =  100
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
pbc =  xyz
; Annealing
annealing   = single periodic
annealing_time  = 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80
annealing_points= 17
annealing_temp  = 300 330 360 390 420 450 480 510 480 450 420 390 
360 330 300 300 300

; Isotropic pressure coupling is now on
Pcoupl  = berendsen
Pcoupltype  = isotropic
compressibility = 4.5e-5
ref_p   =  0.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  350.0
gen_seed=  173529

I've tried turning on Tcoupl and specifying the system as a group, which 
requires a reference temperature and a time constant. I don't think 
annealing and coupling to a bath makes sense, but when I do it I just 
get the same error.

Certainly it there is some simple issue?


Several, actually.

1. You need to use some sort of thermostat, or else nothing is controlling the 
temperature.


2. You haven't defined any tc-grps, but you're implicitly creating two groups 
(based on "annealing = single periodic").  This is where the fatal error is 
coming from - 2 annealing groups, but one tc-grp (System, implicitly, since you 
haven't defined any).


3. "annealing_points" is not a real keyword, but "annealing_npoints" is.

4. You're generating velocities at 350 K, but starting annealing at 300 K.  This 
is not an error as such, but it's probably going to affect how well you move 
through the target temperatures.


There is an example of proper annealing usage in the online manual:

http://manual.gromacs.org/current/online/mdp_opt.html#sa

-Justin


Will Welch



--


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] Annealing--Fatal Error message can't be right.

[William Welch]

Dear kind helpers,
I am using GROMACS 4.0.5.  I cannot find an answer to my exact problem in
the archives.  I am getting the error message "not enough annealing values 2
for 1 group"  but I do not have 2 values specified for annealing--not for
any of the variables. I tried reading the source code in the file specified
in the error message, but I don't know what all the variables are.  I can't
figure out where it thinks I have 2 values specified. My annealing section
follows what is given in the manual.   I am using a simple mdp file adapted
from the the tutorial files which is as follows:


title   =  Yo
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.001 ; ps !
nsteps  =  48 ; total 500 ps.
nstcomm =  1
nstxout =  50
nstvout =  100
nstfout =  0
nstlog  =  100
nstenergy   =  100
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
pbc =  xyz
; Annealing
annealing   = single periodic
annealing_time  = 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80
annealing_points= 17
annealing_temp  = 300 330 360 390 420 450 480 510 480 450 420 390 360
330 300 300 300
; Isotropic pressure coupling is now on
Pcoupl  = berendsen
Pcoupltype  = isotropic
compressibility = 4.5e-5
ref_p   =  0.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  350.0
gen_seed=  173529

I've tried turning on Tcoupl and specifying the system as a group, which
requires a reference temperature and a time constant. I don't think
annealing and coupling to a bath makes sense, but when I do it I just get
the same error.
Certainly it there is some simple issue?
Will Welch
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Re: [gmx-users] PRODRG

[Justin A. Lemkul]

The OP's question is easily answered by referring to the PRODRG FAQ in dealing 
with proper protonation.


As for Antechamber and the like, these are good tools, but do not produce 
GROMOS-compatible topologies, if that is indeed the underlying goal.  We've done 
thorough analysis of various QM calculation methods for GROMOS charges, and none 
of them produce completely satisfactory topologies.  Antechamber, Spartan, 
Gaussian, etc are good for initial charge calculations, but IMHO do not qualify 
as an "end result" for GROMOS parameterization due to the empirical refinement 
used in the force field derivation.  All of that makes GROMOS parameterization 
somewhat tricky, and hence why force field choice is so incredibly important 
when designing projects... ;)


-Justin

TJ Mustard wrote:



Yes I would recommend acpype.

On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote:

 > I think that is better to use antechamber tools.
 >
 >
 > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
 > >> Dear Users
 > >>
 > >> I am using PRODRG to make topology for my drug
 > >> It addes Hydrogenes but in wrong way.
 > >> My Nitrogen atom is bonded to 2 Carbos,
 > >> and PRODRG addes 2 Hydrogenes to it .
 > >> Please let me know how can I do.
 > >> Thanks in advance
 > >
 > > This is not really the forum to get help about that. You need to read
 > > how to PRODRG needs input, and supply something it can deal with. Then
 > > do a whole bunch more work testing what it produced.
 > >
 > > Mark
 > > --
 > > 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!
 > > Please don't post (un)subscribe requests to the list. Use the
 > > www interface or send it to gmx-users-requ...@gromacs.org.
 > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 > >
 >
 >
 > --
 > Jorge R. Quintero
 > Químico
 > Universidad Industrial de Santander
 > Bucaramanga, Santander - Colombia
 >
 > --
 > 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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 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >

 


TJ Mustard
Email: musta...@onid.orst.edu



--


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] PRODRG

[TJ Mustard]

  

  
Yes I would recommend acpype. 



  On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote:
  
  > I think that is better to use antechamber tools.
  >
  >
  > > On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
  > >> Dear Users
  > >>
  > >> I am using PRODRG to make topology for my drug
  > >> It addes Hydrogenes but in wrong way.
  > >> My Nitrogen atom is bonded to 2 Carbos,
  > >> and PRODRG addes 2 Hydrogenes to it .
  > >> Please let me know how can I do.
  > >> Thanks in advance
  > >
  > > This is not really the forum to get help about that. You need to read
  > > how to PRODRG needs input, and supply something it can deal with. Then
  > > do a whole bunch more work testing what it produced.
  > >
  > > Mark
  > > --
  > > gmx-users mailing list    gmx-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!
  > > Please don't post (un)subscribe requests to the list. Use the
  > > www interface or send it to gmx-users-requ...@gromacs.org.
  > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  > >
  >
  >
  > --
  > Jorge R. Quintero
  > Químico
  > Universidad Industrial de Santander
  > Bucaramanga, Santander - Colombia
  >
  > --
  > gmx-users mailing list    gmx-users@gromacs.org
  > http://lists.gromacs.org/mailman/listinfo/gmx-users
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  >


 

TJ Mustard
Email: musta...@onid.orst.edu
  

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Re: [gmx-users] PRODRG

[jorge_quintero]

I think that is better to use antechamber tools.


> On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:
>> Dear Users
>>
>> I am using PRODRG to make topology for my drug
>> It addes Hydrogenes but in wrong way.
>> My Nitrogen atom is bonded to 2 Carbos,
>> and PRODRG addes 2 Hydrogenes to it .
>> Please let me know how can I do.
>> Thanks in advance
>
> This is not really the forum to get help about that. You need to read
> how to PRODRG needs input, and supply something it can deal with. Then
> do a whole bunch more work testing what it produced.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>


-- 
Jorge R. Quintero
Químico
Universidad Industrial de Santander
Bucaramanga, Santander - Colombia

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Re: [gmx-users] Dangling phospholipids

[Justin A. Lemkul]

Dr. Ramón Garduño-Juárez wrote:

Dear All,

First of all I want to tank Justin Lemkul and Thomas Piggot for their 
useful comments that helped me to resolve my previous questions 
regarding the construction of a lipid membrane.


Now I would like to post this question to this forum.

I got through placing a putative ion channel into a DPPC bilayer. I 
managed to expand this sytem -> minimize it -> shrink it (several times) 
-> minimize it (several times) until I got an adequate lipid density.


After viewing the final results I noticed that there are several lipid 
molecules that are dangling at the end of the periodic box.


Is this normal, or I did something wrong?. If this is expected, How do I 
get rid of the dangling lipid molecules before I start a MD simulation?




By "dangling" do you mean that they are somewhat isolated from the rest of the 
lipids?  If so, how many are there?  Usually this just indicates that you're not 
done shrinking the membrane back to appropriate dimensions.  The final box 
vectors achieved through shrinking should usually be fairly close to the 
original dimensions of the system.  If this is not the case, then you're not 
done building your system.


-Justin


Waiting for your replies...

Sincerely,
Ramon Garduno



--


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] Dangling phospholipids

[Dr. Ramón Garduño-Juárez]

Dear All,

First of all I want to tank Justin Lemkul and Thomas Piggot for their 
useful comments that helped me to resolve my previous questions 
regarding the construction of a lipid membrane.


Now I would like to post this question to this forum.

I got through placing a putative ion channel into a DPPC bilayer. I 
managed to expand this sytem -> minimize it -> shrink it (several times) 
-> minimize it (several times) until I got an adequate lipid density.


After viewing the final results I noticed that there are several lipid 
molecules that are dangling at the end of the periodic box.


Is this normal, or I did something wrong?. If this is expected, How do I 
get rid of the dangling lipid molecules before I start a MD simulation?


Waiting for your replies...

Sincerely,
Ramon Garduno
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Re: [gmx-users] PRODRG

[Mark Abraham]

On 10/02/2011 3:40 AM, mohsen ramezanpour wrote:

Dear Users

I am using PRODRG to make topology for my drug
It addes Hydrogenes but in wrong way.
My Nitrogen atom is bonded to 2 Carbos,
and PRODRG addes 2 Hydrogenes to it .
Please let me know how can I do.
Thanks in advance


This is not really the forum to get help about that. You need to read 
how to PRODRG needs input, and supply something it can deal with. Then 
do a whole bunch more work testing what it produced.


Mark
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[gmx-users] PRODRG

[mohsen ramezanpour]

Dear Users

I am using PRODRG to make topology for my drug
It addes Hydrogenes but in wrong way.
My Nitrogen atom is bonded to 2 Carbos,
and PRODRG addes 2 Hydrogenes to it .
Please let me know how can I do.
Thanks in advance
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Re: [gmx-users] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water

[wezhao]

Hi XAvier,

Thanks for your help! I will try it now.
Have a great day!
Wei

>
> Hi Wei,
>
> What you need here is to increase the rdd to 1.4/1.5 nm. You can do that
> using the -rdd option of mdrun.
>
> Turning pme on would have no effect.
>
> XAvier.
>
> On Feb 8, 2011, at 20:56, wez...@ucalgary.ca wrote:
>
>> Dear All,
>>
>> I have performed a simulation of POPC with polarisable water model in
>> presence of 0.2 mol CaCl2 based on MARTINI CG model. I used shift for
>> the
>> electrostatic interactions and the job was done on a 8-core node with
>> domain decomposition 2 2 2. The lipid bilayer consists of 512 lipid and
>> 16000 water. However, the simulation crashed after about 100 ns.
>>
>> The error message is given by:
>> DD  step 5103999 load imb.: force  5.1%
>>
>>   Step   Time Lambda
>>5104000   102080.00.0
>>
>>   Energies (kJ/mol)
>>   Bond   G96AngleLJ (SR)   Coulomb (SR)
>> Potential
>>1.18271e+046.29597e+04   -4.34519e+05   -3.22701e+05
>> -6.82433e+05
>>Kinetic En.   Total EnergyTemperature Pressure (bar)  Cons. rmsd
>> ()
>>1.66874e+05   -5.15560e+053.10498e+021.50257e+01
>> 1.85079e-04
>>
>>
>> Not all bonded interactions have been properly assigned to the domain
>> decomposition cells
>>
>> A list of missing interactions:
>>G96Angle of  19936 missing  1
>>
>> Molecule type 'POPC'
>> the first 10 missing interactions, except for exclusions:
>>G96Angle atoms456  global  3696  3697  3698
>>
>> ---
>> Program mdrun_s_mpi, VERSION 4.0.7
>> Source code file: domdec_top.c, line: 341
>>
>> Fatal error:
>> 1 of the 56736 bonded interactions could not be calculated because some
>> atoms involved moved further apart than the multi-body cut-off distance
>> (1
>> nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for
>> pairs
>> and tabulated bonds also see option -ddcheck
>>
>> I turned on PME for testing, but it crashed within 1 ns. Could somebody
>> give me some suggestion on how to solve this problem?
>> Thanks!
>>
>> Wei Zhao
>>
>>
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>


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Re: [gmx-users] pull code

[Justin A. Lemkul]

Poojari, Chetan wrote:

Hi,

I am using umbrella sampling to pull my peptide (peptide starting from above 
the lipid bilayer) into the hydrophobic core of the lipid bilayer.

Following are my inputs i have used:

title   = Umbrella pulling simulation
define  = -DPOSRES_LIPID
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 25; 500 ps
nstcomm = 1
.
.
; Pull code
pull= umbrella
pull_geometry   = direction
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = POPC
pull_group1 = Protein
pull_vec1   = 0.0 0.0 -1.0
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2


After running the this step:  grompp -f md_pull.mdp -c npt.gro -p topol.top -n 
index.ndx -t npt.cpt -o pull.tpr

i get grompp output as such:

Pull group  natoms  pbc atom  distance at start reference at t=0
   0  6656  3433
   1   10553  -4.132-4.132

I am starting to pull my peptide from 1nm above the upper leaf headgroup. I am 
using POPC lipids and distance between 2 adjacent headgroups seem to be around 
4.2 nm.

I want the peptide to be pulled into the bilayer till the lower leaf lipid 
headgroups, but the peptide is being pulled only till middle of the hydrophobic 
core of the bilayer.

Please can I know what might be the problem ?



Either you're (1) not pulling for sufficient time, (2) not pulling hard enough, 
or (3) the physical properties of the system don't allow for such a position.


For (2), using a harmonic potential to try to force a peptide into a membrane is 
probably not a great idea.  A constraint force is probably better.  For (3), 
what does "POSRES_LIPID" refer to?  Are you keeping the lipids too rigid by 
doing so?




While viewing the conf.*gro file outputed  from the traj. (after extracting the 
frames), i found few lipid molecules to be broken. Please can I know if there 
is a way to avoid these broken structures??? Is there a possibility that I am 
not able to pull the peptide into the lower leaf head group due to these broken 
lipid structures?




Please become comfortable with the concept of periodic boundary conditions.

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

-Justin




Any suggestions will be helpful.


Kind regards,
chetan.



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt




--


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] pull code

[Poojari, Chetan]

Hi,

I am using umbrella sampling to pull my peptide (peptide starting from above 
the lipid bilayer) into the hydrophobic core of the lipid bilayer.

Following are my inputs i have used:

title   = Umbrella pulling simulation
define  = -DPOSRES_LIPID
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 25; 500 ps
nstcomm = 1
.
.
; Pull code
pull= umbrella
pull_geometry   = direction
pull_dim= N N Y
pull_start  = yes   ; define initial COM distance > 0
pull_ngroups= 1
pull_group0 = POPC
pull_group1 = Protein
pull_vec1   = 0.0 0.0 -1.0
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2


After running the this step:  grompp -f md_pull.mdp -c npt.gro -p topol.top -n 
index.ndx -t npt.cpt -o pull.tpr

i get grompp output as such:

Pull group  natoms  pbc atom  distance at start reference at t=0
   0  6656  3433
   1   10553  -4.132-4.132

I am starting to pull my peptide from 1nm above the upper leaf headgroup. I am 
using POPC lipids and distance between 2 adjacent headgroups seem to be around 
4.2 nm.

I want the peptide to be pulled into the bilayer till the lower leaf lipid 
headgroups, but the peptide is being pulled only till middle of the hydrophobic 
core of the bilayer.

Please can I know what might be the problem ?


While viewing the conf.*gro file outputed  from the traj. (after extracting the 
frames), i found few lipid molecules to be broken. Please can I know if there 
is a way to avoid these broken structures??? Is there a possibility that I am 
not able to pull the peptide into the lower leaf head group due to these broken 
lipid structures?




Any suggestions will be helpful.


Kind regards,
chetan.



Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt


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Re: [gmx-users] solvation_box_preparation

[Justin A. Lemkul]

shahid nayeem wrote:

I ran normal MD and it runs fine. Today I used six 10ps MD keeping
temperature 300 K and each time gradually increasing pressure from 1
bar to 5 bar to 25, 50, 75 and then 100bar. It all ran successfully.
Thereafter doing simulated annealing for cooling and heating and
equilibration. It all ran successfully without any LINC warning. But
should I trust this box because you said parameters assigned by prodrg
are none-sense.


I've made my thoughts on that matter pretty clear, I think.  You have to justify 
to reviewers that your parameters are accurate.  We recently published a paper 
detailing the artifacts that can arise from using unrefined PRODRG topologies; 
the incorrect results are quite pronounced.  You need to derive suitable charges 
in conjunction with sensible charge groups.  Garbage in, garbage out.


-Justin


shahid Nayeem

On Wed, Feb 9, 2011 at 5:26 PM, Justin A. Lemkul  wrote:


shahid nayeem wrote:

Hi Justin
Thanks a lot.
I tried doing energy minimization and th lowering emtotal to 200 and
the system converged to
Steepest Descents converged to Fmax < 200 in 1411 steps
Potential Energy  = -3.9063050e+05
Maximum force =  1.3442458e+02 on atom 927
Norm of force =  1.4758101e+01

OK, so energy minimization was fine.


 For equilibration of solvation box I am following a biophys j paper
in which protocol for urea box preparation is given. A simulated
annealing under high pressure (ref_p=100) to cool system from 300 to
0K thereafter heating back to 300K at ref_p=1. Again 1ns MD at same
condition. If this way is harsh treatment of system then suggest me
the way out.
My sa.mdp sa_hot.mdp and sa_equilibriation.mdp as well as chaps.itp
are attached with this mail

There's nothing obviously wrong with the .mdp file.  Have you tried running
"normal" MD to check for stability?  I suggested that before, and I'm still
curious.

Also, your CHAPS topology makes no sense.  The haphazard charge assignment
and nonsensical charge groups indicate to me that PRODRG has done its usual
job of assigning funny parameters.  Even if you could get the simulations to
run, they shouldn't be trusted, and bad parameters could well be the source
of your problem.  Parameterization is time-consuming and difficult, but so
is generated quality, usable data :)

-Justin


Shahid Nayeem
On Mon, Jan 31, 2011 at 9:47 AM, Justin A. Lemkul  wrote:

shahid nayeem wrote:

Please tell me where I am wrong. I downloaded pdb of chaps and used
prodrg server to get .itp and .gro file. Then I checked .itp for any
missing charge and I found it correct. Then I created 6.0x6.0x6.0 box

PRODRG doesn't have a problem of missing charges.  It provides
notoriously
incorrect charges.


with genbox inserting 7 molecules of chaps.gro. Then again using
genbox and -maxsol I put 510 spc.itp in the box to get a density
approaching 1. Then I did steepest descent energy minimization with
constraints = none, for emtotal=2000 and emstep=3000. Up to this the

These settings make no sense.  An emtol of 2000 is very high, and emstep
of
3000 is total nonsense.  How well did you EM converge?  What were the
values
of the potential energy and maximum force?


gromacs runs fine. when I start simulated annealing for cooling at
high pressure with constraint = all_bonds the programme gives fatal
error linc warning and stops. If I do energy minimization with
constraint =all_bonds then also with some error of linc wrning the
minimization is completed. When I do minimization without adding water
then there is no linc warning and minimization is completed but with
final positive potential energy. Then as suggested by Justin I used
smaller box and there also in simulated annealing stage the system
gives linc warning and the programme stops with fatal error. Please
tell me where I am wrong.

How about simplifying the problem.  Does the system run under normal
conditions?  In other words, can you run normal MD?  You're treating the
system very harshly with the combination of high pressure and annealing.
 Without seeing your .mdp file for this process, it's impossible to say
how
reasonable your settings are.

It is also possible that your parameters for CHAPS (if they are the
default
ones from PRODRG) are incorrect.  The charges and charge groups nearly
always are. Without seeing them, there's nothing better to offer.

-Justin


shahid nayeem

On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham 
wrote:

On 28/01/2011 3:51 PM, shahid nayeem wrote:

Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with constraint all bonds it starts giving link
warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
94 and 117) and a list of bond thar rotated more than 30 degree almost
atom number belonging to chaps molecule.

You've set up a system that isn't stab

Re: [gmx-users] error in equilibration

[Justin A. Lemkul]

Mark Abraham wrote:

  On 9/02/2011 11:07 PM, shiva birgani wrote:

Dear Justin
I fallowed your tutorial of "Protein-Ligand Complex" to simulate a 
peptide associated with acetic acid. All the step was good but in 
Equilibration phase 1 I encountered with this error


WARNING 1 [file nvt.mdp, line unknown]:
  Unknown left-hand 'continuation' in parameter file

checking input for internal consistency...
calling cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds into constraints...
Excluding 3 bonded neighbours for ACY 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 6648
turning all bonds into constraints...
Excluding 1 bonded neighbours for NA+ 1
turning all bonds into constraints...
Excluding 1 bonded neighbours for CL- 0
turning all bonds into constraints...
NOTE:
  System has non-zero total charge: -9.99e-01



Mark's conclusion is correct.  The tutorial is for version 4.5.3, as stated in 
the introduction.  In addition, you should note here that you're not ready to 
equilibrate.  You've got a half-neutralized system, still with a -1 charge.


-Justin


processing coordinates...
double-checking input for internal consistency...
WARNING 2 [file "topol.top", line 1453]:
  For energy conservation with LINCS, lincs_iter should be 2 or larger.
  You can safely ignore this if your system doesn't have any
  LINCS-constrained bonds;
  for water molecules we normally use the analytical SETTLE algorithm
  instead.
Setting gen_seed to 261405
Velocities were taken from a Maxwell distribution at 300 K

There were 2 warnings

---
Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 1132

Fatal error:
There were 1 error(s) processing your input
---

how should I do correct it?


You're probably using a version of GROMACS that is years older than the 
tutorial, and so will have minor compatibility issues. More recent 
versions offer much better performance.


Mark



--


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] error in equilibration

[Mark Abraham]

On 9/02/2011 11:07 PM, shiva birgani wrote:

Dear Justin
I fallowed your tutorial of "Protein-Ligand Complex" to simulate a 
peptide associated with acetic acid. All the step was good but in 
Equilibration phase 1 I encountered with this error


WARNING 1 [file nvt.mdp, line unknown]:
  Unknown left-hand 'continuation' in parameter file

checking input for internal consistency...
calling cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds into constraints...
Excluding 3 bonded neighbours for ACY 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 6648
turning all bonds into constraints...
Excluding 1 bonded neighbours for NA+ 1
turning all bonds into constraints...
Excluding 1 bonded neighbours for CL- 0
turning all bonds into constraints...
NOTE:
  System has non-zero total charge: -9.99e-01

processing coordinates...
double-checking input for internal consistency...
WARNING 2 [file "topol.top", line 1453]:
  For energy conservation with LINCS, lincs_iter should be 2 or larger.
  You can safely ignore this if your system doesn't have any
  LINCS-constrained bonds;
  for water molecules we normally use the analytical SETTLE algorithm
  instead.
Setting gen_seed to 261405
Velocities were taken from a Maxwell distribution at 300 K

There were 2 warnings

---
Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 1132

Fatal error:
There were 1 error(s) processing your input
---

how should I do correct it?


You're probably using a version of GROMACS that is years older than the 
tutorial, and so will have minor compatibility issues. More recent 
versions offer much better performance.


Mark
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[gmx-users] error in equilibration

[shiva birgani]

Dear Justin
I fallowed your tutorial of "Protein-Ligand Complex" to simulate a peptide
associated with acetic acid. All the step was good but in Equilibration
phase 1 I encountered with this error

WARNING 1 [file nvt.mdp, line unknown]:
  Unknown left-hand 'continuation' in parameter file

checking input for internal consistency...
calling cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
turning all bonds into constraints...
Excluding 3 bonded neighbours for ACY 1
turning all bonds into constraints...
Excluding 2 bonded neighbours for SOL 6648
turning all bonds into constraints...
Excluding 1 bonded neighbours for NA+ 1
turning all bonds into constraints...
Excluding 1 bonded neighbours for CL- 0
turning all bonds into constraints...
NOTE:
  System has non-zero total charge: -9.99e-01

processing coordinates...
double-checking input for internal consistency...
WARNING 2 [file "topol.top", line 1453]:
  For energy conservation with LINCS, lincs_iter should be 2 or larger.
  You can safely ignore this if your system doesn't have any
  LINCS-constrained bonds;
  for water molecules we normally use the analytical SETTLE algorithm
  instead.
Setting gen_seed to 261405
Velocities were taken from a Maxwell distribution at 300 K

There were 2 warnings

---
Program grompp, VERSION 3.3.3
Source code file: grompp.c, line: 1132

Fatal error:
There were 1 error(s) processing your input
---

how should I do correct it?
thanks in advance
Shiva
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Re: [gmx-users] solvation_box_preparation

[Justin A. Lemkul]

shahid nayeem wrote:

Hi Justin
Thanks a lot.
I tried doing energy minimization and th lowering emtotal to 200 and
the system converged to
Steepest Descents converged to Fmax < 200 in 1411 steps
Potential Energy  = -3.9063050e+05
Maximum force =  1.3442458e+02 on atom 927
Norm of force =  1.4758101e+01


OK, so energy minimization was fine.


 For equilibration of solvation box I am following a biophys j paper
in which protocol for urea box preparation is given. A simulated
annealing under high pressure (ref_p=100) to cool system from 300 to
0K thereafter heating back to 300K at ref_p=1. Again 1ns MD at same
condition. If this way is harsh treatment of system then suggest me
the way out.
My sa.mdp sa_hot.mdp and sa_equilibriation.mdp as well as chaps.itp
are attached with this mail


There's nothing obviously wrong with the .mdp file.  Have you tried running
"normal" MD to check for stability?  I suggested that before, and I'm still 
curious.

Also, your CHAPS topology makes no sense.  The haphazard charge assignment and
nonsensical charge groups indicate to me that PRODRG has done its usual job of
assigning funny parameters.  Even if you could get the simulations to run, they
shouldn't be trusted, and bad parameters could well be the source of your
problem.  Parameterization is time-consuming and difficult, but so is generated
quality, usable data :)

-Justin


Shahid Nayeem
On Mon, Jan 31, 2011 at 9:47 AM, Justin A. Lemkul  wrote:


shahid nayeem wrote:

Please tell me where I am wrong. I downloaded pdb of chaps and used
prodrg server to get .itp and .gro file. Then I checked .itp for any
missing charge and I found it correct. Then I created 6.0x6.0x6.0 box

PRODRG doesn't have a problem of missing charges.  It provides notoriously
incorrect charges.


with genbox inserting 7 molecules of chaps.gro. Then again using
genbox and -maxsol I put 510 spc.itp in the box to get a density
approaching 1. Then I did steepest descent energy minimization with
constraints = none, for emtotal=2000 and emstep=3000. Up to this the

These settings make no sense.  An emtol of 2000 is very high, and emstep of
3000 is total nonsense.  How well did you EM converge?  What were the values
of the potential energy and maximum force?


gromacs runs fine. when I start simulated annealing for cooling at
high pressure with constraint = all_bonds the programme gives fatal
error linc warning and stops. If I do energy minimization with
constraint =all_bonds then also with some error of linc wrning the
minimization is completed. When I do minimization without adding water
then there is no linc warning and minimization is completed but with
final positive potential energy. Then as suggested by Justin I used
smaller box and there also in simulated annealing stage the system
gives linc warning and the programme stops with fatal error. Please
tell me where I am wrong.

How about simplifying the problem.  Does the system run under normal
conditions?  In other words, can you run normal MD?  You're treating the
system very harshly with the combination of high pressure and annealing.
 Without seeing your .mdp file for this process, it's impossible to say how
reasonable your settings are.

It is also possible that your parameters for CHAPS (if they are the default
ones from PRODRG) are incorrect.  The charges and charge groups nearly
always are. Without seeing them, there's nothing better to offer.

-Justin


shahid nayeem

On Fri, Jan 28, 2011 at 10:59 AM, Mark Abraham 
wrote:

On 28/01/2011 3:51 PM, shahid nayeem wrote:

Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with constraint all bonds it starts giving link
warning in 0 step with rms 7407.805164, max 66989.116545 (between atom
94 and 117) and a list of bond thar rotated more than 30 degree almost
atom number belonging to chaps molecule.

You've set up a system that isn't stable, but we don't have enough
information to have any idea why. "I tried with new box size" doesn't go
close to describing your method in enough detail for anyone to know where
you went wrong.

See http://www.gromacs.org/Documentation/Terminology/Blowing_Up for
generic
tips

Mark


Please help.
shahid Nayeem

On Thu, Jan 27, 2011 at 7:06 PM, Justin A. Lemkul
 wrote:

shahid nayeem wrote:

Dear All

I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.

Original messge:

I am trying to prepare a solvation box of chaps. After generating .itp
and .gro at ProDrg and thorough check of charges, I started with a box
size of 6x6x6. Energy minimization, simulated annealing (Cooling under
high pressure and again heating at normal pressure) as well as final
equilibration ran smoothly. But finally I get a box where all water
molecules get accumulated in two three small region 

Re: [gmx-users] gen_vel during gradual NVT equilibration

[Erik Marklund]

Why don't you try simulated anealing instead? The you get a continous 
increase of the temprature over time.


Erik

bipin singh skrev 2011-02-09 12.27:

Hi,

I want to run NVT equilibration for a protein molecule and want to 
increase temperature gradually i.e.

from 0 to 300 K over a 20 ps, but i have some doubts regarding this:

1)Whether I should read velocities from previous steps of NVT during 
gradual heating or every time i have to generate velocities for the 
new temperature.

2)Whether the 20ps time is appropriate for this purpose.

--
/
-
Thanks and regards
/Bipin Singh/
/
/
/




--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] gen_vel during gradual NVT equilibration

[Justin A. Lemkul]

bipin singh wrote:

Hi,

I want to run NVT equilibration for a protein molecule and want to 
increase temperature gradually i.e.

from 0 to 300 K over a 20 ps, but i have some doubts regarding this:

1)Whether I should read velocities from previous steps of NVT during 
gradual heating or every time i have to generate velocities for the new 
temperature.


Simulated annealing does this for you, as long as you want linear heating.


2)Whether the 20ps time is appropriate for this purpose.


That's for you to decide, based on what your results indicate.

-Justin



--
/
-
Thanks and regards
/Bipin Singh/
/
/
/



--


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] gen_vel during gradual NVT equilibration

[bipin singh]

Hi,

I want to run NVT equilibration for a protein molecule and want to increase
temperature gradually i.e.
from 0 to 300 K over a 20 ps, but i have some doubts regarding this:

1)Whether I should read velocities from previous steps of NVT during gradual
heating or every time i have to generate velocities for the new temperature.
2)Whether the 20ps time is appropriate for this purpose.

-- 
*
-
Thanks and regards
Bipin Singh
*
*
*
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Re: [gmx-users] OPLS and RB parameters in GROMACS

[sulatha M. S]

Dear Rainer,

Thankyou very much. I read the abstract of this paper and it says torsional
parameters fro alkanes have been updated. I do not have access to full
contents of this paper, so could not get it.
Thanks again.

Sulatha

On Wed, Feb 9, 2011 at 2:27 PM, Rainer Boeckmann <
rainer.boeckm...@biologie.uni-erlangen.de> wrote:

> Dear Sulatha,
>
> these are probably the more recent parameters from
>
> Price, M. L. P., D. Ostrovsky, and W. L. Jorgensen. 2001. Gas-phase and
> liquid-state properties of
> 8esters, nitriles, and nitro compounds with the opls-aa force field. J.
> Comput. Chem. 22:1340–
> 1352.
>
> Best
> Rainer
>
> On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote:
>
> I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121,
> 20, 4831, 1999), the aliphatic torsional parameters are the same as those
> from 1996. here are the values,
>
>
>V1
> V2V3 (kcal/mol)
> CT-CT-CT-CT  1.740   -0.157 0.279
>
> HC-CT-CT-CT  0.0000.0000.366
>
> HC-CT-CT-HC 0.000 0.000   0.318
>
>
> Values calculated from the equation given in p.62 of the manual in kJ/mol
> are
>
>  c0   c1
>   c2 c3
> CT-CT-CT-CT 3.56686-1.88907
> 0.65688-2.33467
>
> HC-CT-CT-CT  0.66526   1.99577
> 0.000 -2.66102
>
> HC-CT-CT-HC 0.76567-2.29702   0.000
> -3.06269
>
> and the values given in ffoplsaabon.itp are:
>
> CT-CT-CT-CT 2.9288-1.46440.2092
>   -1.6736
>
> HC-CT-CT-CT 0.6276   1.88280
> 0.000  -2.5104
>
> HC-CT-CT-HC 0.62761.8828
> 0.000   -2.5104
>
> So there is a difference. Which of these is correct ? Any help is highly
> appreciated.
>
> Sulatha
>
>
>
> On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch  wrote:
>
>> There is no error. The alkane dihedral parameters were updated in 1999,
>> and differ from those originally published in 1996.
>>
>> Andrew
>>
>> On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S  wrote:
>>
>>> Hi all,
>>>
>>> Hi
>>>
>>>
>>>
>>> I've converted the OPLS-AA torsional potential parameters for the
>>>
>>> alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
>>>
>>> C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
>>>
>>> OPLS format given in Jorgensen et al, JACS 118, 11225 (1996)
>>>
>>> to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found
>>>
>>> that the calculated values are different.
>>>
>>>
>>>
>>> A previous post to the gmx-users mailing list on March 27, 2008,
>>>
>>> pointed out this issue for the H-C-C-H torsional potential but there was no 
>>> response to that.
>>>
>>>
>>>
>>> Does anyone know if there is an error in the ffoplsaabon.itp file? Or
>>>
>>> is there a newer set of OPLS-AA parameters?
>>>
>>>
>>>
>>> For the OPLS-AA parameters (in kcal/mol), I used:
>>>
>>>
>>>
>>> dihedral  V1  V2 V3
>>>
>>> C-C-C-C1.740  -0.157 0.279
>>>
>>> C-C-C-H 0.0  0.00.366
>>>
>>> H-C-C-H 0.0  0.00.318
>>>
>>>
>>>
>>> from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:
>>>
>>>
>>>
>>> dihedral  C0  C1 C2   C3
>>>
>>> C-C-C-C3.56686   -1.889076   0.65688   -2.33467
>>>
>>> C-C-C-H 0.66526   1.99577 0.0   -2.661024
>>>
>>> H-C-C-H 0.76567   -2.297020.0   -3.06269
>>>
>>>
>>>
>>> the parameters in the ffoplsaabon.itp file are:
>>>
>>>
>>>
>>> dihedral  C0  C1 C2   C3
>>>
>>> C-C-C-C   2.9288  -1.4644  0.2092 -1.6736
>>>
>>> C-C-C-H   0.6276   1.882800.0   -2.5104
>>>
>>> H-C-C-H   0.6276   1.8828  0.0   -2.5104
>>>
>>>
>>>
>>> Thankyou for any clarification.
>>>
>>> Sulatha
>>>
>>> --
>>> 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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>>>
>>
>>
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Re: [gmx-users] add force field

[lina zhao]

I do believe so. ^_^

it works beautifully with the newly-added force field.

Thanks,

lina

On Wed, Feb 9, 2011 at 5:11 PM, Mark Abraham wrote:

>  On 9/02/2011 7:47 PM, lina zhao wrote:
>
>
> Hi, it works
>
> before I thought it might share some similarity with 4.0.7 which some bash
> file helps to update the ff information.
>
>
> The mechanism changed in 4.5. Now "forcefield.*" files do something
> significant. Look at the contents and see.
>
> Mark
>
>
> Thanks,
>
> lina
>
>
>
>
> On Wed, Feb 9, 2011 at 4:02 PM, David van der Spoel 
> wrote:
>
>>  On 2011-02-09 08.56, lina zhao wrote:
>>
>>> Hi,
>>>
>>> Anyone has successfully tried to add some new force field in the default
>>> force field (in 4.5)
>>>
>>> so pdb2gmx can show up the (newly-added) force field which will also be
>>> recognized by gromacs,
>>>
>>> Thanks,
>>>
>>> lina
>>>
>>>   Yes it's easy technically.
>> Just copy e.g. oplsaa.ff to new.ff and edit the files in that directory
>> (not easy).
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>>  --
>> 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!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] OPLS and RB parameters in GROMACS

[Rainer Boeckmann]

Dear Sulatha,

these are probably the more recent parameters from

Price, M. L. P., D. Ostrovsky, and W. L. Jorgensen. 2001. Gas-phase and 
liquid-state properties of
8esters, nitriles, and nitro compounds with the opls-aa force field. J. Comput. 
Chem. 22:1340–
1352.

Best
Rainer

On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote:

> I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, 
> 4831, 1999), the aliphatic torsional parameters are the same as those from 
> 1996. here are the values,
>  
> 
>V1V2   
>  V3 (kcal/mol)
> CT-CT-CT-CT  1.740   -0.157 0.279
> 
> HC-CT-CT-CT  0.0000.0000.366
> 
> HC-CT-CT-HC 0.000 0.000   0.318
> 
> 
> Values calculated from the equation given in p.62 of the manual in kJ/mol are 
> 
>  c0   c1  
>  c2 c3
> CT-CT-CT-CT 3.56686-1.889070.65688
> -2.33467
> 
> HC-CT-CT-CT  0.66526   1.995770.000   
>   -2.66102
> 
> HC-CT-CT-HC 0.76567-2.29702   0.000   
>   -3.06269
> 
> and the values given in ffoplsaabon.itp are:
> 
> CT-CT-CT-CT 2.9288-1.46440.2092   
> -1.6736
> 
> HC-CT-CT-CT 0.6276   1.88280   0.000  
> -2.5104
> 
> HC-CT-CT-HC 0.62761.8828   0.000  
>  -2.5104
> 
> So there is a difference. Which of these is correct ? Any help is highly 
> appreciated.
> 
> Sulatha
> 
> 
> 
> On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch  wrote:
> There is no error. The alkane dihedral parameters were updated in 1999, and 
> differ from those originally published in 1996.
> 
> Andrew
> 
> On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S  wrote:
> Hi all,
> Hi
>  
> I've converted the OPLS-AA torsional potential parameters for the
> alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
> C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
> OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) 
> to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found
> that the calculated values are different.
>  
> A previous post to the gmx-users mailing list on March 27, 2008,
> pointed out this issue for the H-C-C-H torsional potential but there was no 
> response to that.
>  
> Does anyone know if there is an error in the ffoplsaabon.itp file? Or
> is there a newer set of OPLS-AA parameters?
>  
> For the OPLS-AA parameters (in kcal/mol), I used:
>  
> dihedral  V1  V2 V3
> C-C-C-C1.740  -0.157 0.279
> C-C-C-H 0.0  0.00.366
> H-C-C-H 0.0  0.00.318
>  
> from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:
>  
> dihedral  C0  C1 C2   C3
> C-C-C-C3.56686   -1.889076   0.65688   -2.33467
> C-C-C-H 0.66526   1.99577 0.0   -2.661024
> H-C-C-H 0.76567   -2.297020.0   -3.06269
>  
> the parameters in the ffoplsaabon.itp file are:
>  
> dihedral  C0  C1 C2   C3
> C-C-C-C   2.9288  -1.4644  0.2092 -1.6736
> C-C-C-H   0.6276   1.882800.0   -2.5104
> H-C-C-H   0.6276   1.8828  0.0   -2.5104
> 
> 
> Thankyou for any clarification.
> 
> Sulatha
> 
> --
> 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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> 
> 
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> 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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> 
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> 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/Suppor

Re: [gmx-users] OPLS and RB parameters in GROMACS

[Rainer Boeckmann]

Dear Sulatha,

these are probably the more recent parameters from

Price, M. L. P., D. Ostrovsky, and W. L. Jorgensen. 2001. Gas-phase and 
liquid-state properties of
8esters, nitriles, and nitro compounds with the opls-aa force field. J. Comput. 
Chem. 22:1340–
1352.

Best
Rainer



On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote:

> I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, 
> 4831, 1999), the aliphatic torsional parameters are the same as those from 
> 1996. here are the values,
>  
> 
>V1V2   
>  V3 (kcal/mol)
> CT-CT-CT-CT  1.740   -0.157 0.279
> 
> HC-CT-CT-CT  0.0000.0000.366
> 
> HC-CT-CT-HC 0.000 0.000   0.318
> 
> 
> Values calculated from the equation given in p.62 of the manual in kJ/mol are 
> 
>  c0   c1  
>  c2 c3
> CT-CT-CT-CT 3.56686-1.889070.65688
> -2.33467
> 
> HC-CT-CT-CT  0.66526   1.995770.000   
>   -2.66102
> 
> HC-CT-CT-HC 0.76567-2.29702   0.000   
>   -3.06269
> 
> and the values given in ffoplsaabon.itp are:
> 
> CT-CT-CT-CT 2.9288-1.46440.2092   
> -1.6736
> 
> HC-CT-CT-CT 0.6276   1.88280   0.000  
> -2.5104
> 
> HC-CT-CT-HC 0.62761.8828   0.000  
>  -2.5104
> 
> So there is a difference. Which of these is correct ? Any help is highly 
> appreciated.
> 
> Sulatha
> 
> 
> 
> On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch  wrote:
> There is no error. The alkane dihedral parameters were updated in 1999, and 
> differ from those originally published in 1996.
> 
> Andrew
> 
> On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S  wrote:
> Hi all,
> Hi
>  
> I've converted the OPLS-AA torsional potential parameters for the
> alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation),
> C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the
> OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) 
> to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found
> that the calculated values are different.
>  
> A previous post to the gmx-users mailing list on March 27, 2008,
> pointed out this issue for the H-C-C-H torsional potential but there was no 
> response to that.
>  
> Does anyone know if there is an error in the ffoplsaabon.itp file? Or
> is there a newer set of OPLS-AA parameters?
>  
> For the OPLS-AA parameters (in kcal/mol), I used:
>  
> dihedral  V1  V2 V3
> C-C-C-C1.740  -0.157 0.279
> C-C-C-H 0.0  0.00.366
> H-C-C-H 0.0  0.00.318
>  
> from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as:
>  
> dihedral  C0  C1 C2   C3
> C-C-C-C3.56686   -1.889076   0.65688   -2.33467
> C-C-C-H 0.66526   1.99577 0.0   -2.661024
> H-C-C-H 0.76567   -2.297020.0   -3.06269
>  
> the parameters in the ffoplsaabon.itp file are:
>  
> dihedral  C0  C1 C2   C3
> C-C-C-C   2.9288  -1.4644  0.2092 -1.6736
> C-C-C-H   0.6276   1.882800.0   -2.5104
> H-C-C-H   0.6276   1.8828  0.0   -2.5104
> 
> 
> Thankyou for any clarification.
> 
> Sulatha
> 
> --
> 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!
> Please don't post (un)subscribe requests to the list. Use the
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> --
> 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
> 
> -- 
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> 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.
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Re: [gmx-users] add force field

[Mark Abraham]

On 9/02/2011 7:47 PM, lina zhao wrote:


Hi, it works

before I thought it might share some similarity with 4.0.7 which some 
bash file helps to update the ff information.


The mechanism changed in 4.5. Now "forcefield.*" files do something 
significant. Look at the contents and see.


Mark


Thanks,

lina




On Wed, Feb 9, 2011 at 4:02 PM, David van der Spoel 
mailto:sp...@xray.bmc.uu.se>> wrote:


On 2011-02-09 08.56, lina zhao wrote:

Hi,

Anyone has successfully tried to add some new force field in
the default
force field (in 4.5)

so pdb2gmx can show up the (newly-added) force field which
will also be
recognized by gromacs,

Thanks,

lina

Yes it's easy technically.
Just copy e.g. oplsaa.ff to new.ff and edit the files in that
directory (not easy).

-- 
David van der Spoel, Ph.D., Professor of Biology

Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se 
http://folding.bmc.uu.se
-- 
gmx-users mailing list gmx-users@gromacs.org


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Re: [gmx-users] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water

[XAvier Periole]

Hi Wei,

What you need here is to increase the rdd to 1.4/1.5 nm. You can do that using 
the -rdd option of mdrun. 

Turning pme on would have no effect. 

XAvier. 

On Feb 8, 2011, at 20:56, wez...@ucalgary.ca wrote:

> Dear All,
> 
> I have performed a simulation of POPC with polarisable water model in
> presence of 0.2 mol CaCl2 based on MARTINI CG model. I used shift for the
> electrostatic interactions and the job was done on a 8-core node with
> domain decomposition 2 2 2. The lipid bilayer consists of 512 lipid and
> 16000 water. However, the simulation crashed after about 100 ns.
> 
> The error message is given by:
> DD  step 5103999 load imb.: force  5.1%
> 
>   Step   Time Lambda
>5104000   102080.00.0
> 
>   Energies (kJ/mol)
>   Bond   G96AngleLJ (SR)   Coulomb (SR)  Potential
>1.18271e+046.29597e+04   -4.34519e+05   -3.22701e+05   -6.82433e+05
>Kinetic En.   Total EnergyTemperature Pressure (bar)  Cons. rmsd ()
>1.66874e+05   -5.15560e+053.10498e+021.50257e+011.85079e-04
> 
> 
> Not all bonded interactions have been properly assigned to the domain
> decomposition cells
> 
> A list of missing interactions:
>G96Angle of  19936 missing  1
> 
> Molecule type 'POPC'
> the first 10 missing interactions, except for exclusions:
>G96Angle atoms456  global  3696  3697  3698
> 
> ---
> Program mdrun_s_mpi, VERSION 4.0.7
> Source code file: domdec_top.c, line: 341
> 
> Fatal error:
> 1 of the 56736 bonded interactions could not be calculated because some
> atoms involved moved further apart than the multi-body cut-off distance (1
> nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs
> and tabulated bonds also see option -ddcheck
> 
> I turned on PME for testing, but it crashed within 1 ns. Could somebody
> give me some suggestion on how to solve this problem?
> Thanks!
> 
> Wei Zhao
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
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Re: [gmx-users] add force field

[lina zhao]

Hi, it works

before I thought it might share some similarity with 4.0.7 which some bash
file helps to update the ff information.

Thanks,

lina




On Wed, Feb 9, 2011 at 4:02 PM, David van der Spoel wrote:

> On 2011-02-09 08.56, lina zhao wrote:
>
>> Hi,
>>
>> Anyone has successfully tried to add some new force field in the default
>> force field (in 4.5)
>>
>> so pdb2gmx can show up the (newly-added) force field which will also be
>> recognized by gromacs,
>>
>> Thanks,
>>
>> lina
>>
>>  Yes it's easy technically.
> Just copy e.g. oplsaa.ff to new.ff and edit the files in that directory
> (not easy).
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> 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!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] add force field

[David van der Spoel]

On 2011-02-09 08.56, lina zhao wrote:

Hi,

Anyone has successfully tried to add some new force field in the default
force field (in 4.5)

so pdb2gmx can show up the (newly-added) force field which will also be
recognized by gromacs,

Thanks,

lina


Yes it's easy technically.
Just copy e.g. oplsaa.ff to new.ff and edit the files in that directory 
(not easy).


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
gmx-users mailing listgmx-users@gromacs.org
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