[gmx-users] mdrun_mpi -rerun bonded interactions

[Vasileios Tatsis]

Dear GRomacs users,

I am using the -rerun option of mdrun to read the coordinates of a trajectory 
and to compute the potential energy of a molecule during MD. 

This operation when performed in parallel, using mdrun_mpi, the energy of the 
bonded interactions is not computed. But using one core, with the option -nt 1, 
all interactions are computed. 


I am using the md-vv integrator.


Thanks in advance for your help
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Re: [gmx-users] calculation of density for martini coarse-grained

[mohammad agha]

Dear Prof.

Thank you for your reply.
I'm really sorry for my mistake in writing the density!! my calculated density 
become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?

In the martini_v2.0.itp file, has been written "all particle masses are set to 
72 amu". May I know my mistake, Please?

My solvent molecules aren't named "SOL".

Command lines and terminal outputs:

1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro
output of terminal is:
Output configuration contains 755 atoms in 151 residues
Volume :    1000 (nm^3)
Density    : 15.8111 (g/l)
Number of SOL molecules:  0   
2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 -center 
7.4 7.4 7.4 
Output of terminal:
Read 755 atoms
Volume: 1000 nm^3, corresponds to roughly 45 electrons
No velocities found
    system size :  9.803  9.897  9.978 (nm)
    diameter    : 13.969   (nm)
    center  :  5.239  4.900  4.932 (nm)
    box vectors : 10.000 10.000 10.000 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  :1000.00   (nm^3)
    shift   :  2.161  2.500  2.468 (nm)
new center  :  7.400  7.400  7.400 (nm)
new box vectors : 14.800 14.800 14.800 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :3241.79   (nm^3)

3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr
output of terminal:
NOTE 1 [file topol.top, line 22]:
  System has non-zero total charge: 1.51e+02

3- mdrun -v -deffnm e1 
 
4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551 
output of terminal: 
Output configuration contains 33306 atoms in 32702 residues
Volume : 3241.79 (nm^3)
Density    : 3070.15 (g/l)
Number of SOL molecules:  0   
___
I have a problem about density in step 4 after adding water, again!!!
___
5- grompp -f em.mdp -c 3.gro -p topol.top -o e3.tpr 
output of terminal: 
NOTE 1 [file topol.top, line 22]:
  System has non-zero total charge: 1.51e+02
  
Analysing residue names:
There are: 32702  Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
groups...
Number of degrees of freedom in T-Coupling group rest is 99915.00
This run will generate roughly 49 Mb of data

There was 1 note

6- mdrun -v -deffnm e3


7-  genion -s e3.tpr -o 4.gro -p topol.top -nname cl- -nn 151
output of terminal:
Reading file e3.tpr, VERSION 4.5.4 (single precision)
Using a coulomb cut-off of 1.2 nm
Will try to add 0 NA ions and 151 cl- ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 33306 elements
Group 1 (  Other) has 33306 elements
Group 2 (    CA) has   755 elements
Group 3 (  W) has 32551 elements
Select a group: 3

__

Adding ions was done successfully but in the genion.log file had been written 
"System total charge: 151.000"

__

8- grompp -f em.mdp -c 4.gro -p topol.top -o e4.tpr -maxwarn 1
output of terminal:
WARNING 1 [file topol.top, line 23]:
  151 non-matching atom names
  atom names from topol.top will be used
  atom names from 4.gro will be ignored

Analysing residue names:
There are: 32702  Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into 
groups...
Number of degrees of freedom in T-Coupling group rest is 99915.00
This run will generate roughly 49 Mb of data

There was 1 warning


My topol.top file is:
#include "martini_v2.0.itp"
#include "martini_v2.0_ions.itp"
#include "martini_v2.0_lipids.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ system ]
CA in water

[ molecules ]
CA  151
W   32400
cl- 151
___


Best RegardsSara 


 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Thursday, December 15, 2011 11:19 AM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
 

On 15/12/2011 5:59 PM, mohammad agha wrote: 
Dear Prof.
>May I ask you two questions, Please?
>1- I work with MARTINI force field. I have a surfactant molecule
consists of 5 beads. After I placed 151 surfactants into my
simulation box (cubic) with length of 10 nm, Gromacs reported:
>
>Volume = 1000 nm3
>Density = 15.8111 gr/l
>
>My volume is right: 10 nm * 10 nm * 10 nm = 1000 nm3 =
1000*10e-24 L, but about density, I think

Re: [gmx-users] calculation of density for martini coarse-grained

[Mark Abraham]

On 16/12/2011 1:36 AM, mohammad agha wrote:

Dear Prof.

Thank you for your reply.
I'm really sorry for my mistake in writing the density!! my calculated 
density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?
In the martini_v2.0.itp file, has been written "all particle masses 
are set to 72 amu". May I know my mistake, Please?


My solvent molecules aren't named "SOL".

Command lines and terminal outputs:

1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro
output of terminal is:
Output configuration contains 755 atoms in 151 residues
Volume :1000 (nm^3)
Density: 15.8111 (g/l)
Number of SOL molecules:  0


One possibility is that the Martini force field doesn't have the masses 
set up correctly for genbox to match from the coordinate file. Perhaps 
in share/top/atommass.dat?


2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 
-center 7.4 7.4 7.4

Output of terminal:
Read 755 atoms
Volume: 1000 nm^3, corresponds to roughly 45 electrons
No velocities found
system size :  9.803  9.897  9.978 (nm)
diameter: 13.969   (nm)
center  :  5.239  4.900  4.932 (nm)
box vectors : 10.000 10.000 10.000 (nm)
box angles  :  90.00  90.00  90.00 (degrees)
box volume  :1000.00   (nm^3)
shift   :  2.161  2.500  2.468 (nm)
new center  :  7.400  7.400  7.400 (nm)
new box vectors : 14.800 14.800 14.800 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :3241.79   (nm^3)


So the box volume of 2.gro is not 1000 nm^3.



3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr
output of terminal:
NOTE 1 [file topol.top, line 22]:
  System has non-zero total charge: 1.51e+02

3- mdrun -v -deffnm e1

4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551
output of terminal:
Output configuration contains 33306 atoms in 32702 residues
Volume : 3241.79 (nm^3)
Density: 3070.15 (g/l)
Number of SOL molecules:  0
___
I have a problem about density in step 4 after adding water, again!!!


Could be the same issue - apparently the water is something like three 
times as heavy as normal water (whose density is around 1000g/L).



___
5- grompp -f em.mdp -c 3.gro -p topol.top -o e3.tpr
output of terminal:
NOTE 1 [file topol.top, line 22]:
  System has non-zero total charge: 1.51e+02

Analysing residue names:
There are: 32702  Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and 
splitting into groups...

Number of degrees of freedom in T-Coupling group rest is 99915.00
This run will generate roughly 49 Mb of data

There was 1 note

6- mdrun -v -deffnm e3

7-  genion -s e3.tpr -o 4.gro -p topol.top -nname cl- -nn 151
output of terminal:
Reading file e3.tpr, VERSION 4.5.4 (single precision)
Using a coulomb cut-off of 1.2 nm
Will try to add 0 NA ions and 151 cl- ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 33306 elements
Group 1 (  Other) has 33306 elements
Group 2 (CA) has   755 elements
Group 3 (  W) has 32551 elements
Select a group: 3
__
Adding ions was done successfully but in the genion.log file had been 
written "System total charge: 151.000"


That would be normal before adding ions, and indicative of a problem 
after adding ions, but you haven't made this clear... You say it was 
successful, and then announce that it reports a total charge consistent 
with failure. If genion succeeded in changing some solute to ions, its 
output is very clear about this.



__
8- grompp -f em.mdp -c 4.gro -p topol.top -o e4.tpr -maxwarn 1
output of terminal:
WARNING 1 [file topol.top, line 23]:
  151 non-matching atom names
  atom names from topol.top will be used
  atom names from 4.gro will be ignored


Don't use -maxwarn unless you can write down why it is OK... fix the 
problem. Apparently one file doesn't have the changes to the ions.


Mark



Analysing residue names:
There are: 32702  Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and 
splitting into groups...

Number of degrees of freedom in T-Coupling group rest is 99915.00
This run will generate roughly 49 Mb of data

There was 1 warning

My topol.top file is:
#include "martini_v2.0.itp"
#include "martini_v2.0_ions.itp"
#include "martini_v2.0_lipids.itp"
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ sy

Fw: [gmx-users] Re: submission error

[aiswarya . pawar]

Lina,

I used the same script for mpi ie other than usr/bin/poe I have given 
usr/bin/mpirun I still receive the same errorOn 15/12/2011 4:51 PM, aiswarya pawar wrote:
>
> Hi,
>
>
> When i tried running mdrun without mip i received the same error ie
>
> when i gave mdrun -deffnm md
>
> i got=
> Back Off! I just backed up md.log to ./#md.log.1#
> Getting Loaded...
> Reading file md.tpr, VERSION 4.5.4 (single precision)
> Loaded with Money
>
> p0_23443:  p4_error: interrupt SIGx: 4

The job you ran below with poe did not have the MPI suffix, so I am not 
convinced you are doing appropriate things with appropriate executables. 
Above, a p4_error is consistent with an MPI-enabled executable.

Get an MPI "hello world" program and get it running before worrying 
about GROMACS. Follow the user guide for your cluster. Get your 
MPI-enabled mdrun suffixed with _mpi like the installation guides recommend.

Mark

>
>
> Thanks,
> Aiswarya
>
> On Wed, Dec 14, 2011 at 5:00 PM, aiswarya pawar 
> mailto:aiswarya.pa...@gmail.com>> wrote:
>
> Hi users,
>
> I have a submission script for gromacs mdrun to be used on IBM
> cluster, but i get an error while running it. the script goes like
> this=
>
> #!/bin/sh
> # @ error   = job1.$(Host).$(Cluster).$(Process).err
> # @ output  = job1.$(Host).$(Cluster).$(Process).out
> # @ class = ptask32
> # @ job_type = parallel
> # @ node = 1
> # @ tasks_per_node = 4
> # @ queue
>
> echo "_"
> echo "LOADL_STEP_ID=$LOADL_STEP_ID"
> echo "_"
>
> machine_file="/tmp/machinelist.$LOADL_STEP_ID"
> rm -f $machine_file
> for node in $LOADL_PROCESSOR_LIST
> do
> echo $node >> $machine_file
> done
> machine_count=`cat /tmp/machinelist.$LOADL_STEP_ID|wc -l`
> echo $machine_count
> echo MachineList:
> cat /tmp/machinelist.$LOADL_STEP_ID
> echo "_"
> unset LOADLBATCH
> env  |grep LOADLBATCH
> cd /home/staff/1adf/
> /usr/bin/poe /home/gromacs-4.5.5/bin/mdrun -deffnm
> /home/staff/1adf/md -procs $machine_count -hostfile
> /tmp/machinelist.$LOADL_STEP_ID
> rm /tmp/machinelist.$LOADL_STEP_ID
>
>
> i get an out file as=
> _
> LOADL_STEP_ID=cnode39.97541.0
> _
> 4
> MachineList:
> cnode62
> cnode7
> cnode4
> cnode8
> _
> p0_25108:  p4_error: interrupt SIGx: 4
> p0_2890:  p4_error: interrupt SIGx: 4
> p0_2901:  p4_error: interrupt SIGx: 15
> p0_22760:  p4_error: interrupt SIGx: 15
>
>
> an error file =
>
> Reading file /home/staff/1adf/md.tpr, VERSION 4.5.4 (single precision)
> Sorry couldn't backup /home/staff/1adf/md.log to
> /home/staff/1adf/#md.log.14#
>
> Back Off! I just backed up /home/staff/1adf/md.log to
> /home/staff/1adf/#md.log.14#
> ERROR: 0031-300  Forcing all remote tasks to exit due to exit code
> 1 in task 0
>
> Please anyone can help with this error.
>
> Thanks
>
>
>
>
>
>



Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!

-Original Message-
From: Mark Abraham 
Sender: gmx-users-boun...@gromacs.org
Date: Thu, 15 Dec 2011 17:03:12 
To: Discussion list for GROMACS users
Reply-To: Discussion list for GROMACS users 
Subject: Re: [gmx-users] Re: submission error

-- 
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Re: [gmx-users] calculation of density for martini coarse-grained

[mohammad agha]

thanks for your reply.

Best Regards

Sara



 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Thursday, December 15, 2011 6:31 PM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
 

On 16/12/2011 1:36 AM, mohammad agha wrote: 
Dear Prof.
>
>
>Thank you for your reply.
>I'm really sorry for my mistake in writing the density!! my calculated density 
>become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?
>In the martini_v2.0.itp file, has been written "all particle masses are set to 
>72 amu". May I know my mistake, Please?
>
>
>My solvent molecules aren't named "SOL".
>
>
>Command lines and terminal outputs:
>
>
>1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro
>output of terminal is:
>Output configuration contains 755 atoms in 151 residues
>Volume :    1000 (nm^3)
>Density    : 15.8111 (g/l)
>Number of SOL molecules:  0   
One possibility is that the Martini force field doesn't have the
masses set up correctly for genbox to match from the coordinate
file. Perhaps in share/top/atommass.dat?


2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 -center 
7.4 7.4 7.4 
>Output of terminal:
>Read 755 atoms
>Volume: 1000 nm^3, corresponds to roughly 45 electrons
>No velocities found
>    system size :  9.803  9.897  9.978 (nm)
>    diameter    : 13.969   (nm)
>    center  :  5.239  4.900  4.932 (nm)
>    box vectors : 10.000 10.000 10.000 (nm)
>    box angles  :  90.00  90.00  90.00 (degrees)
>    box volume  :1000.00   (nm^3)
>    shift   :  2.161  2.500  2.468 (nm)
>new center  :  7.400  7.400  7.400 (nm)
>new box vectors : 14.800 14.800 14.800 (nm)
>new box angles  :  90.00  90.00  90.00 (degrees)
>new box volume  :3241.79   (nm^3)
>
So the box volume of 2.gro is not 1000 nm^3.



>3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr
>output of terminal:
>NOTE 1 [file topol.top, line 22]:
>  System has non-zero total charge: 1.51e+02
>
>3- mdrun -v -deffnm e1 
> 
>4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551 
>output of terminal: 
>Output configuration contains 33306 atoms in 32702 residues
>Volume : 3241.79 (nm^3)
>Density    : 3070.15 (g/l)
>Number of SOL molecules:  0   
>___
>I have a problem about density in step 4 after adding water,
again!!!
>
Could be the same issue - apparently the water is something like
three times as heavy as normal water (whose density is around
1000g/L).


___
>5- grompp -f em.mdp -c 3.gro -p topol.top -o e3.tpr 
>output of terminal: 
>NOTE 1 [file topol.top, line 22]:
>  System has non-zero total charge: 1.51e+02
>  
>Analysing residue names:
>There are: 32702  Other residues
>Analysing residues not classified as Protein/DNA/RNA/Water and
splitting into groups...
>Number of degrees of freedom in T-Coupling group rest is
99915.00
>This run will generate roughly 49 Mb of data
>
>There was 1 note
>
>6- mdrun -v -deffnm e3
>
>
>
>7-  genion -s e3.tpr -o 4.gro -p topol.top -nname cl- -nn 151
>output of terminal:
>Reading file e3.tpr, VERSION 4.5.4 (single precision)
>Using a coulomb cut-off of 1.2 nm
>Will try to add 0 NA ions and 151 cl- ions.
>Select a continuous group of solvent molecules
>Group 0 ( System) has 33306 elements
>Group 1 (  Other) has 33306 elements
>Group 2 (    CA) has   755 elements
>Group 3 (  W) has 32551 elements
>Select a group: 3
>
>__
>
>Adding ions was done successfully but in the genion.log file had been written 
>"System total charge: 151.000"
>
That would be normal before adding ions, and indicative of a problem
after adding ions, but you haven't made this clear... You say it was
successful, and then announce that it reports a total charge
consistent with failure. If genion succeeded in changing some solute
to ions, its output is very clear about this.


__
>
>8- grompp -f em.mdp -c 4.gro -p topol.top -o e4.tpr -maxwarn 1
>output of terminal:
>WARNING 1 [file topol.top, line 23]:
>  151 non-matching atom names
>  atom names from topol.top will be used
>  atom names from 4.gro will be ignored
>
Don't use -maxwarn unless you can write down why it is OK... fix the
problem. Apparently one file doesn't have the changes to the ions.

Mark



>Analysing residue names:
>There are: 32702  Other residues
>Analysing residues not classified as Protein/DNA/RNA/Water and
  splitting into groups...
>Numb

Re: [gmx-users] calculation of density for martini coarse-grained

[mohammad agha]

Dear Prof.

Thank you very much.

Excuse me, I am beginner in gromacs and my experience about warnings is low, 
but I think my problem return to this warning:
WARNING: masses and atomic (Van der Waals) radii will be determined
 based on residue and atom names. These numbers can deviate
 from the correct mass and radius of the atom type.

I checked mailing list but I didn't find my answer!
Please help me.

Best Regards

Sara



 From: Mark Abraham 
To: Discussion list for GROMACS users  
Sent: Thursday, December 15, 2011 6:31 PM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
 

On 16/12/2011 1:36 AM, mohammad agha wrote: 
Dear Prof.
>
>
>Thank you for your reply.
>I'm really sorry for my mistake in writing the density!! my calculated density 
>become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?
>In the martini_v2.0.itp file, has been written "all particle masses are set to 
>72 amu". May I know my mistake, Please?
>
>
>My solvent molecules aren't named "SOL".
>
>
>Command lines and terminal outputs:
>
>
>1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro
>output of terminal is:
>Output configuration contains 755 atoms in 151 residues
>Volume :    1000 (nm^3)
>Density    : 15.8111 (g/l)
>Number of SOL molecules:  0   
One possibility is that the Martini force field doesn't have the
masses set up correctly for genbox to match from the coordinate
file. Perhaps in share/top/atommass.dat?


2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 -center 
7.4 7.4 7.4 
>Output of terminal:
>Read 755 atoms
>Volume: 1000 nm^3, corresponds to roughly 45 electrons
>No velocities found
>    system size :  9.803  9.897  9.978 (nm)
>    diameter    : 13.969   (nm)
>    center  :  5.239  4.900  4.932 (nm)
>    box vectors : 10.000 10.000 10.000 (nm)
>    box angles  :  90.00  90.00  90.00 (degrees)
>    box volume  :1000.00   (nm^3)
>    shift   :  2.161  2.500  2.468 (nm)
>new center  :  7.400  7.400  7.400 (nm)
>new box vectors : 14.800 14.800 14.800 (nm)
>new box angles  :  90.00  90.00  90.00 (degrees)
>new box volume  :3241.79   (nm^3)
>
So the box volume of 2.gro is not 1000 nm^3.



>3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr
>output of terminal:
>NOTE 1 [file topol.top, line 22]:
>  System has non-zero total charge: 1.51e+02
>
>3- mdrun -v -deffnm e1 
> 
>4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551 
>output of terminal: 
>Output configuration contains 33306 atoms in 32702 residues
>Volume : 3241.79 (nm^3)
>Density    : 3070.15 (g/l)
>Number of SOL molecules:  0   
>___
>I have a problem about density in step 4 after adding water,
again!!!
>
Could be the same issue - apparently the water is something like
three times as heavy as normal water (whose density is around
1000g/L).


___
>5- grompp -f em.mdp -c 3.gro -p topol.top -o e3.tpr 
>output of terminal: 
>NOTE 1 [file topol.top, line 22]:
>  System has non-zero total charge: 1.51e+02
>  
>Analysing residue names:
>There are: 32702  Other residues
>Analysing residues not classified as Protein/DNA/RNA/Water and
splitting into groups...
>Number of degrees of freedom in T-Coupling group rest is
99915.00
>This run will generate roughly 49 Mb of data
>
>There was 1 note
>
>6- mdrun -v -deffnm e3
>
>
>
>7-  genion -s e3.tpr -o 4.gro -p topol.top -nname cl- -nn 151
>output of terminal:
>Reading file e3.tpr, VERSION 4.5.4 (single precision)
>Using a coulomb cut-off of 1.2 nm
>Will try to add 0 NA ions and 151 cl- ions.
>Select a continuous group of solvent molecules
>Group 0 ( System) has 33306 elements
>Group 1 (  Other) has 33306 elements
>Group 2 (    CA) has   755 elements
>Group 3 (  W) has 32551 elements
>Select a group: 3
>
>__
>
>Adding ions was done successfully but in the genion.log file had been written 
>"System total charge: 151.000"
>
That would be normal before adding ions, and indicative of a problem
after adding ions, but you haven't made this clear... You say it was
successful, and then announce that it reports a total charge
consistent with failure. If genion succeeded in changing some solute
to ions, its output is very clear about this.


__
>
>8- grompp -f em.mdp -c 4.gro -p topol.top -o e4.tpr -maxwarn 1
>output of terminal:
>WARNING 1 [file topol.top, line 23]:
>  151 non-matching atom names
>

Re: [gmx-users] calculation of density for martini coarse-grained

[Justin A. Lemkul]

mohammad agha wrote:

Dear Prof.

Thank you very much.
Excuse me, I am beginner in gromacs and my experience about warnings is 
low, but I think my problem return to this warning:


WARNING: masses and atomic (Van der Waals) radii will be determined
 based on residue and atom names. These numbers can deviate
 from the correct mass and radius of the atom type.



The warning indicates that names may give misleading values for masses and van 
der Waals interactions.  For instance, is "CA" an alpha-carbon, or calcium?  In 
this context, the program reporting the error doesn't know.  Since MARTINI uses 
lots of weird atom names for its structures, the program is warning you that the 
output may be incorrect, or perhaps it may not; hence why it is a warning and 
not an error.


-Justin


I checked mailing list but I didn't find my answer!
Please help me.

Best Regards

Sara

*From:* Mark Abraham 
*To:* Discussion list for GROMACS users 
*Sent:* Thursday, December 15, 2011 6:31 PM
*Subject:* Re: [gmx-users] calculation of density for martini coarse-grained

On 16/12/2011 1:36 AM, mohammad agha wrote:

Dear Prof.

Thank you for your reply.
I'm really sorry for my mistake in writing the density!! my calculated 
density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?
In the martini_v2.0.itp file, has been written "all particle masses 
are set to 72 amu". May I know my mistake, Please?


My solvent molecules aren't named "SOL".

Command lines and terminal outputs:

1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro
output of terminal is:
Output configuration contains 755 atoms in 151 residues
Volume :1000 (nm^3)
Density: 15.8111 (g/l)
Number of SOL molecules:  0  


One possibility is that the Martini force field doesn't have the masses 
set up correctly for genbox to match from the coordinate file. Perhaps 
in share/top/atommass.dat?


2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 
-center 7.4 7.4 7.4

Output of terminal:
Read 755 atoms
Volume: 1000 nm^3, corresponds to roughly 45 electrons
No velocities found
system size :  9.803  9.897  9.978 (nm)
diameter: 13.969   (nm)
center  :  5.239  4.900  4.932 (nm)
box vectors : 10.000 10.000 10.000 (nm)
box angles  :  90.00  90.00  90.00 (degrees)
box volume  :1000.00   (nm^3)
shift   :  2.161  2.500  2.468 (nm)
new center  :  7.400  7.400  7.400 (nm)
new box vectors : 14.800 14.800 14.800 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  :3241.79   (nm^3)


So the box volume of 2.gro is not 1000 nm^3.



3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr
output of terminal:
NOTE 1 [file topol.top, line 22]:
  System has non-zero total charge: 1.51e+02

3- mdrun -v -deffnm e1
 
4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551

output of terminal:
Output configuration contains 33306 atoms in 32702 residues
Volume : 3241.79 (nm^3)
Density: 3070.15 (g/l)
Number of SOL molecules:  0  
___

I have a problem about density in step 4 after adding water, again!!!


Could be the same issue - apparently the water is something like three 
times as heavy as normal water (whose density is around 1000g/L).



___
5- grompp -f em.mdp -c 3.gro -p topol.top -o e3.tpr
output of terminal:
NOTE 1 [file topol.top, line 22]:
  System has non-zero total charge: 1.51e+02
 
Analysing residue names:

There are: 32702  Other residues
Analysing residues not classified as Protein/DNA/RNA/Water and 
splitting into groups...

Number of degrees of freedom in T-Coupling group rest is 99915.00
This run will generate roughly 49 Mb of data

There was 1 note

6- mdrun -v -deffnm e3

7-  genion -s e3.tpr -o 4.gro -p topol.top -nname cl- -nn 151
output of terminal:
Reading file e3.tpr, VERSION 4.5.4 (single precision)
Using a coulomb cut-off of 1.2 nm
Will try to add 0 NA ions and 151 cl- ions.
Select a continuous group of solvent molecules
Group 0 ( System) has 33306 elements
Group 1 (  Other) has 33306 elements
Group 2 (CA) has   755 elements
Group 3 (  W) has 32551 elements
Select a group: 3
__
Adding ions was done successfully but in the genion.log file had been 
written "System total charge: 151.000"


That would be normal before adding ions, and indicative of a problem 
after adding ions, but you haven't made this clear... You say it was 
successful, and then announce that it reports a total charge consistent 
with

Re: [gmx-users] calculation of density for martini coarse-grained

[Justin A. Lemkul]

mohammad agha wrote:

Thank you very much for your reply.

I experienced "genbox" for gromos force field for my molecules and for 
dspc molecules in martini tutorial in lipid_tutorial.tar.gz, I took the 
same warning for all them!!!

May I know that what should I do, Please ?



Probably nothing.  If you use a coordinate file as input into a number of tools 
you'll likely get the same.  As I said, it is a warning, not an error that needs 
fixing.  It is up to you, as the user, to verify that the output of the program 
is what you want it to be.  Issues related to measured density as you've been 
reporting are likely a consequence of bizarre atom names that Gromacs doesn't 
understand.  You have to (correctly) do the math to find what the density should be.


-Justin


Best Regards
Sara

*From:* Justin A. Lemkul 
*To:* mohammad agha ; Discussion list for GROMACS 
users 

*Sent:* Thursday, December 15, 2011 9:26 PM
*Subject:* Re: [gmx-users] calculation of density for martini coarse-grained



mohammad agha wrote:
 > Dear Prof.
 >
 > Thank you very much.
 > Excuse me, I am beginner in gromacs and my experience about warnings 
is low, but I think my problem return to this warning:

 >
 > WARNING: masses and atomic (Van der Waals) radii will be determined
 >  based on residue and atom names. These numbers can deviate
 >  from the correct mass and radius of the atom type.
 >

The warning indicates that names may give misleading values for masses 
and van der Waals interactions.  For instance, is "CA" an alpha-carbon, 
or calcium?  In this context, the program reporting the error doesn't 
know.  Since MARTINI uses lots of weird atom names for its structures, 
the program is warning you that the output may be incorrect, or perhaps 
it may not; hence why it is a warning and not an error.


-Justin

 > I checked mailing list but I didn't find my answer!
 > Please help me.
 >
 > Best Regards
 >
 > Sara
 > 
 > *From:* Mark Abraham >
 > *To:* Discussion list for GROMACS users >

 > *Sent:* Thursday, December 15, 2011 6:31 PM
 > *Subject:* Re: [gmx-users] calculation of density for martini 
coarse-grained

 >
 > On 16/12/2011 1:36 AM, mohammad agha wrote:
 >> Dear Prof.
 >>
 >> Thank you for your reply.
 >> I'm really sorry for my mistake in writing the density!! my 
calculated density become: 90.254026 gr/l while gromacs reported 
15.8111g/l! why?
 >> In the martini_v2.0.itp file, has been written "all particle masses 
are set to 72 amu". May I know my mistake, Please?

 >>
 >> My solvent molecules aren't named "SOL".
 >>
 >> Command lines and terminal outputs:
 >>
 >> 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro
 >> output of terminal is:
 >> Output configuration contains 755 atoms in 151 residues
 >> Volume:1000 (nm^3)
 >> Density:15.8111 (g/l)
 >> Number of SOL molecules:  0 
 >
 > One possibility is that the Martini force field doesn't have the 
masses set up correctly for genbox to match from the coordinate file. 
Perhaps in share/top/atommass.dat?

 >
 >> 2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 
14.8 -center 7.4 7.4 7.4

 >> Output of terminal:
 >> Read 755 atoms
 >> Volume: 1000 nm^3, corresponds to roughly 45 electrons
 >> No velocities found
 >>system size :  9.803  9.897  9.978 (nm)
 >>diameter: 13.969  (nm)
 >>center  :  5.239  4.900  4.932 (nm)
 >>box vectors : 10.000 10.000 10.000 (nm)
 >>box angles  :  90.00  90.00  90.00 (degrees)
 >>box volume  :1000.00  (nm^3)
 >>shift  :  2.161  2.500  2.468 (nm)
 >> new center  :  7.400  7.400  7.400 (nm)
 >> new box vectors : 14.800 14.800 14.800 (nm)
 >> new box angles  :  90.00  90.00  90.00 (degrees)
 >> new box volume  :3241.79  (nm^3)
 >
 > So the box volume of 2.gro is not 1000 nm^3.
 >
 >>
 >> 3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr
 >> output of terminal:
 >> NOTE 1 [file topol.top, line 22]:
 >>  System has non-zero total charge: 1.51e+02
 >>
 >> 3- mdrun -v -deffnm e1
 >>  4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551
 >> output of terminal:
 >> Output configuration contains 33306 atoms in 32702 residues
 >> Volume:3241.79 (nm^3)
 >> Density:3070.15 (g/l)
 >> Number of SOL molecules:  0  
___

 >> I have a problem about density in step 4 after adding water, again!!!
 >
 > Could be the same issue - apparently the water is something like 
three times as heavy as normal water (whose density is around 1000g/L).

 >
 >> 

Re: [gmx-users] calculation of density for martini coarse-grained

[mohammad agha]

Thank you very much.

Best Regards

Sara




 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Thursday, December 15, 2011 10:02 PM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
 


mohammad agha wrote:
> Thank you very much for your reply.
> 
> I experienced "genbox" for gromos force field for my molecules and for dspc 
> molecules in martini tutorial in lipid_tutorial.tar.gz, I took the same 
> warning for all them!!!
> May I know that what should I do, Please ?
> 

Probably nothing.  If you use a coordinate file as input into a number of tools 
you'll likely get the same.  As I said, it is a warning, not an error that 
needs fixing.  It is up to you, as the user, to verify that the output of the 
program is what you want it to be.  Issues related to measured density as 
you've been reporting are likely a consequence of bizarre atom names that 
Gromacs doesn't understand.  You have to (correctly) do the math to find what 
the density should be.

-Justin

> Best Regards
> Sara
> 
> *From:* Justin A. Lemkul 
> *To:* mohammad agha ; Discussion list for GROMACS users 
> 
> *Sent:* Thursday, December 15, 2011 9:26 PM
> *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained
> 
> 
> 
> mohammad agha wrote:
>  > Dear Prof.
>  >
>  > Thank you very much.
>  > Excuse me, I am beginner in gromacs and my experience about warnings is 
>low, but I think my problem return to this warning:
>  >
>  > WARNING: masses and atomic (Van der Waals) radii will be determined
>  >          based on residue and atom names. These numbers can deviate
>  >          from the correct mass and radius of the atom type.
>  >
> 
> The warning indicates that names may give misleading values for masses and 
> van der Waals interactions.  For instance, is "CA" an alpha-carbon, or 
> calcium?  In this context, the program reporting the error doesn't know.  
> Since MARTINI uses lots of weird atom names for its structures, the program 
> is warning you that the output may be incorrect, or perhaps it may not; hence 
> why it is a warning and not an error.
> 
> -Justin
> 
>  > I checked mailing list but I didn't find my answer!
>  > Please help me.
>  >
>  > Best Regards
>  >
>  > Sara
>  > 
>  > *From:* Mark Abraham >
>  > *To:* Discussion list for GROMACS users >
>  > *Sent:* Thursday, December 15, 2011 6:31 PM
>  > *Subject:* Re: [gmx-users] calculation of density for martini 
>coarse-grained
>  >
>  > On 16/12/2011 1:36 AM, mohammad agha wrote:
>  >> Dear Prof.
>  >>
>  >> Thank you for your reply.
>  >> I'm really sorry for my mistake in writing the density!! my calculated 
>density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?
>  >> In the martini_v2.0.itp file, has been written "all particle masses are 
>set to 72 amu". May I know my mistake, Please?
>  >>
>  >> My solvent molecules aren't named "SOL".
>  >>
>  >> Command lines and terminal outputs:
>  >>
>  >> 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro
>  >> output of terminal is:
>  >> Output configuration contains 755 atoms in 151 residues
>  >> Volume                :        1000 (nm^3)
>  >> Density                :    15.8111 (g/l)
>  >> Number of SOL molecules:      0  >
>  > One possibility is that the Martini force field doesn't have the masses 
>set up correctly for genbox to match from the coordinate file. Perhaps in 
>share/top/atommass.dat?
>  >
>  >> 2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 
>-center 7.4 7.4 7.4
>  >> Output of terminal:
>  >> Read 755 atoms
>  >> Volume: 1000 nm^3, corresponds to roughly 45 electrons
>  >> No velocities found
>  >>    system size :  9.803  9.897  9.978 (nm)
>  >>    diameter    : 13.969              (nm)
>  >>    center      :  5.239  4.900  4.932 (nm)
>  >>    box vectors : 10.000 10.000 10.000 (nm)
>  >>    box angles  :  90.00  90.00  90.00 (degrees)
>  >>    box volume  :1000.00              (nm^3)
>  >>    shift      :  2.161  2.500  2.468 (nm)
>  >> new center      :  7.400  7.400  7.400 (nm)
>  >> new box vectors : 14.800 14.800 14.800 (nm)
>  >> new box angles  :  90.00  90.00  90.00 (degrees)
>  >> new box volume  :3241.79              (nm^3)
>  >
>  > So the box volume of 2.gro is not 1000 nm^3.
>  >
>  >>
>  >> 3- grompp -f em.mdp -c 2.gro -p topol.top -o e1.tpr
>  >> output of terminal:
>  >> NOTE 1 [file topol.top, line 22]:
>  >>  System has non-zero total charge: 1.51e+02
>  >>
>  >> 3- mdrun -v -deffnm e1
>  >>  4- genbox -cp e1.gro -cs water.gro -o 3.gro -maxsol 32551
>  >> output of terminal:
>  >> Output configuration contains 33306 atoms in 32702 residues
>  >> Volume                :    3241.79 (nm^3)
>  >> Density                :    3070.15 (g/l)
>  >

[gmx-users] Eigenvalue values from PCA (a general question)

[R.S.K.Vijayan]

Hi all

I have a query about  the eigenvalue values obtained from g_covar and
g_anaeig

I performed essential dynamics using  PCA on my system (Protein-DNA
complex) considering BB of the protein and the phosphate and sugar of the
DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the top 10
principal components are stated below

 1 10.1064
 2 4.78616
 3 4.07406
 4 3.48535
 5 2.7176
 6 2.13348
 7 1.75909
 8 1.45699
 9 1.12932
10 0.893933

What i infer from this is that the cumulative variance experienced by  the
top 10 PC is  hardly ~ 30 %.

so my questions are

a) does this imply inadequate sampling by MD or a limited conformational
change happening  in the system
b) is it wise to consider the Nucleic acid during essential dynamics or
should it be discared and only the Protein BB or CA be considered.

Thanking you in advance for your suggestions. My apologies since it sound
to be a very general question and rather not very specific to Gromacs.

Regards
Vijayan.R
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[gmx-users] free energy and UB term

[lq z]

Dear GMXers,

I'm trying to manually add two sets of Urey-Bradley terms to the topology
file (in [angle] entry with type 5). However, it seems it is not allowed. I
got the following error:

Incorrect number of parameters - found 8, expected 4 or 4 for U-B.

Is it true that I can't do this in gromacs? Thanks.

Luke
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Re: [gmx-users] Eigenvalue values from PCA (a general question)

[Tsjerk Wassenaar]

Hi Vijayan R.,

> What i infer from this is that the cumulative variance experienced by  the
> top 10 PC is  hardly ~ 30 %.

Not experienced...; It's the variance captured by the first ten PC's.

> a) does this imply inadequate sampling by MD or a limited conformational
> change happening  in the system

No, not at all. It shows that the motions in your system can not be
adequately captured by linear combinations of atom fluctuations. The
system may be too flexible and/or there may be a lot of rotational
motion.

> b) is it wise to consider the Nucleic acid during essential dynamics or
> should it be discared and only the Protein BB or CA be considered.

Analysis with and without nucleic acids are just two different things.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] Eigenvalue values from PCA (a general question)

[R.S.K.Vijayan]

Hi Tsjerk

Many thanks for your response. Do you think NMA is worth considering in
such cases like this?

Regards
Vijayan.R

On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar  wrote:

> Hi Vijayan R.,
>
> > What i infer from this is that the cumulative variance experienced by
> the
> > top 10 PC is  hardly ~ 30 %.
>
> Not experienced...; It's the variance captured by the first ten PC's.
>
> > a) does this imply inadequate sampling by MD or a limited conformational
> > change happening  in the system
>
> No, not at all. It shows that the motions in your system can not be
> adequately captured by linear combinations of atom fluctuations. The
> system may be too flexible and/or there may be a lot of rotational
> motion.
>
> > b) is it wise to consider the Nucleic acid during essential dynamics or
> > should it be discared and only the Protein BB or CA be considered.
>
> Analysis with and without nucleic acids are just two different things.
>
> Cheers,
>
> Tsjerk
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> 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] Eigenvalue values from PCA (a general question)

[Tsjerk Wassenaar]

Hi Vijayan.R,

Not really. NMA also assumes linear relationships.

Cheers,

Tsjerk

On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan  wrote:
> Hi Tsjerk
>
> Many thanks for your response. Do you think NMA is worth considering in such
> cases like this?
>
> Regards
> Vijayan.R
>
> On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar  wrote:
>>
>> Hi Vijayan R.,
>>
>> > What i infer from this is that the cumulative variance experienced by
>> > the
>> > top 10 PC is  hardly ~ 30 %.
>>
>> Not experienced...; It's the variance captured by the first ten PC's.
>>
>> > a) does this imply inadequate sampling by MD or a limited conformational
>> > change happening  in the system
>>
>> No, not at all. It shows that the motions in your system can not be
>> adequately captured by linear combinations of atom fluctuations. The
>> system may be too flexible and/or there may be a lot of rotational
>> motion.
>>
>> > b) is it wise to consider the Nucleic acid during essential dynamics or
>> > should it be discared and only the Protein BB or CA be considered.
>>
>> Analysis with and without nucleic acids are just two different things.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>> --
>> 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
>
>
>
> --
> 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



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] Eigenvalue values from PCA (a general question)

[R.S.K.Vijayan]

Thanks Tsjerk

On Thu, Dec 15, 2011 at 4:55 PM, Tsjerk Wassenaar  wrote:

> Hi Vijayan.R,
>
> Not really. NMA also assumes linear relationships.
>
> Cheers,
>
> Tsjerk
>
> On Thu, Dec 15, 2011 at 10:48 PM, R.S.K.Vijayan 
> wrote:
> > Hi Tsjerk
> >
> > Many thanks for your response. Do you think NMA is worth considering in
> such
> > cases like this?
> >
> > Regards
> > Vijayan.R
> >
> > On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar 
> wrote:
> >>
> >> Hi Vijayan R.,
> >>
> >> > What i infer from this is that the cumulative variance experienced by
> >> > the
> >> > top 10 PC is  hardly ~ 30 %.
> >>
> >> Not experienced...; It's the variance captured by the first ten PC's.
> >>
> >> > a) does this imply inadequate sampling by MD or a limited
> conformational
> >> > change happening  in the system
> >>
> >> No, not at all. It shows that the motions in your system can not be
> >> adequately captured by linear combinations of atom fluctuations. The
> >> system may be too flexible and/or there may be a lot of rotational
> >> motion.
> >>
> >> > b) is it wise to consider the Nucleic acid during essential dynamics
> or
> >> > should it be discared and only the Protein BB or CA be considered.
> >>
> >> Analysis with and without nucleic acids are just two different things.
> >>
> >> Cheers,
> >>
> >> Tsjerk
> >>
> >> --
> >> Tsjerk A. Wassenaar, Ph.D.
> >>
> >> post-doctoral researcher
> >> Molecular Dynamics Group
> >> * Groningen Institute for Biomolecular Research and Biotechnology
> >> * Zernike Institute for Advanced Materials
> >> University of Groningen
> >> The Netherlands
> >> --
> >> 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
> >
> >
> >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Re: Eigenvalue values from PCA (a general question)

[Niesen, Michiel]

>Date: Thu, 15 Dec 2011 15:11:12 -0500
>From: "R.S.K.Vijayan" 
>Subject: [gmx-users] Eigenvalue values from PCA (a general question)
>To: gmx-users@gromacs.org
>Message-ID:
>   
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi all
>
>I have a query about  the eigenvalue values obtained from g_covar and
>g_anaeig
>
>I performed essential dynamics using  PCA on my system (Protein-DNA
>complex) considering BB of the protein and the phosphate and sugar of the
>DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the top 10
>principal components are stated below
>
> 1 10.1064
> 2 4.78616
> 3 4.07406
> 4 3.48535
> 5 2.7176
> 6 2.13348
> 7 1.75909
> 8 1.45699
> 9 1.12932
>10 0.893933
>
>What i infer from this is that the cumulative variance experienced by  the
>top 10 PC is  hardly ~ 30 %.

The cumulative variance described by a set of PCs is not the sum of their 
eigenvalues. You have to take the sum of the first x eigenvalues as a 
percentage of the sum of all eigenvalues to get the cumulative variance.

>a) does this imply inadequate sampling by MD or a limited conformational
>change happening  in the system
>b) is it wise to consider the Nucleic acid during essential dynamics or
>should it be discared and only the Protein BB or CA be considered.
>
>Thanking you in advance for your suggestions. My apologies since it sound
>to be a very general question and rather not very specific to Gromacs.
>
>Regards
>Vijayan.R


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Re: [gmx-users] Re: Eigenvalue values from PCA (a general question)

[R.S.K.Vijayan]

Thanks Micheal for pointing out the mistake

On Fri, Dec 16, 2011 at 4:20 AM, Niesen, Michiel  wrote:

> >Date: Thu, 15 Dec 2011 15:11:12 -0500
> >From: "R.S.K.Vijayan" 
> >Subject: [gmx-users] Eigenvalue values from PCA (a general question)
> >To: gmx-users@gromacs.org
> >Message-ID:
> >   <
> camm9pawrymqrgzheriarvovk7qwuzpfwrm_owc_0+cemezm...@mail.gmail.com>
> >Content-Type: text/plain; charset="iso-8859-1"
> >
> >Hi all
> >
> >I have a query about  the eigenvalue values obtained from g_covar and
> >g_anaeig
> >
> >I performed essential dynamics using  PCA on my system (Protein-DNA
> >complex) considering BB of the protein and the phosphate and sugar of the
> >DNA for a 50 ns trajectory. The eigenvalue which i do obtain for the top
> 10
> >principal components are stated below
> >
> > 1 10.1064
> > 2 4.78616
> > 3 4.07406
> > 4 3.48535
> > 5 2.7176
> > 6 2.13348
> > 7 1.75909
> > 8 1.45699
> > 9 1.12932
> >10 0.893933
> >
> >What i infer from this is that the cumulative variance experienced by  the
> >top 10 PC is  hardly ~ 30 %.
>
> The cumulative variance described by a set of PCs is not the sum of their
> eigenvalues. You have to take the sum of the first x eigenvalues as a
> percentage of the sum of all eigenvalues to get the cumulative variance.
>
> >a) does this imply inadequate sampling by MD or a limited conformational
> >change happening  in the system
> >b) is it wise to consider the Nucleic acid during essential dynamics or
> >should it be discared and only the Protein BB or CA be considered.
> >
> >Thanking you in advance for your suggestions. My apologies since it sound
> >to be a very general question and rather not very specific to Gromacs.
> >
> >Regards
> >Vijayan.R
>
>
> -
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Re: [gmx-users] free energy and UB term

[Mark Abraham]

On 16/12/2011 7:22 AM, lq z wrote:

Dear GMXers,

I'm trying to manually add two sets of Urey-Bradley terms to the 
topology file (in [angle] entry with type 5). However, it seems it is 
not allowed. I got the following error:


Incorrect number of parameters - found 8, expected 4 or 4 for U-B.

Is it true that I can't do this in gromacs? Thanks.


You can add any interaction you like. What you can't get is useful help 
if you don't show what you've tried. :-)


Mark
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[gmx-users] good reference for PCA in gromacs

[Sanku M]

Hi,
  I am wondering whether someone can suggest a reference paper based on which 
all gromacs principal component analysis (PCA) analysis ( i.e g_covar and 
g_anaeig tools) tools are based . Or, any other review articles on  PCA 
analysis  is based will also be useful.
Thanks
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Re: [gmx-users] good reference for PCA in gromacs

[Mark Abraham]

On 16/12/2011 10:47 AM, Sanku M wrote:

Hi,
  I am wondering whether someone can suggest a reference paper based 
on which all gromacs principal component analysis (PCA) analysis ( i.e 
g_covar and g_anaeig tools) tools are based . Or, any other review 
articles on  PCA analysis  is based will also be useful.




I would recommend sections 8.10-8.11 of the manual and refs therein.

Mark
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Re: [gmx-users] Re: Eigenvalue values from PCA (a general question)

[Tsjerk Wassenaar]

Hi Michiel,

I disagree, and so does semantics. The cumulative variance of a pc is the
variance of it plus the sum of the preceding ones. You're talking about the
cumulative fraction of the total variance.

Cheers,

Tajerk

On Dec 16, 2011 12:07 AM, "Niesen, Michiel"  wrote:

>Date: Thu, 15 Dec 2011 15:11:12 -0500
>From: "R.S.K.Vijayan" 
>Subject: [gmx-users] Eigenvalue values from PCA (a general question)
>To: gmx-users@gromacs.org
>Message-ID:
>   
>Content-Type: text/plain; charset="iso-8859-1"

> >Hi all > >I have a query about the eigenvalue values obtained from
g_covar and >g_anaeig > >I pe...

>What i infer from this is that the cumulative variance experienced by the
>top 10 PC is hardly ~ ...
The cumulative variance described by a set of PCs is not the sum of their
eigenvalues. You have to take the sum of the first x eigenvalues as a
percentage of the sum of all eigenvalues to get the cumulative variance.

>a) does this imply inadequate sampling by MD or a limited conformational
>change happening in the...

>b) is it wise to consider the Nucleic acid during essential dynamics or
>should it be discared and ...

>Thanking you in advance for your suggestions. My apologies since it sound
>to be a very general que...
-
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[gmx-users] compatible gromacs

[aiswarya pawar]

Hi users,

i would like to know which version of gromacs would be compatible with the
cluster architecture =

Linux cnode39 2.6.5-7.244-pseries64 #1 SMP Mon Dec 12 18:32:25 UTC 2005
ppc64 ppc64 ppc64 GNU/Linux

And which gromacs version would be compatible with the mpi version =
mpich-1.2.7


Thanks,
Aiswarya
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Re: [gmx-users] calculation of density for martini coarse-grained

[mohammad agha]

Excuse me, I did all of examples in my system with different molecules (even 
water alone) and with different force fields and I took this warning for all of 
them by doing genbox command!!!

WARNING: masses and atomic (Van der Waals) radii will be determined
 based on residue and atom names. These numbers can deviate
 from the correct mass and radius of the atom type.


Is this warning for all in this command, always? If not, then why have I that 
always? My density is calculated wrong in gromacs and density is important for 
me!  

Please help me.

Best Regards
Sara



 From: mohammad agha 
To: "jalem...@vt.edu" ; Discussion list for GROMACS users 
 
Sent: Thursday, December 15, 2011 10:28 PM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
 

Thank you very much.

Best Regards

Sara



 From: Justin A. Lemkul 
To: Discussion list for GROMACS users  
Sent: Thursday, December 15, 2011 10:02 PM
Subject: Re: [gmx-users] calculation of density for martini coarse-grained
 


mohammad agha wrote:
> Thank you very much for your reply.
> 
> I experienced "genbox" for gromos force field for my molecules and for dspc 
> molecules in martini tutorial in lipid_tutorial.tar.gz, I took the same 
> warning for all them!!!
> May I know that what should I do, Please ?
> 

Probably nothing.  If you use a coordinate file as input into a number of tools 
you'll likely get the same.  As I said, it is a warning, not an error that 
needs fixing.  It is up to you, as the user, to verify that the output of the 
program is what you want it to be.  Issues related to measured density as 
you've been reporting are likely a consequence of bizarre atom names that 
Gromacs doesn't understand.  You have to (correctly) do the math to find what 
the density should be.

-Justin

> Best Regards
> Sara
>
 
> *From:* Justin A. Lemkul 
> *To:* mohammad agha ; Discussion list for GROMACS users 
> 
> *Sent:* Thursday, December 15, 2011 9:26 PM
> *Subject:* Re: [gmx-users] calculation of density for martini coarse-grained
> 
> 
> 
> mohammad agha wrote:
>  > Dear Prof.
>  >
>  > Thank you very much.
>  > Excuse me, I am beginner in gromacs and my experience about warnings is 
>low, but I think my problem return to this warning:
>  >
>  > WARNING: masses and atomic (Van
 der Waals) radii will be determined
>  >          based on residue and atom names. These numbers can deviate
>  >          from the correct mass and radius of the atom type.
>  >
> 
> The warning indicates that names may give misleading values for masses and 
> van der Waals interactions.  For instance, is "CA" an alpha-carbon, or 
> calcium?  In this context, the program reporting the error doesn't know.  
> Since MARTINI uses lots of weird atom names for its structures, the program 
> is warning you that the output may be incorrect, or perhaps it may not; hence 
> why it is a warning and not an error.
> 
> -Justin
> 
>  > I checked mailing list but I didn't find my answer!
>  > Please help me.
>  >
>  > Best Regards
>  >
>  > Sara
>  >
 
>  > *From:* Mark Abraham >
>  > *To:* Discussion list for GROMACS users >
>  > *Sent:* Thursday, December 15, 2011 6:31 PM
>  > *Subject:* Re: [gmx-users] calculation of density for martini 
>coarse-grained
>  >
>  > On 16/12/2011 1:36 AM, mohammad agha wrote:
>  >> Dear Prof.
>  >>
>  >>
 Thank you for your reply.
>  >> I'm really sorry for my mistake in writing the density!! my calculated 
>density become: 90.254026 gr/l while gromacs reported 15.8111g/l! why?
>  >> In the martini_v2.0.itp file, has been written "all particle masses are 
>set to 72 amu". May I know my mistake, Please?
>  >>
>  >> My solvent molecules aren't named "SOL".
>  >>
>  >> Command lines and terminal outputs:
>  >>
>  >> 1- genbox -ci cg.gro -nmol 151 -box 10 10 10 -o 1.gro
>  >> output of terminal is:
>  >> Output configuration contains 755 atoms in 151 residues
>  >> Volume                :        1000 (nm^3)
>  >> Density                :    15.8111
 (g/l)
>  >> Number of SOL molecules:      0  >
>  > One possibility is that the Martini force field doesn't have the masses 
>set up correctly for genbox to match from the coordinate file. Perhaps in 
>share/top/atommass.dat?
>  >
>  >> 2- editconf -f 1.gro -o 2.gro -c -d 1.0 -bt cubic -box 14.8 14.8 14.8 
>-center 7.4 7.4 7.4
>  >> Output of terminal:
>  >> Read 755 atoms
>  >> Volume: 1000 nm^3, corresponds to roughly 45 electrons
>  >> No velocities found
>  >>    system size :  9.803  9.897  9.978 (nm)
>  >>    diameter    : 13.969              (nm)
>  >>    center      :  5.239  4.900  4.932 (nm)
>  >>   
 box vectors : 10.000 10.000 10.000 (nm)
>  >>    box angles  :  90.00  90.00  90.00 (degrees)
>  >>

[gmx-users] Re: Eigenvalue values from PCA (a general question)

[Niesen, Michiel]

>Hi Michiel,
>
>I disagree, and so does semantics. The cumulative variance of a pc is the
>variance of it plus the sum of the preceding ones. You're talking about the
>cumulative fraction of the total variance.

You are right about the proper word usage. It seemed to me from his question, 
the use of a % mark when discussing the variance covered by the first 10 PCs, 
and the conclusions drawn from the value he calculated, that Vijayan meant the 
cumulative fraction of the total variance. I should name it properly, but I 
still believe that cumulative fraction of the total variance is the property 
Vijayan would be interested in.

Regards, 
 Michiel


>
>Cheers,
>
>Tajerk
>
>On Dec 16, 2011 12:07 AM, "Niesen, Michiel"  wrote:
>
>>Date: Thu, 15 Dec 2011 15:11:12 -0500
>>From: "R.S.K.Vijayan" 
>>Subject: [gmx-users] Eigenvalue values from PCA (a general question)
>>To: gmx-users@gromacs.org
>>Message-ID:
>>   
>>Content-Type: text/plain; charset="iso-8859-1"
>
>> >Hi all > >I have a query about the eigenvalue values obtained from
>g_covar and >g_anaeig > >I pe...
>
>>What i infer from this is that the cumulative variance experienced by the
>>top 10 PC is hardly ~ ...
>The cumulative variance described by a set of PCs is not the sum of their
>eigenvalues. You have to take the sum of the first x eigenvalues as a
>percentage of the sum of all eigenvalues to get the cumulative variance.
>
>>a) does this imply inadequate sampling by MD or a limited conformational
>>change happening in the...
>
>>b) is it wise to consider the Nucleic acid during essential dynamics or
>>should it be discared and ...
>
>>Thanking you in advance for your suggestions. My apologies since it sound
>>to be a very general que...

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[gmx-users] Regarding free energy calculation

[bipin singh]

Hello,

I am willing to study the free energy of binding of a cation (Ca++) to
the protein and I am following the free energy tutorial
provided by Justin
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy
).
Please let me know whether the settings for this type of study would
be same as given in the tutorial for ligand-Protein
binding free energy calculation or it need some different approach:
The setting from the ligand-Protein binding free energy calculation
are given as:


 van der Waals coupling:

 sc-alpha  = 0.5 ; use soft-core for LJ (de)coupling
 sc-sigma  = 0.3
 sc-power  = 1
 couple-moltype= LIG
 couple-intramol   = no
 couple-lambda0= none; non-interacting dummy in state A
 couple-lambda1= vdw ; only vdW terms on in state B

Coulombic coupling:

 sc-alpha  = 0   ; soft-core during (dis)charging can
be unstable!
 sc-sigma  = 0
 couple-moltype= LIG
 couple-intramol   = no
 couple-lambda0= vdw ; only vdW terms in state A (the
previous state B is now A)
 couple-lambda1= vdw-q   ; all nonbonded interactions are on in state B


-- 
---
Regards,
Bipin Singh
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