[gmx-users] continuing the terminated simulation

[delara aghaie]

Dear Gromacs users
Hello,
I use gromacs version 4.5.5. I have started with Lysozime in water simulation. 
(Justin tutorials)
The md part of simulation was terminated. Now I want to continue the simulation 
from the interruption point. Is this command line correct?
mdrun -deffnm md_0_1  -s    md_0_1.tpr   -cpi  md_0_1.tpr.cpt???

I am not sure whether to use only -cpi md_0_1.tpr.cpt with mdrun command or 
both .tpr and .cpt files???

another question is that whether continuing the simulation should be done via 
file md_0_1.tpr.cpt  or md_0_1.tpr_prev.cpt ? and what in the difference 
between them?

Thanks in advance
Regards
D.M
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Re: [gmx-users] continuing the terminated simulation

[Ankita Naithani]

Hi Delara,

To continue a crashed simulation you just need to type in the following
command without deffnm md.

mdrun -s md_0_1.tpr -cpi md_0_1.cpt

You can check the link here:
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts

The continuation is down via the .cpt file. the _prev.cpt is just a backup
copy and you need only .cpt file to begin the crashed run.
The difference is explained here:
http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File

Cheers,

Ankita




On Wed, Oct 30, 2013 at 9:26 AM, delara aghaie  wrote:

> Dear Gromacs users
> Hello,
> I use gromacs version 4.5.5. I have started with Lysozime in water
> simulation. (Justin tutorials)
> The md part of simulation was terminated. Now I want to continue the
> simulation from the interruption point. Is this command line correct?
> mdrun -deffnm md_0_1  -smd_0_1.tpr   -cpi
> md_0_1.tpr.cpt???
>
> I am not sure whether to use only -cpi md_0_1.tpr.cpt with mdrun command
> or both .tpr and .cpt files???
>
> another question is that whether continuing the simulation should be done
> via file md_0_1.tpr.cpt  or md_0_1.tpr_prev.cpt ? and what in the
> difference between them?
>
> Thanks in advance
> Regards
> D.M
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[gmx-users] Lysozime in Water

[Negar Parvizi]

Dear Gromacs users
Hello, 
I use gromacs version 4.5.5. I have started with Lysozime in water
simulation. (Justin tutorials)
The md part of simulation was terminated. Now I want to continue the
simulation from the interruption point. Is this command line correct?
mdrun -deffnm md_0_1  -smd_0_1.tpr   -cpi  md_0_1.tpr.cpt???

I am not sure whether to use only *-cpi md_0_1.tpr.cpt* with mdrun command
or both *.tpr* and .*cpt* files???
another question is that whether continuing the simulation should be done
via file *md_0_1.tpr.cpt*  or *md_0_1.tpr_prev.cpt* ? and what in the 
difference between them?

Thanks in advance
Regards
Negar
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Re: [gmx-users] Lysozime in Water

[jkrieger]

Yes, I would use the same command to continue the simulation after
stopping with the addition of -cpi

Every time a .cpt is made, the previous one is renamed _prev.cpt so that
you can still get it in case something happened in between the two.
Normally I would use the .cpt but if that doesn't work then try the
_prev.cpt

I think someone already replied to this question but I guess that didn't
help enough. Hopefully this reply does.

> Dear Gromacs users
> Hello,
> I use gromacs version 4.5.5. I have started with Lysozime in water
> simulation. (Justin tutorials)
> The md part of simulation was terminated. Now I want to continue the
> simulation from the interruption point. Is this command line correct?
> mdrun -deffnm md_0_1  -smd_0_1.tpr   -cpi
> md_0_1.tpr.cpt???
>
> I am not sure whether to use only *-cpi md_0_1.tpr.cpt* with mdrun command
> or both *.tpr* and .*cpt* files???
> another question is that whether continuing the simulation should be done
> via file *md_0_1.tpr.cpt*  or *md_0_1.tpr_prev.cpt* ? and what in
> the difference between them?
>
> Thanks in advance
> Regards
> Negar
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Re: [gmx-users] continuing the terminated simulation

[Pavan Ghatty]

mdrun -deffnm md_0_1
If the above crashed, do the following:
mdrun -s md_0_1.tpr -cpi md_0_1.cpt -deffnm md_0_2
This way, pre-crash files are called md_0_1 and post-crash file will be
named md_0_2[.cpt.gro.xtc.trr...]. The simulation will end when it reaches
the number of steps entered in the initial .tpr file which is md_0_1.tpr in
your case.

hth
Pavan


On Wed, Oct 30, 2013 at 5:36 AM, Ankita Naithani
wrote:

> Hi Delara,
>
> To continue a crashed simulation you just need to type in the following
> command without deffnm md.
>
> mdrun -s md_0_1.tpr -cpi md_0_1.cpt
>
> You can check the link here:
> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
>
> The continuation is down via the .cpt file. the _prev.cpt is just a backup
> copy and you need only .cpt file to begin the crashed run.
> The difference is explained here:
> http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File
>
> Cheers,
>
> Ankita
>
>
>
>
> On Wed, Oct 30, 2013 at 9:26 AM, delara aghaie  wrote:
>
> > Dear Gromacs users
> > Hello,
> > I use gromacs version 4.5.5. I have started with Lysozime in water
> > simulation. (Justin tutorials)
> > The md part of simulation was terminated. Now I want to continue the
> > simulation from the interruption point. Is this command line correct?
> > mdrun -deffnm md_0_1  -smd_0_1.tpr   -cpi
> > md_0_1.tpr.cpt???
> >
> > I am not sure whether to use only -cpi md_0_1.tpr.cpt with mdrun command
> > or both .tpr and .cpt files???
> >
> > another question is that whether continuing the simulation should be done
> > via file md_0_1.tpr.cpt  or md_0_1.tpr_prev.cpt ? and what in the
> > difference between them?
> >
> > Thanks in advance
> > Regards
> > D.M
> > --
> > gmx-users mailing listgmx-users@gromacs.org
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> >
>
>
>
> --
> Ankita Naithani
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[gmx-users] Re: periodic surface minimization

[escajarro]

I found the problem finally. It had to do with the fact that my charge groups
contained atoms in different residue. I just defined one charge group for
every atom, and everything worked.

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[gmx-users] single point calculation with gromacs

[fantasticqhl]

Dear All,

I want to do the single point calculations for my systems with gromacs, I
used the method mentioned on the gmx's website.

mdrun -s sp.tpr -rerun configuration.pdb.

However, I have some questions on how to generate the tpr file for single
point calculation. It didn't work if I used a mdp files of minimization to
generate the tpr file. It worked if I used a mdp files of md in vacuum, but
the energies were much higher than those reported by the 0-step
minimization. I guess that there might be some problem.

Could some one give me some suggestion on the mdp file for this kind of
single point callculations? Thanks very much!


All the best,
Qinghua

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[gmx-users] binding energy (score) of single trajectory frames

[Knapp Bernhard]

Hi users,

I was wondering if there is an easy and quick way to get a frame-wise 
binding energy between 2 groups of chains (chain ABC vs DE) in an 
existing trajectory. This is not indented to be an actual binding free 
energy approach but rather a rough indicator if the binding between two 
chains increases or decreases during simulation time. This should work 
like a protein/protein docking scoring function which assigns binding 
scores to single conformations. Is there a direct approach on an 
existing xtc (even if water was removed and not all steps were written)? 
Maybe like g_hbond but in addition with terms like Gvdw, Gdeformation, 
Ghydrophobic etc. Alternatively (and probably much more time and 
resource consuming), would it be possible to obtain this by the rerun 
option of mdrun (adjusted energy monitoring groups (the original setup 
was "energygrps =  protein	SOL"))?


Cheers,
Bernhard
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[gmx-users] pbc off

[jwillcox]

Hey everyone,

If I ran my simulations with periodic boundary conditions, is there a way
in Gromacs to get a trajectory file tracking the diffusion of the
molecules in the first time frame (i.e. not allow them to exit one side of
the box and reenter the other side)?

If not, can I specify this in the run parameters before doing the simulation?

Thanks!

Jon

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Re: [gmx-users] single point calculation with gromacs

[Justin Lemkul]

On 10/30/13 9:31 AM, fantasticqhl wrote:

Dear All,

I want to do the single point calculations for my systems with gromacs, I
used the method mentioned on the gmx's website.

mdrun -s sp.tpr -rerun configuration.pdb.

However, I have some questions on how to generate the tpr file for single
point calculation. It didn't work if I used a mdp files of minimization to
generate the tpr file. It worked if I used a mdp files of md in vacuum, but
the energies were much higher than those reported by the 0-step
minimization. I guess that there might be some problem.



Maybe this?

http://redmine.gromacs.org/issues/1341


Could some one give me some suggestion on the mdp file for this kind of
single point callculations? Thanks very much!



It would help if you posted the .mdp file(s) that you're using.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] pbc off

[Justin Lemkul]

On 10/30/13 11:42 AM, jwill...@andrew.cmu.edu wrote:

Hey everyone,

If I ran my simulations with periodic boundary conditions, is there a way
in Gromacs to get a trajectory file tracking the diffusion of the
molecules in the first time frame (i.e. not allow them to exit one side of
the box and reenter the other side)?



trjconv -pbc nojump

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] binding energy (score) of single trajectory frames

[Justin Lemkul]

On 10/30/13 11:26 AM, Knapp Bernhard wrote:

Hi users,

I was wondering if there is an easy and quick way to get a frame-wise binding
energy between 2 groups of chains (chain ABC vs DE) in an existing trajectory.
This is not indented to be an actual binding free energy approach but rather a
rough indicator if the binding between two chains increases or decreases during
simulation time. This should work like a protein/protein docking scoring
function which assigns binding scores to single conformations. Is there a direct
approach on an existing xtc (even if water was removed and not all steps were
written)? Maybe like g_hbond but in addition with terms like Gvdw, Gdeformation,
Ghydrophobic etc. Alternatively (and probably much more time and resource
consuming), would it be possible to obtain this by the rerun option of mdrun
(adjusted energy monitoring groups (the original setup was "energygrps =
proteinSOL"))?



Using energygrps is the closest you'll get without modifying the code.  You'll 
get decomposed short-range nonbonded terms, which can perhaps provide some 
indicator of the strength of the interaction between the two entities.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] SHAKE for water

[Guillaume Chevrot]

Hi,

I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).

Thanks!

Guillaume
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Re: [gmx-users] SHAKE for water

[Justin Lemkul]

On 10/30/13 12:00 PM, Guillaume Chevrot wrote:

Hi,

I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).



Never tried it, but I would assume

define = -DFLEXIBLE
constraint-algorithm = shake

would do the trick.  Of course, that assumes that your water model was not 
parametrized to stay rigid with SETTLE (which most were) and that you're OK 
using SHAKE for everything else in your system, since you can only use one 
constraint algorithm.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] SHAKE for water

[Guillaume Chevrot]

Hi,

2013/10/30 Justin Lemkul 

>
>
> On 10/30/13 12:00 PM, Guillaume Chevrot wrote:
>
>> Hi,
>>
>> I was wondering if there is an option or a way to use the algorithm SHAKE
>> for the water molecules (instead of SETTLE).
>>
>>
> Never tried it, but I would assume
>
> define = -DFLEXIBLE
> constraint-algorithm = shake
>
>
thanks for the trick, I'll try.


> would do the trick.  Of course, that assumes that your water model was not
> parametrized to stay rigid with SETTLE (which most were)


Does that mean changing [ settle ] by [ constraints ] in the file spce.itp
is sufficient?

Thanks again!

Guillaume









> and that you're OK using SHAKE for everything else in your system, since
> you can only use one constraint algorithm.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
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[gmx-users] (no subject)

[Hari Pandey]

Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of  "mass of input".  I tried to resolve 
this problem but failed. Previously I was doing AOt but now I just found that 
the molecule OS1 =O2L  showing error . Here I posted my A.pdb, RM.rtp 
atomtypes.atp.  The mass of input  should be 15.99940  but it showing 222. 
Please help me whether this is bug or something wrong with my GROMACS. Its 
GROMACS version 5.4.5. I calculate for just 1 atom to see error

I have just 1  atom in my pdb  so only on  in .rtp too
A.pdb
CRYST1   12.000   12.000   12.000  90.00  90.00  90.00 P 1         1
 MODEL        1 
ATOM       1  OS1    AOT   151       7.820  -5.791  -0.815  1.00  0.00          
 O 
ENDMDL
TER

RM.rtp
[AOT ] ;
 [ atoms ]
        OS1     O2L     -0.6000         1
  [ bonds ]

atomtypes.atp
NTL     14.007000 ;     ammonium nitrogen
NH3L    14.007000 ;     nitrogen phosphatidylethanolamine
OBL     15.999400 ;     acetic acid carboxyl oxygen (e. to protein OB)
OCL     15.999400 ;     acetate oxygen
OSL     15.999400 ;     ester oxygen
OSLP    15.999400 ;     Phosphate oxygen, to avoid conflict with methylacetate 
type O
O2L     15.999400 ;     Nucleic acid =O in phosphate or sulfate
OHL     15.999400 ;     Nucleic acid phosphate hydroxyl oxygen
PL      30.974000 ;     phosphorus
SL      32.06 ;     Sulfate sulfur
SOD     22.989770 ;     Sodium Ion
MG      24.305000 ;     Magnesium Ion

OUTPUT OF editconf

Volume  of input 125 (nm^3)
Mass    of input 222.295 (a.m.u.)   This is incorrect, even to much incorrect. 
It should be 15.40
Density of input 2.95304 (g/l)
Scaling all box vectors by 0.143468
new system size :  0.000  0.000  0.000
    shift       :  2.141  2.141  2.141 (nm)
new center      :  2.500  2.500  2.500 (nm)
new box vectors :  5.000  5.000  5.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 125.00               (nm^3)

Many Many Thanks for your help
Hari
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[gmx-users] "editconf" displays incorrect mass of input, GROMACS version 4.5.4

[Hari Pandey]

Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of  "mass of input".  I tried to resolve 
this problem but failed. Previously I was doing AOt but now I just found that 
the molecule OS1 =O2L  showing error . Here I posted my A.pdb, RM.rtp 
atomtypes.atp.  The mass of input  should be 15.99940  but it showing 222. 
Please help me whether this is bug or something wrong with my GROMACS. Its 
GROMACS version 4.5.4. I tested for just 1 atom to see error

I have just 1  atom in my pdb  so only on  in .rtp too
A.pdb
CRYST1   12.000   12.000   12.000  90.00  90.00  90.00 P 1         1
 MODEL        1 
ATOM       1  OS1    AOT   151       7.820  -5.791  -0.815  1.00  0.00          
 O 
ENDMDL
TER

RM.rtp
[ AOT ] ;
 [ atoms ]
        OS1     O2L     -0.6000         1
  [ bonds ]

atomtypes.atp
NTL     14.007000 ;     ammonium nitrogen
NH3L    14.007000 ;     nitrogen phosphatidylethanolamine
OBL     15.999400 ;     acetic acid carboxyl oxygen (e. to protein OB)
OCL     15.999400 ;     acetate oxygen
OSL     15.999400 ;     ester oxygen
OSLP    15.999400 ;     Phosphate oxygen, to avoid conflict with methylacetate 
type O
O2L     15.999400 ;     Nucleic acid =O in phosphate or sulfate
OHL     15.999400 ;     Nucleic acid phosphate hydroxyl oxygen
PL      30.974000 ;     phosphorus
SL      32.06 ;     Sulfate sulfur
SOD     22.989770 ;     Sodium Ion
MG      24.305000 ;     Magnesium Ion

OUTPUT OF editconf

Volume  of input 125 (nm^3)
Mass    of input 222.295 (a.m.u.)   This is incorrect, even to much incorrect. 
It should be 15.40
Density of input 2.95304 (g/l)
Scaling all box vectors by 0.143468
new system size :  0.000  0.000  0.000
    shift       :  2.141  2.141  2.141 (nm)
new center      :  2.500  2.500  2.500 (nm)
new box vectors :  5.000  5.000  5.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 125.00               (nm^3)

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Re: [gmx-users] "editconf" displays incorrect mass of input, GROMACS version 4.5.4

[Justin Lemkul]

On 10/30/13 2:34 PM, Hari Pandey wrote:

Dear Gromacs users,
Please somebody help .
editconf computs the incorrect value of  "mass of input".  I tried to resolve 
this problem but failed. Previously I was doing AOt but now I just found that the 
molecule OS1 =O2L  showing error . Here I posted my A.pdb, RM.rtp atomtypes.atp.  The 
mass of input  should be 15.99940  but it showing 222. Please help me whether this is bug 
or something wrong with my GROMACS. Its GROMACS version 4.5.4. I tested for just 1 atom 
to see error

I have just 1  atom in my pdb  so only on  in .rtp too
A.pdb
CRYST1   12.000   12.000   12.000  90.00  90.00  90.00 P 1 1
  MODEL1
ATOM   1  OS1AOT   151   7.820  -5.791  -0.815  1.00  0.00  
 O
ENDMDL
TER

RM.rtp
[ AOT ] ;
  [ atoms ]
 OS1 O2L -0.6000 1
   [ bonds ]

atomtypes.atp
NTL 14.007000 ; ammonium nitrogen
NH3L14.007000 ; nitrogen phosphatidylethanolamine
OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB)
OCL 15.999400 ; acetate oxygen
OSL 15.999400 ; ester oxygen
OSLP15.999400 ; Phosphate oxygen, to avoid conflict with methylacetate 
type O
O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate
OHL 15.999400 ; Nucleic acid phosphate hydroxyl oxygen
PL  30.974000 ; phosphorus
SL  32.06 ; Sulfate sulfur
SOD 22.989770 ; Sodium Ion
MG  24.305000 ; Magnesium Ion

OUTPUT OF editconf

Volume  of input 125 (nm^3)
Massof input 222.295 (a.m.u.)   This is incorrect, even to much incorrect. 
It should be 15.40
Density of input 2.95304 (g/l)
Scaling all box vectors by 0.143468
new system size :  0.000  0.000  0.000
 shift   :  2.141  2.141  2.141 (nm)
new center  :  2.500  2.500  2.500 (nm)
new box vectors :  5.000  5.000  5.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 125.00   (nm^3)



I cannot reproduce the problem with 4.6.3.  I get correct output:

Volume  of input 1.728 (nm^3)
Massof input 15.9994 (a.m.u.)
Density of input 15.3748 (g/l)
Scaling all box vectors by 0.248658
new system size :  0.000  0.000  0.000
shift   :  2.326  2.480  2.480 (nm)
new center  :  2.500  2.500  2.500 (nm)
new box vectors :  5.000  5.000  5.000 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 125.00   (nm^3)

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] SHAKE for water

[Justin Lemkul]

On 10/30/13 1:46 PM, Guillaume Chevrot wrote:

Hi,

2013/10/30 Justin Lemkul 




On 10/30/13 12:00 PM, Guillaume Chevrot wrote:


Hi,

I was wondering if there is an option or a way to use the algorithm SHAKE
for the water molecules (instead of SETTLE).



Never tried it, but I would assume

define = -DFLEXIBLE
constraint-algorithm = shake



thanks for the trick, I'll try.



would do the trick.  Of course, that assumes that your water model was not
parametrized to stay rigid with SETTLE (which most were)



Does that mean changing [ settle ] by [ constraints ] in the file spce.itp
is sufficient?



Sufficient for what?  What type of replacement are you making?  If you're just 
trying to use SHAKE, you don't have to modify the topology at all; the .mdp 
options are sufficient to produce the behavior you want.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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RE: [gmx-users] RE: Gibbs Energy Calculation and charges

[Dallas Warren]

Michael, thanks for taking the time to comment and have a look.

The real issue I am having is a bit deeper into the topic than that, my last 
reply was just an observation on something else.  Will summarise what I have 
been doing etc.

I have a molecule that are calculating the Gibbs energy of hydration and 
solvation (octanol).  In a second topology the only difference is that the 
atomic charges have been doubled.  Considering that charges are scaled linearly 
with lambda, the normal charge values of dH/dl from lambda 0 to 1 obtained 
should reproduce that of the double charged molecule from lambda 0.5 to 1.0.  
Is that a correct interpretation?  Since the only difference should be that 
charge of the atoms and over that range the charge will be identical.

I was using couple-intramol = no and the following are the results from those 
simulations.

For the OE atom within the molecule, I have plotted the following graphs of 
dH/dl versus charge of that atom for both of the topologies.
octanol - http://ozreef.org/stuff/octanol.gif
water - http://ozreef.org/stuff/water.gif
mdp file - http://ozreef.org/stuff/gromacs/mdout.mdp

The mismatch between the two topologies is the real issue that I am having.  I 
was hoping to get the two to overlap.

My conclusion based on this is that there is actually something else being 
changed with the topology by GROMACS when the simulations are being run.  The 
comments in the manual allude to that, but not entirely sure what is going on.

> From the manual:
>
>couple-intramol:
>
>no
> All intra-molecular non-bonded interactions for moleculetype
>couple-moltype are replaced by exclusions and explicit pair
>interactions. In this manner the decoupled state of the molecule
>corresponds to the proper vacuum state without periodicity effects.
>yes
> The intra-molecular Van der Waals and Coulomb interactions are
>also turned on/off. This can be useful for partitioning free-energies
>of relatively large molecules, where the intra-molecular non-bonded
>interactions might lead to kinetically trapped vacuum conformations.
>The 1-4 pair interactions are not turned off.

Chris Neale commented:
>Ah, I see. I guess that you are using couple-intramol = no (the default in 
>v4.6.3 at least). That means
>that the intramolecular charge-charge interactions are always at full-strength 
>(and therefore different).
>I would expect that normal at lambda=0 should be the same as double at 
>lambda=0.5 only for
>couple-intramol = yes
>If you were using couple-intramol = yes already, then I am as confused as you 
>are.

>From Chris' comment, I then went back and repeated the calculation using 
>couple-intramol = yes with the results of this in the below image (plus the 
>previous when set to no for comparison)

http://ozreef.org/stuff/gromacs/couple-intramol.png

My rather garbled comment that you saw was my attempt to make sense of the fact 
that this setting made things worse (and try to add something to get this issue 
to have another pass on the list, hoping someone like yourself will comment), 
and the value of dH/dl for c-i=yes at lambda=1 matches with c-i=no at lambad=0. 
 This you can see with the previously linked to graphs.

Hopefully that helps understand what I have been doing and the issues.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 
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Re: [gmx-users] RE: Gibbs Energy Calculation and charges

[Michael Shirts]

I likely won't have much time to look at it tonight, but you can see
exactly what the option is doing to the topology.  run gmxdump on the
tpr.  All of the stuff that couple-intramol does is in grompp, so the
results will show up in the detailed listings of the interactions, and
which ones have which values set for the A and B states.

On Wed, Oct 30, 2013 at 5:36 PM, Dallas Warren  wrote:
> Michael, thanks for taking the time to comment and have a look.
>
> The real issue I am having is a bit deeper into the topic than that, my last 
> reply was just an observation on something else.  Will summarise what I have 
> been doing etc.
>
> I have a molecule that are calculating the Gibbs energy of hydration and 
> solvation (octanol).  In a second topology the only difference is that the 
> atomic charges have been doubled.  Considering that charges are scaled 
> linearly with lambda, the normal charge values of dH/dl from lambda 0 to 1 
> obtained should reproduce that of the double charged molecule from lambda 0.5 
> to 1.0.  Is that a correct interpretation?  Since the only difference should 
> be that charge of the atoms and over that range the charge will be identical.
>
> I was using couple-intramol = no and the following are the results from those 
> simulations.
>
> For the OE atom within the molecule, I have plotted the following graphs of 
> dH/dl versus charge of that atom for both of the topologies.
> octanol - http://ozreef.org/stuff/octanol.gif
> water - http://ozreef.org/stuff/water.gif
> mdp file - http://ozreef.org/stuff/gromacs/mdout.mdp
>
> The mismatch between the two topologies is the real issue that I am having.  
> I was hoping to get the two to overlap.
>
> My conclusion based on this is that there is actually something else being 
> changed with the topology by GROMACS when the simulations are being run.  The 
> comments in the manual allude to that, but not entirely sure what is going on.
>
>> From the manual:
>>
>>couple-intramol:
>>
>>no
>> All intra-molecular non-bonded interactions for moleculetype
>>couple-moltype are replaced by exclusions and explicit pair
>>interactions. In this manner the decoupled state of the molecule
>>corresponds to the proper vacuum state without periodicity effects.
>>yes
>> The intra-molecular Van der Waals and Coulomb interactions are
>>also turned on/off. This can be useful for partitioning free-energies
>>of relatively large molecules, where the intra-molecular non-bonded
>>interactions might lead to kinetically trapped vacuum conformations.
>>The 1-4 pair interactions are not turned off.
>
> Chris Neale commented:
>>Ah, I see. I guess that you are using couple-intramol = no (the default in 
>>v4.6.3 at least). That means
>>that the intramolecular charge-charge interactions are always at 
>>full-strength (and therefore different).
>>I would expect that normal at lambda=0 should be the same as double at 
>>lambda=0.5 only for
>>couple-intramol = yes
>>If you were using couple-intramol = yes already, then I am as confused as you 
>>are.
>
> >From Chris' comment, I then went back and repeated the calculation using 
> >couple-intramol = yes with the results of this in the below image (plus the 
> >previous when set to no for comparison)
>
> http://ozreef.org/stuff/gromacs/couple-intramol.png
>
> My rather garbled comment that you saw was my attempt to make sense of the 
> fact that this setting made things worse (and try to add something to get 
> this issue to have another pass on the list, hoping someone like yourself 
> will comment), and the value of dH/dl for c-i=yes at lambda=1 matches with 
> c-i=no at lambad=0.  This you can see with the previously linked to graphs.
>
> Hopefully that helps understand what I have been doing and the issues.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a 
> nail.
> --
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