[gmx-users] forcefield and setting

[fatemeh ramezani]

 Dear Justin
I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for 
water.

em.mdp file:
title   =  n.pdb
cpp =  /lib/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  steep
nsteps  =  4
constraint_algorithm  =
shake_tol   = 0.0001
nstenergy   =  10
nstxtcout   =  1
nstlist =  5
nstcomm =  1
ns_type =  grid
rlist   =  1
coulombtype =  PME
rcoulomb    =  1
rvdw    =  1
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  8
ewald_rtol  =  1e-5
optimize_fft    =  yes
emtol   =  1000.0
emstep  =  0.01

md.mdp file:
title   =  n.pdb restraining
cpp =  /lib/cpp
constraints =  none
integrator  =  md 
dt  =  0.0008
nsteps  =  2500
nstcomm =  10
comm_mode   =  
nstxout =  250
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  0.9
coulombtype =  PME
rcoulomb    =  0.9
rcoulomb-switch =  1
rvdw    =  0.5
vdwtype =  shift
;rvdw-switch =  0.6
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft    =  yes
  

; Berendsen temperature coupling is on in three groups
Tcoupl  =  V-rescale
tau_t   =  0.1   0.1
tc-grps            =  Protein   Non-Protein
ref_t   =  300   300
; Pressure coupling is  on
;Pcoupl  =  berendsen
Pcoupl  =  no
Pcoupltype =  isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp    =  300.0
gen_seed    =  173529
energygrps  = Protein  Sol 



Fatemeh Ramezani
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Re: [gmx-users] forcefield and setting

[Justin Lemkul]

On 9/19/13 11:59 AM, fatemeh ramezani wrote:



  Dear Justin
I used gromacs OPLSAA forcefield for simulation of protein and TIP3P model for 
water.

em.mdp file:
title   =  n.pdb
cpp =  /lib/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  steep
nsteps  =  4
constraint_algorithm  =
shake_tol   = 0.0001
nstenergy   =  10
nstxtcout   =  1
nstlist =  5
nstcomm =  1
ns_type =  grid
rlist   =  1
coulombtype =  PME
rcoulomb=  1
rvdw=  1
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  8
ewald_rtol  =  1e-5
optimize_fft=  yes
emtol   =  1000.0
emstep  =  0.01

md.mdp file:
title   =  n.pdb restraining
cpp =  /lib/cpp
constraints =  none
integrator  =  md
dt  =  0.0008
nsteps  =  2500
nstcomm =  10
comm_mode   =
nstxout =  250
nstvout =  1000
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  0.9
coulombtype =  PME
rcoulomb=  0.9
rcoulomb-switch =  1
rvdw=  0.5
vdwtype =  shift


Your van der Waals settings make no sense.  I strongly suspect that this is 
inducing very nasty artifacts.


-Justin


;rvdw-switch =  0.6
fourierspacing  =  0.12
fourier_nx  =  0
fourier_ny  =  0
fourier_nz  =  0
pme_order   =  6
ewald_rtol  =  1e-5
optimize_fft=  yes


; Berendsen temperature coupling is on in three groups
Tcoupl  =  V-rescale
tau_t   =  0.1   0.1
tc-grps=  Protein   Non-Protein
ref_t   =  300   300
; Pressure coupling is  on
;Pcoupl  =  berendsen
Pcoupl  =  no
Pcoupltype =  isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  300.0
gen_seed=  173529
energygrps  = Protein  Sol



Fatemeh Ramezani



--
==

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

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Re: [gmx-users] Forcefield parameters for AcetylCoA

[Justin A. Lemkul]

Please keep the discussion on the gmx-users mailing list.

On 7/11/12 10:43 AM, panbazha wrote:

Dear Justin,
That file was generated by me in ATB, The issue is when i looked into
the united atom itp file, I found many bonds and angles has not determined. So,
just wondering if there are any published reports to edit it manually.



A quick literature search should turn something up.  Google returns lots of 
results if you search "Gromos96 acetyl CoA" (without the quotes).


I looked at the missing bonded parameters and they should all be quite easy to 
define based on known values in ffbonded.itp - it is not clear to me why they 
are missing.  Most, if not all, of the missing bonds are between OA and H atoms, 
which are simple alcohol groups (bond type gb_1).


-Justin


Best regards





Quoting "Justin A. Lemkul" :




On 7/11/12 8:18 AM, Padmanabhan Anbazhagan wrote:

Dear All,
Could anyone please suggest me some article or information that contains
force field parameters (gromacs53A6) for acetyl Coenzyme A



Google turned up:

http://compbio.biosci.uq.edu.au/atb/download.py?molid=5470

-Justin

--


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




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




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Re: [gmx-users] Forcefield parameters for AcetylCoA

[Justin A. Lemkul]

On 7/11/12 8:18 AM, Padmanabhan Anbazhagan wrote:

Dear All,
Could anyone please suggest me some article or information that contains
force field parameters (gromacs53A6) for acetyl Coenzyme A



Google turned up:

http://compbio.biosci.uq.edu.au/atb/download.py?molid=5470

-Justin

--


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




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[gmx-users] Forcefield parameters for AcetylCoA

[Padmanabhan Anbazhagan]

Dear All,
Could anyone please suggest me some article or information that contains
force field parameters (gromacs53A6) for acetyl Coenzyme A

Thanks in advance.

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Re: [gmx-users] Forcefield question

[Mark Abraham]

On 13/02/2012 9:46 PM, Matthias Ernst wrote:

Hi,

I am currently working with the AMBER forcefields provided by GROMACS. 
I noticed there are atoms in the forcefields (e.g. amber99 or amber03) 
with LJ parameters of 0.0 for sigma and epsilon. For example, the HO 
atom type is sometimes used (e.g. in SER or in the terminal Hs of DNA 
residues) but has such paramaters (see below).
I do not understand (yet) how that can give physically meaningful 
results. For sigma, I could understand that with combination rule 2, 
the resulting sigma for a bond is not zero. But the contribution to 
the total energy vanishes because of epsilon being zero and as such, I 
think clashes between such an atom and some other atom cannot be 
avoided because there is no energetic "penalty" for this.
Am I getting something wrong? Are there some default values that are 
applied if sigma and epsilon are zero or are those values stored 
somewhere else but not in ffnonbonded.itp?


No, but the HO atom type is for modelling X-O-H where X is not H. The 
water model(s) which which AMBER are parameterized do not have VDW 
parameters for H in water, and likely the absence of them on alcoholic H 
is for consistency with that. The theory goes that H is too small and 
too labile by comparison with the O, so it may as well not occupy volume.


You may find the issue discussed in the AMBER papers, or confirmed in 
the AMBER force field files (which I hope are freely downloadable 
somewhere).


Mark



Thank you for your help,
Matthias

===
This is part of amber ffnonbonded.itp:

[ atomtypes ]
; name  at.num  mass charge ptype  sigma  epsilon
Br  35  79.900.  A   0.0e+00  0.0e+00
HO   1   1.008   0.  A   0.0e+00  0.0e+00
HW   1   1.008   0.  A   0.0e+00  0.0e+00
FE  26  55.000.  A   0.0e+00  0.0e+00


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[gmx-users] Forcefield question

[Matthias Ernst]

Hi,

I am currently working with the AMBER forcefields provided by GROMACS. I 
noticed there are atoms in the forcefields (e.g. amber99 or amber03) 
with LJ parameters of 0.0 for sigma and epsilon. For example, the HO 
atom type is sometimes used (e.g. in SER or in the terminal Hs of DNA 
residues) but has such paramaters (see below).
I do not understand (yet) how that can give physically meaningful 
results. For sigma, I could understand that with combination rule 2, the 
resulting sigma for a bond is not zero. But the contribution to the 
total energy vanishes because of epsilon being zero and as such, I think 
clashes between such an atom and some other atom cannot be avoided 
because there is no energetic "penalty" for this.
Am I getting something wrong? Are there some default values that are 
applied if sigma and epsilon are zero or are those values stored 
somewhere else but not in ffnonbonded.itp?


Thank you for your help,
Matthias

===
This is part of amber ffnonbonded.itp:

[ atomtypes ]
; name  at.num  mass charge ptype  sigma  epsilon
Br  35  79.900.  A   0.0e+00  0.0e+00
HO   1   1.008   0.  A   0.0e+00  0.0e+00
HW   1   1.008   0.  A   0.0e+00  0.0e+00
FE  26  55.000.  A   0.0e+00  0.0e+00
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Re: [gmx-users] Forcefield for Lipids

[Justin A. Lemkul]

Saumya wrote:

Hello all,

I am trying to simulate the DMPC Lipid Bilayer with water molecules. I 
am using Charmm27 forcefield for that. I obtain the starting structure 
from Charmm-GUI. The pdb file that I obtain has "DMPC" as the residue 
name for the lipid molecules. I checked the "lipid.rtp" file in Charmm27 
and it has DMPC in the list of lipids. But, when I generate the topology 
using pdb2gmx, it says that it does not recognize the the DMPC residue. 


Please copy and paste the exact error message.

Therefore, the resulting topology file does not include any information 
about the lipids and only states the solvent information.
How can I generate a topology that will include the DMPC lipids too and 
what residues name is recognized by Gromacs for the DMPC lipid? 


Without seeing the error, it's hard to say.  Also note that pdb2gmx is not 
typically used for many-molecule systems like bilayers.  You'll get a redundant 
topology that is not wrong, but will be very cumbersome to use and understand.


The better approach is to:

1. Isolate a single DMPC lipid from your .pdb file
2. Run pdb2gmx on this single lipid
3. Modify the resulting .top into a .itp file (see 
http://www.gromacs.org/Documentation/File_Formats/.itp_File)

4. Construct a simple topology, i.e.:

#include "charmm27.ff/forcefield.itp"
#include "dmpc.itp"
#include (water model you need)

[ system ]
whatever

[ molecules ]
(fill this in)

-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] Forcefield for Lipids

[Saumya]

Hello all,

I am trying to simulate the DMPC Lipid Bilayer with water molecules. I am
using Charmm27 forcefield for that. I obtain the starting structure from
Charmm-GUI. The pdb file that I obtain has "DMPC" as the residue name for
the lipid molecules. I checked the "lipid.rtp" file in Charmm27 and it has
DMPC in the list of lipids. But, when I generate the topology using pdb2gmx,
it says that it does not recognize the the DMPC residue. Therefore, the
resulting topology file does not include any information about the lipids
and only states the solvent information.
How can I generate a topology that will include the DMPC lipids too and what
residues name is recognized by Gromacs for the DMPC lipid?
Kindly guide.

Regards,
Saumya
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Re: [gmx-users] Forcefield parameters

[Mark Abraham]

On 28/10/2010 3:03 AM, Sai Pooja wrote:

Hi Mark,
I am familiar with the section, however, I have a few doubts.
When you say ...
So modified protein-water VDW interactions can be introduced by 
defining all relevant "protein atom"-"TIP3P oxygen" [nonbond_params] 
terms.
Do you mean that I can introduce [pairtypes] specifying interactions 
of all "relevant protein atoms" with "tip3p atoms"?

No, [pairtypes] are not relevant.
and I do not understand - It may be simpler to modify the [atomtypes] 
to generate the "modified" VDW from the combination rule
Would this not alter all non-bonded interactions for the atomtypes 
defined? I think I haven't understood thsi properly...


I was thinking of a flawed procedure. Ignore this part.

Mark


Pooja

On Tue, Oct 26, 2010 at 8:21 PM, Mark Abraham <mailto:mark.abra...@anu.edu.au>> wrote:


I think manual 5.3.3 covers the relevant points. Let me know what
is not clear.

Mark


- Original Message -
From: Sai Pooja mailto:saipo...@gmail.com>>
    Date: Wednesday, October 27, 2010 9:41
Subject: Re: [gmx-users] Forcefield parameters
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>

>
>
> On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham
 wrote:

>
>
> - Original Message -
    > From: Sai Pooja 
> Date: Wednesday, October 27, 2010 8:52
> Subject: Re: [gmx-users] Forcefield parameters
> To: Discussion list for GROMACS users 
>
> > On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul
 wrote:

> >
> >
> > Sai Pooja wrote:

> >
> >
> > On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>> wrote:
> >
> >
> >
> >Sai Pooja wrote:
> >
> >Hi,
> > I want to change the non-bonded parameters
to modify the
> >interaction between water molecules and
protein molecules.
> > I am using CHARMM forcefield with Tip3p water.
> > The ffnonbonded.itp file of the forcefield
has non-bonded
> >parameters for tip3p water. Can I achieve
the above by changing
> >these parameters?
> >
> >
> >That depends on your definition of "modify,"
but yes, in a way, you
> >can make changes here.
> >   1) Modify - Multiply sigma and epsilon by a constant
> >
> >If yes, will this also change the
non-bonded parameters for
> >water - water interaction?
> >
> > 2) Is there a way to add a new ifdef perhaps such
that a modified sigma and epsilon can be used for
water-protein interactions and the unmodified
parameters can be used for water-water interactions?
> >

> >
> > Nonbonded interactions are calculated during the
simulation by applying the combination rules defined by
the force field.  There is no simple way to do this with
an ifdef, since that is just in the topology.  You can't
conditionally apply nonbonded parameters.  That just
sounds like a recipe for breaking a force field.

>
> Not quite right. Parameters for VDW are calculated from the
combination rules from the atom-specific values given in
[atomtypes] only as a last resort. [nonbond_params] are used
in preference to such.
>
> So modified protein-water VDW interactions can be introduced
by defining all relevant "protein atom"-"TIP3P oxygen"
[nonbond_params] terms. It may be simpler to modify the
[atomtypes] to generate the "modified" VDW from the
combination rule, and introduce the "normal" TIP3P
oxygen-oxygen interaction via [nonbond_params].

>
> Mark, could you please elaborate the method?

>
> Mark
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Re: [gmx-users] Forcefield parameters

[Mark Abraham]

I think manual 5.3.3 covers the relevant points. Let me know what is not clear.

Mark

- Original Message -
From: Sai Pooja 
Date: Wednesday, October 27, 2010 9:41
Subject: Re: [gmx-users] Forcefield parameters
To: Discussion list for GROMACS users 

> 
> 
 > On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham  
 > wrote:
  > 
> 
> - Original Message -
> From: Sai Pooja 
> Date: Wednesday, October 27, 2010 8:52
> Subject: Re: [gmx-users] Forcefield parameters
>   To: Discussion list for GROMACS users 
> 
 > > On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul  wrote:
   > > 
  > > 
> > Sai Pooja wrote:  
 > > 
  > > 
> > On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul  > <mailto:jalem...@vt.edu>> wrote:
  > > 
> > 
  > > 
> >Sai Pooja wrote:
  > > 
> >Hi,
  > > I want to change the non-bonded parameters to modify the
> >interaction between water molecules and protein molecules.
  > > I am using CHARMM forcefield with Tip3p water.
> > The ffnonbonded.itp file of the forcefield has non-bonded
  > >parameters for tip3p water. Can I achieve the above by changing
> >these parameters?
  > > 
> > 
  > >That depends on your definition of "modify," but yes, in a way, you
> >can make changes here. 
  > >   1) Modify - Multiply sigma and epsilon by a constant
> > 
  > >If yes, will this also change the non-bonded parameters for
> >water - water interaction?
  > > 
> > 2) Is there a way to add a new ifdef perhaps such that a modified sigma and 
> > epsilon can be used for water-protein interactions and the unmodified 
> > parameters can be used for water-water interactions?
  > >  
> > 
  > > Nonbonded interactions are calculated during the simulation by applying 
the combination rules defined by the force field.  There is no simple way to do 
this with an ifdef, since that is just in the topology.  You can't 
conditionally apply nonbonded parameters.  That just sounds like a recipe for 
breaking a force field.
  > 
> Not quite right. Parameters for VDW are calculated from the combination rules 
> from the atom-specific values given in [atomtypes] only as a last resort. 
> [nonbond_params] are used in preference to such.
  > 
> So modified protein-water VDW interactions can be introduced by defining all 
> relevant "protein atom"-"TIP3P oxygen" [nonbond_params] terms. It may be 
> simpler to modify the [atomtypes] to generate the "modified" VDW from the 
> combination rule, and introduce the "normal" TIP3P oxygen-oxygen interaction 
> via [nonbond_params].
   >   > Mark, could you please elaborate the method? > 
> Mark 
> --
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  > 
> > 
> -- 
> Quaerendo Invenietis-Seek and you shall discover.
 > -- 
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Re: [gmx-users] Forcefield parameters

[Sai Pooja]

On Tue, Oct 26, 2010 at 6:04 PM, Mark Abraham wrote:

>
>
> - Original Message -
> From: Sai Pooja 
> Date: Wednesday, October 27, 2010 8:52
> Subject: Re: [gmx-users] Forcefield parameters
> To: Discussion list for GROMACS users 
>
> > On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul wrote:
>
>> >
>> >
>> > Sai Pooja wrote:
>>
>> >
>>> >
>>> > On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>> >
>>> >
>>> >
>>> >Sai Pooja wrote:
>>> >
>>> >Hi,
>>> > I want to change the non-bonded parameters to modify the
>>> >interaction between water molecules and protein molecules.
>>> > I am using CHARMM forcefield with Tip3p water.
>>> > The ffnonbonded.itp file of the forcefield has non-bonded
>>> >parameters for tip3p water. Can I achieve the above by changing
>>> >these parameters?
>>> >
>>> >
>>> >That depends on your definition of "modify," but yes, in a way, you
>>> >can make changes here.
>>> >   1) Modify - Multiply sigma and epsilon by a constant
>>> >
>>> >If yes, will this also change the non-bonded parameters for
>>> >water - water interaction?
>>> >
>>> > 2) Is there a way to add a new ifdef perhaps such that a modified
>>> sigma and epsilon can be used for water-protein interactions and the
>>> unmodified parameters can be used for water-water interactions?
>>> >
>>>
>> >
>> > Nonbonded interactions are calculated during the simulation by applying
>> the combination rules defined by the force field.  There is no simple way to
>> do this with an ifdef, since that is just in the topology.  You can't
>> conditionally apply nonbonded parameters.  That just sounds like a recipe
>> for breaking a force field.
>>
>
> Not quite right. Parameters for VDW are calculated from the combination
> rules from the atom-specific values given in [atomtypes] only as a last
> resort. [nonbond_params] are used in preference to such.
>
> So modified protein-water VDW interactions can be introduced by defining
> all relevant "protein atom"-"TIP3P oxygen" [nonbond_params] terms. It may be
> simpler to modify the [atomtypes] to generate the "modified" VDW from the
> combination rule, and introduce the "normal" TIP3P oxygen-oxygen interaction
> via [nonbond_params].
>

Mark, could you please elaborate the method?

>
> Mark
> --
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Re: [gmx-users] Forcefield parameters

[Mark Abraham]

- Original Message -
From: Sai Pooja 
Date: Wednesday, October 27, 2010 8:52
Subject: Re: [gmx-users] Forcefield parameters
To: Discussion list for GROMACS users 

> On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul  wrote:
 > 
> 
> Sai Pooja wrote:  
 > 
> 
> On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul  <mailto:jalem...@vt.edu>> wrote:
  > 
> 
> 
>Sai Pooja wrote:
> 
>Hi,
> I want to change the non-bonded parameters to modify the
>interaction between water molecules and protein molecules.
> I am using CHARMM forcefield with Tip3p water.
>   The ffnonbonded.itp file of the forcefield has non-bonded
>parameters for tip3p water. Can I achieve the above by changing
>these parameters?
> 
> 
>That depends on your definition of "modify," but yes, in a way, you
>  can make changes here. 
>   1) Modify - Multiply sigma and epsilon by a constant
> 
>If yes, will this also change the non-bonded parameters for
>water - water interaction?
> 
> 2) Is there a way to add a new ifdef perhaps such that a modified sigma and 
> epsilon can be used for water-protein interactions and the unmodified 
> parameters can be used for water-water interactions?
>
> 
> Nonbonded interactions are calculated during the simulation by applying the 
> combination rules defined by the force field.  There is no simple way to do 
> this with an ifdef, since that is just in the topology.  You can't 
> conditionally apply nonbonded parameters.  That just sounds like a recipe for 
> breaking a force field.

Not quite right. Parameters for VDW are calculated from the combination rules 
from the atom-specific values given in [atomtypes] only as a last resort. 
[nonbond_params] are used in preference to such.

So modified protein-water VDW interactions can be introduced by defining all 
relevant "protein atom"-"TIP3P oxygen" [nonbond_params] terms. It may be 
simpler to modify the [atomtypes] to generate the "modified" VDW from the 
combination rule, and introduce the "normal" TIP3P oxygen-oxygen interaction 
via [nonbond_params].

Mark

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Re: [gmx-users] Forcefield parameters

[Justin A. Lemkul]

Sai Pooja wrote:
On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul > wrote:




Sai Pooja wrote:



On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Sai Pooja wrote:

   Hi,
I want to change the non-bonded parameters to modify the
   interaction between water molecules and protein molecules.
I am using CHARMM forcefield with Tip3p water.
The ffnonbonded.itp file of the forcefield has non-bonded
   parameters for tip3p water. Can I achieve the above by
changing
   these parameters?
   


   That depends on your definition of "modify," but yes, in a
way, you
   can make changes here.
  1) Modify - Multiply sigma and epsilon by a constant

   If yes, will this also change the non-bonded parameters for
   water - water interaction?

2) Is there a way to add a new ifdef perhaps such that a
modified sigma and epsilon can be used for water-protein
interactions and the unmodified parameters can be used for
water-water interactions?
 



Nonbonded interactions are calculated during the simulation by
applying the combination rules defined by the force field.  There is
no simple way to do this with an ifdef, since that is just in the
topology.  You can't conditionally apply nonbonded parameters.  That
just sounds like a recipe for breaking a force field.

 
In that case, changing sigma and epsilon of tip3p water molecules in the 
ffnonbonded.itp files will change both water-protein and water-water Vdw 
interactions.
Also if I multiply q for tip3p water molecules in the same file, I can 
modify the water-water and water-coulomb interactions.
 


Any change you might make to the TIP3P parameters (LJ parameters or charges) 
will inherently change the intermolecular interactions between whatever species 
are in your system.


-Justin


-Pooja

-Justin

Pooja
 
   


   Yes.

   -Justin


   Pooja

   -- Quaerendo Invenietis-Seek and you shall discover.


   -- 

   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

   >

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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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--


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] Forcefield parameters

[Sai Pooja]

On Tue, Oct 26, 2010 at 4:04 PM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>
>>
>> On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Sai Pooja wrote:
>>
>>Hi,
>> I want to change the non-bonded parameters to modify the
>>interaction between water molecules and protein molecules.
>> I am using CHARMM forcefield with Tip3p water.
>> The ffnonbonded.itp file of the forcefield has non-bonded
>>parameters for tip3p water. Can I achieve the above by changing
>>these parameters?
>>
>>
>>That depends on your definition of "modify," but yes, in a way, you
>>can make changes here.
>>   1) Modify - Multiply sigma and epsilon by a constant
>>
>>If yes, will this also change the non-bonded parameters for
>>water - water interaction?
>>
>> 2) Is there a way to add a new ifdef perhaps such that a modified sigma
>> and epsilon can be used for water-protein interactions and the unmodified
>> parameters can be used for water-water interactions?
>>
>>
>
> Nonbonded interactions are calculated during the simulation by applying the
> combination rules defined by the force field.  There is no simple way to do
> this with an ifdef, since that is just in the topology.  You can't
> conditionally apply nonbonded parameters.  That just sounds like a recipe
> for breaking a force field.
>

In that case, changing sigma and epsilon of tip3p water molecules in the
ffnonbonded.itp files will change both water-protein and water-water Vdw
interactions.
Also if I multiply q for tip3p water molecules in the same file, I can
modify the water-water and water-coulomb interactions.

-Pooja

> -Justin
>
>  Pooja
>>
>>
>>
>>Yes.
>>
>>-Justin
>>
>>
>>Pooja
>>
>>-- Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>-- 
>>
>>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
>>
>>
>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
> --
> 
>
> 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
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Re: [gmx-users] Forcefield parameters

[Justin A. Lemkul]

Sai Pooja wrote:



On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul > wrote:




Sai Pooja wrote:

Hi,
 I want to change the non-bonded parameters to modify the
interaction between water molecules and protein molecules.
 I am using CHARMM forcefield with Tip3p water.
 The ffnonbonded.itp file of the forcefield has non-bonded
parameters for tip3p water. Can I achieve the above by changing
these parameters?
 



That depends on your definition of "modify," but yes, in a way, you
can make changes here. 

   
1) Modify - Multiply sigma and epsilon by a constant


If yes, will this also change the non-bonded parameters for
water - water interaction?

2) Is there a way to add a new ifdef perhaps such that a modified sigma 
and epsilon can be used for water-protein interactions and the 
unmodified parameters can be used for water-water interactions?
 


Nonbonded interactions are calculated during the simulation by applying the 
combination rules defined by the force field.  There is no simple way to do this 
with an ifdef, since that is just in the topology.  You can't conditionally 
apply nonbonded parameters.  That just sounds like a recipe for breaking a force 
field.


-Justin


Pooja
 

 



Yes.

-Justin


Pooja

-- 
Quaerendo Invenietis-Seek and you shall discover.



-- 



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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--
Quaerendo Invenietis-Seek and you shall discover.



--


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] Forcefield parameters

[Sai Pooja]

On Tue, Oct 26, 2010 at 3:46 PM, Justin A. Lemkul  wrote:

>
>
> Sai Pooja wrote:
>
>> Hi,
>>  I want to change the non-bonded parameters to modify the interaction
>> between water molecules and protein molecules.
>>  I am using CHARMM forcefield with Tip3p water.
>>  The ffnonbonded.itp file of the forcefield has non-bonded parameters for
>> tip3p water. Can I achieve the above by changing these parameters?
>>
>>
>
> That depends on your definition of "modify," but yes, in a way, you can
> make changes here.


1) Modify - Multiply sigma and epsilon by a constant

>  If yes, will this also change the non-bonded parameters for water - water
>> interaction?
>>
>  2) Is there a way to add a new ifdef perhaps such that a modified sigma
and epsilon can be used for water-protein interactions and the unmodified
parameters can be used for water-water interactions?

Pooja


>
>>
>
> Yes.
>
> -Justin
>
>
> Pooja
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
> --
> 
>
> 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] Forcefield parameters

[Justin A. Lemkul]

Sai Pooja wrote:

Hi,
 
I want to change the non-bonded parameters to modify the interaction 
between water molecules and protein molecules.
 
I am using CHARMM forcefield with Tip3p water.
 
The ffnonbonded.itp file of the forcefield has non-bonded parameters for 
tip3p water. Can I achieve the above by changing these parameters?
 


That depends on your definition of "modify," but yes, in a way, you can make 
changes here.


If yes, will this also change the non-bonded parameters for water - 
water interaction?
 


Yes.

-Justin


Pooja

--
Quaerendo Invenietis-Seek and you shall discover.



--


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] Forcefield parameters

[Sai Pooja]

Hi,

I want to change the non-bonded parameters to modify the interaction between
water molecules and protein molecules.

I am using CHARMM forcefield with Tip3p water.

The ffnonbonded.itp file of the forcefield has non-bonded parameters for
tip3p water. Can I achieve the above by changing these parameters?

If yes, will this also change the non-bonded parameters for water - water
interaction?

Pooja

-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
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Re: [gmx-users] forcefield

[Tsjerk Wassenaar]

Hi Lalitha,

Zebularine is beyond the trivial. You may be able to derive something
reasonable from the other bases using 'chemical intuition' (cytidine,
thymidine, uracil), but it's likely that the electronic structure of
the ring is too different to justify an approach like that. Likely you
should perform parameterization the proper way, which is not a
beginners subject. At least have a look at
http://www.gromacs.org/WIKI-import/Parametrization

Cheers,

Tsjerk

On Wed, Oct 14, 2009 at 7:30 AM, lalitha selvam  wrote:
> Hi,
>
> I want to do simulation with the ligand called zebularine. I dont find
> forcefied for that. Also i read prodgr has been deprecated..
> Could you please help me to find out the forcefield for the ligand
> zebularine.
> Thanks in advance
> lalitha
>
> 
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[gmx-users] forcefield

[lalitha selvam]

Hi,

 

I want to do simulation with the ligand called zebularine. I dont find 
forcefied for that. Also i read prodgr has been deprecated..

Could you please help me to find out the forcefield for the ligand zebularine.

Thanks in advance

lalitha
  
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Re: [gmx-users] forcefield for free (neutral) amino acids

[Mark Abraham]

FyD wrote:

Dear chun feng,

I am not a user of GROMACS, but I hope someone who's working on  
protein dynamics can do me a favor here. I am desperately searching  
for a forcefield for free and neutral amino acids. But it seems that 
 the forcefields such as amber and opls only parametrizes amino acids  
in peptides (without OH and H) and terminal amino acids on peptides.


Yes

I know there has to be some forcefield already developed for popular 
 molecules like amino acids, anyone please point me the way! Thanks a  
million!


You could derive your own force field for such amino-acids. You can 
derive RESP and ESP charges for any molecule or molecular fragment 
containing chemical elements up to Bromine using the R.E.D. tools. See 
http://q4md-forcefieldtools.org/


The "Generalized AMBER Force Field" and the AMBER utility program 
antechamber is probably also suited to the task.


Mark
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Re: [gmx-users] forcefield for free (neutral) amino acids

[FyD]

Dear chun feng,

I am not a user of GROMACS, but I hope someone who's working on   
protein dynamics can do me a favor here. I am desperately searching   
for a forcefield for free and neutral amino acids. But it seems that  
 the forcefields such as amber and opls only parametrizes amino  
acids  in peptides (without OH and H) and terminal amino acids on  
peptides.


Yes

I know there has to be some forcefield already developed for popular  
 molecules like amino acids, anyone please point me the way! Thanks  
a  million!


You could derive your own force field for such amino-acids. You can  
derive RESP and ESP charges for any molecule or molecular fragment  
containing chemical elements up to Bromine using the R.E.D. tools. See  
http://q4md-forcefieldtools.org/


regards, Francois


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[gmx-users] forcefield for free (neutral) amino acids

[chun feng]

Hi all:

I am not a user of GROMACS, but I hope someone who's working on protein 
dynamics can do me a favor here. I am desperately searching for a forcefield 
for free and neutral amino acids. But it seems that the forcefields such as 
amber and opls only parametrizes amino acids in peptides (without OH and H) and 
terminal amino acids on peptides. I know there has to be some forcefield 
already developed for popular molecules like amino acids, anyone please point 
me the way! Thanks a million!



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Re: [gmx-users] Forcefield to choose

[Justin A. Lemkul]

vivek sharma wrote:

Hi everybody,
I am running MDS for protein molecule using GROMACS, but I am not sure 
of which forcefield I should use.

Can anybody suggest me the criteria for choosing forcefield ?



Every force field has its inherent benefits and limitations.  There is no 
substitute for studying up on each (by reading the primary literature), and 
choosing the one best suited to your system.  A bit of a shortcut would be to 
look into the literature for similar systems and see what people are using.


Also, I am using drug-enzyme tutorial by John E. Kerrigan titled 
"GROMACS Tutorial for Drug – Enzyme Complex." where it is suggested to 
use PRODRG server for residues whose entry is not available in .rtp. In 
this tutorial it is suggested to edit the .gro and .top file manually, 
Can anybody suggest any other way (may be some tool or command) of doing 
such editing (not manually).


As in, separating the ligand and protein coordinates from each other?  I suppose 
trjconv could do it, but it really is a trivial task to use a text editor... 
IIRC, the tutorial walks you through every step of modifying the 
PRODRG-generated topology.


Also note that if you use PRODRG/PRODRG2.5 your force field has already been 
chosen for you (ffgmx in the case of PRODRG and ffG43a1 for PRODRG2.5).  If this 
is not suitable, then you have a difficult task of parameterization ahead!


-Justin



With Thanks
Vivek




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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Forcefield to choose

[vivek sharma]

Hi everybody,
I am running MDS for protein molecule using GROMACS, but I am not sure of
which forcefield I should use.
Can anybody suggest me the criteria for choosing forcefield ?

Also, I am using drug-enzyme tutorial by John E. Kerrigan titled "GROMACS
Tutorial for Drug – Enzyme Complex." where it is suggested to use PRODRG
server for residues whose entry is not available in .rtp. In this tutorial
it is suggested to edit the .gro and .top file manually, Can anybody suggest
any other way (may be some tool or command) of doing such editing (not
manually).

With Thanks
Vivek
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Re: [gmx-users] forcefield validation

[David Mobley]

>
> First, thanks very much for your instruction. If quantum chemical
> calculation does not have any physical meaning, how should I decide the
> partial charge for a molecule?

David is correct, he was referring to Mulliken charges.

Again, there is no *right* answer to this, the name of the game is
consistency. You need to derive parameters according to the
parameterization procedure for your force field. i.e. AMBER works best
with charges that are like HF 6/31G* RESP charges that the force field
was parameterized with. Presumably there are other answers for CHARMM,
gmx, etc. It's not my job to know all of the answers...

Best wishes,
David

> Any suggestion will be appreciated, thanks very much in advance.
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Re: [gmx-users] forcefield validation

[David Mobley]

Hi,

 Many
> articles didn't give out the validation procedure of their topologies in
> detail, are there some classic articles explaining how the forcefield we
> used today, such as OPLS, GROMOS, AMBER and CHARMM , developed? I want to
> know how they were deduced from the very beginning.


There is also a recent review article from Jay Ponder and someone else
(Dave Case, I think?) relating to this. You can find the reference on
Jay Ponder's web page.

David

> Any suggestion will be appreciated , thanks very much in advance.
>
>
>
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Re: [gmx-users] forcefield validation

[David van der Spoel]

Qin Shanshan wrote:
> 
> First, thanks very much for your instruction. If quantum chemical 
> calculation does not have any physical meaning, how should I decide the 
> partial charge for a molecule?
>  
I think Mark referred to Mulliken charges. Check how your favorite FF
does it and follow the recipe.

> Any suggestion will be appreciated, thanks very much in advance.
> 
> 
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] forcefield validation

[Qin Shanshan]

First, thanks very much for your instruction. If quantum chemical calculation 
does not have any physical meaning, how should I decide the partial charge for 
a molecule?

Any suggestion will be appreciated, thanks very much in advance.___
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Re: [gmx-users] forcefield validation

[Mark Abraham]

Qin Shanshan wrote:
> Thanks very much for your patient explaination.It really is a question 
> confusing me much. What I am interested in is inserting some organic 
> molecules into lipid bilayers. Tieleman's lipid parameters have given 
> out the interactive LJ parameters with ffgmx forcefield. So if I want to 
> simulate lipid with tileman's force field I should use ffgmx for organic 
> molecules. However I have to prove the ffgmx forcefield for organic 
> molecules is correct too. Somebody prove this by calculating the new 
> molecules' melting point or their structures in  solutions to compare 
> with X-ray results. I found
> Monika Holtje's BBA article(Biochimica et Biophysica Acta 1511 (2001) 
> 156^167), they simulated cholesterol and stearic acid and palmitic acid, 
> constructing topology files using Gromos 87 forcefield , and put the 
> Cholesterol topology on Gromacs website.They said " The geometries, 
> conformations and configurations as they occur instandard GROMACS 
> dynamics in vacuo and in water using the parameter set in this file, 
> compared well with crystal structures". In their topology , they set the 
> partial charge like this:
>  
>  
> ;   nrtype   resnr  residuatomcgnrcharge   ; total charge
>  1 CH3   1CHOL C11 0
>  2  CB   1CHOL C22 0
>  3 CH2   1CHOL C33 0
>  4 CH2   1CHOL C44 0
>  5 CH1   1CHOL C55 0.14 ; charges adopted
>  6  OA   1CHOL O65-0.54 ; from Retinol in
>  7  HO   1CHOL H 5 0.40 ; ffgmx.rtp
>  8 CH2   1CHOL C86 0
>  9  CB   1CHOL C97 0
> 10CR61   1CHOL C10   8 0
> 11 CH2   1CHOL C11   9 0
> 12 CH1   1CHOL C12  10 0
> 13 CH1   1CHOL C13  11 0
> 14 CH2   1CHOL C14  12 0
> 15 CH2   1CHOL C15  13 0
> 16  CB   1CHOL C16  14 0
> 17 CH3   1CHOL C17  15 0
> 18 CH1   1CHOL C18  16 0
> 19 CH2   1CHOL C19  17 0
> 20 CH2   1CHOL C20  18 0
> 21 CH1   1CHOL C21  19 0
> 22 CH1   1CHOL C22  20 0
> 23 CH3   1CHOL C23  21 0
> 24 CH2   1CHOL C24  22 0
> 25 CH2   1CHOL C25  23 0
> 26 CH2   1CHOL C26  24 0
> 27 CH1   1CHOL C27  25 0
> 28 CH3   1CHOL C28  26 0
> 29 CH3   1CHOL C29  27 0

This charge distribution looks particularly weird and/or indefensible.

> However when I use B3lyp/6-31G(d,p) to calculate mulliken 
> distribution 

...which doesn't have any physical meaning...

> of cholesterol the charge distribution is rather different. 
> How did they decide their partial charge? 

You'd have to ask them, or read their paper.

> Is it customed to let alkane 
> groups zero charged?

No.

> Many articles didn't give out the validation 
> procedure of their topologies in detail, are there some classic articles 
> explaining how the forcefield we used today, such as OPLS, GROMOS, AMBER 
> and CHARMM , developed? I want to know how they were deduced from the 
> very beginning.

They're all referenced in the GROMACS manual, like you'd expect.

Mark
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[gmx-users] forcefield validation

[Qin Shanshan]

Thanks very much for your patient explaination.It really is a question 
confusing me much. What I am interested in is inserting some organic molecules 
into lipid bilayers. Tieleman's lipid parameters have given out the interactive 
LJ parameters with ffgmx forcefield. So if I want to simulate lipid with 
tileman's force field I should use ffgmx for organic molecules. However I have 
to prove the ffgmx forcefield for organic molecules is correct too. Somebody 
prove this by calculating the new molecules' melting point or their structures 
in  solutions to compare with X-ray results. I found 
Monika Holtje's BBA article(Biochimica et Biophysica Acta 1511 (2001) 156^167), 
they simulated cholesterol and stearic acid and palmitic acid, constructing 
topology files using Gromos 87 forcefield , and put the Cholesterol topology on 
Gromacs website.They said " The geometries, conformations and configurations as 
they occur instandard GROMACS dynamics in vacuo and in water using the 
parameter set in this file, compared well with crystal structures". In their 
topology , they set the partial charge like this:


;   nrtype   resnr  residuatomcgnrcharge   ; total charge
 1 CH3   1CHOL C11 0
 2  CB   1CHOL C22 0
 3 CH2   1CHOL C33 0
 4 CH2   1CHOL C44 0
 5 CH1   1CHOL C55 0.14 ; charges adopted
 6  OA   1CHOL O65-0.54 ; from Retinol in
 7  HO   1CHOL H 5 0.40 ; ffgmx.rtp
 8 CH2   1CHOL C86 0
 9  CB   1CHOL C97 0
10CR61   1CHOL C10   8 0
11 CH2   1CHOL C11   9 0
12 CH1   1CHOL C12  10 0
13 CH1   1CHOL C13  11 0
14 CH2   1CHOL C14  12 0
15 CH2   1CHOL C15  13 0
16  CB   1CHOL C16  14 0
17 CH3   1CHOL C17  15 0
18 CH1   1CHOL C18  16 0
19 CH2   1CHOL C19  17 0
20 CH2   1CHOL C20  18 0
21 CH1   1CHOL C21  19 0
22 CH1   1CHOL C22  20 0
23 CH3   1CHOL C23  21 0
24 CH2   1CHOL C24  22 0
25 CH2   1CHOL C25  23 0
26 CH2   1CHOL C26  24 0
27 CH1   1CHOL C27  25 0
28 CH3   1CHOL C28  26 0
29 CH3   1CHOL C29  27 0

However when I use B3lyp/6-31G(d,p) to calculate mulliken distribution of 
cholesterol the charge distribution is rather different. How did they decide 
their partial charge? Is it customed to let alkane groups zero charged? Many 
articles didn't give out the validation procedure of their topologies in 
detail, are there some classic articles explaining how the forcefield we used 
today, such as OPLS, GROMOS, AMBER and CHARMM , developed? I want to know how 
they were deduced from the very beginning.

Any suggestion will be appreciated , thanks very much in advance.
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[gmx-users] forcefield validation

[Qin Shanshan]

Thanks very much for your patient explaination.It really is a question 
confusing me much. What I am interested in is inserting some organic molecules 
into lipid bilayers. Tieleman's lipid parameters have given out the interactive 
LJ parameters with ffgmx forcefield. So if I want to simulate lipid with 
tileman's force field I should use ffgmx for organic molecules. However I have 
to prove the ffgmx forcefield for organic molecules is correct too. Somebody 
prove this by calculating the new molecules' melting point or their structures 
in  solutions to compare with X-ray results. I found 
Monika Holtje's BBA article(Biochimica et Biophysica Acta 1511 (2001) 156^167), 
they simulated cholesterol and stearic acid and palmitic acid, constructing 
topology files using Gromos 87 forcefield , and put the Cholesterol topology on 
Gromacs website.They said " The geometries, conformations and configurations as 
they occur instandard GROMACS dynamics in vacuo and in water using the 
parameter set in this file, compared well with crystal structures". In their 
topology , they set the partial charge like this:


;   nrtype   resnr  residuatomcgnrcharge   ; total charge
 1 CH3   1CHOL C11 0
 2  CB   1CHOL C22 0
 3 CH2   1CHOL C33 0
 4 CH2   1CHOL C44 0
 5 CH1   1CHOL C55 0.14 ; charges adopted
 6  OA   1CHOL O65-0.54 ; from Retinol in
 7  HO   1CHOL H 5 0.40 ; ffgmx.rtp
 8 CH2   1CHOL C86 0
 9  CB   1CHOL C97 0
10CR61   1CHOL C10   8 0
11 CH2   1CHOL C11   9 0
12 CH1   1CHOL C12  10 0
13 CH1   1CHOL C13  11 0
14 CH2   1CHOL C14  12 0
15 CH2   1CHOL C15  13 0
16  CB   1CHOL C16  14 0
17 CH3   1CHOL C17  15 0
18 CH1   1CHOL C18  16 0
19 CH2   1CHOL C19  17 0
20 CH2   1CHOL C20  18 0
21 CH1   1CHOL C21  19 0
22 CH1   1CHOL C22  20 0
23 CH3   1CHOL C23  21 0
24 CH2   1CHOL C24  22 0
25 CH2   1CHOL C25  23 0
26 CH2   1CHOL C26  24 0
27 CH1   1CHOL C27  25 0
28 CH3   1CHOL C28  26 0
29 CH3   1CHOL C29  27 0

However when I use B3lyp/6-31G(d,p) to calculate mulliken distribution of 
cholesterol the charge distribution is rather different. How did they decide 
their partial charge? Is it customed to let alkane groups zero charged? Many 
articles didn't give out the validation procedure of their topologies in 
detail, are there some classic articles explaining how the forcefield we used 
today, such as OPLS, GROMOS, AMBER and CHARMM , developed? I want to know how 
they were deduced from the very beginning.

Any suggestion will be appreciated , thanks very much in advance.


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Re: [gmx-users] forcefield validation

[David Mobley]

Alan Dodd's suggestion is nice, but there isn't always a lot of
experimental data available for a particular molecule we can compare
with -- or perhaps we want to begin with "good" parameters and then
see if our method can reproduce experiment. Anyway, for whatever
reason it isn't always possible to do the sort of validation he
suggests.

The other basic approach the field takes is to do the following:
(a) Make sure your molecule of interest can be expected to be
well-described by standard parameterization procedures
(b) Pick the force field you want to use for the rest of your system of interest
(c) Derive parameters for your small molecule using the same procedure
as that used for the force field for the rest of the system (b) to
ensure consistency
(d) Assume that the parameters are OK, since they are consistent with
the rest of your force field, and proceed.

Consistency is really the name of the game here when direct comparison
with experiment can't be used for validation. You want to make sure
your parameters are consistent with the rest of the force field which
*has* been validated against experiment. And then, you also assume
that if you follow the procedure that led to that validated force
field, it also should give you good parameters for your small
molecule.

These are certainly important questions.

With regards to prodrg, at the very least you will need to re-derive
partial charges. But you also need to make sure it is consistent with
the rest of the force field you choose to use, which means you need to
look at those other issues as well. In particular, how is prodrg
deriving parameters? Is the procedure the same as that used for your
force field of interest?

I realize this may all seem like a pain in the neck if you just want
to simulate something. But you can't put garbage/inconsistency in and
expect to get something good out.

Best wishes,
David



On 10/16/07, Qin Shanshan <[EMAIL PROTECTED]> wrote:
>
>
> Dear gms-users, I have a fundamental question to put forward. If I want to
> construct a forcefield for an organic molecule of middle size,which has
> about 100 atoms, how can I prove that my forcefield for this molecule is
> correct? Althouth we can get ffgmx itp files from prodrg server, can we be
> sure that these topologies are definitely correct? If we want to convince
> others that our topologies are right, is there any criteria to compare with?
>  If I want to derive a forcefield for a particular molecule, what should I
> do?
> Any suggestion will be appreciated, thanks very much in advance.
> ___
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Re: [gmx-users] forcefield validation

[Alan Dodd]

Use the topologies/forcefields in a simulation/energy minimisation, and check 
that any predictions made by the simulation match up with any available 
experimental evidence.  Hopefully, you'll see that predictions are confirmed by 
existing experiments, and will suggest new experiments to be done.


- Original Message 
From: Qin Shanshan <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Tuesday, October 16, 2007 2:48:44 PM
Subject: [gmx-users] forcefield validation


Dear gms-users, I have a fundamental question to put forward. If I want to 
construct a forcefield for an organic molecule of middle size,which has about 
100 atoms, how can I prove that my forcefield for this molecule is correct? 
Althouth we can get ffgmx itp files from prodrg server, can we be sure that 
these topologies are definitely correct? If we want to convince others that our 
topologies are right, is there any criteria to compare with?  If I want to 
derive a forcefield for a particular molecule, what should I do?
Any suggestion will be appreciated, thanks very much in advance.


   

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[gmx-users] forcefield validation

[Qin Shanshan]

Dear gms-users, I have a fundamental question to put forward. If I want to 
construct a forcefield for an organic molecule of middle size,which has about 
100 atoms, how can I prove that my forcefield for this molecule is correct? 
Althouth we can get ffgmx itp files from prodrg server, can we be sure that 
these topologies are definitely correct? If we want to convince others that our 
topologies are right, is there any criteria to compare with?  If I want to 
derive a forcefield for a particular molecule, what should I do?
Any suggestion will be appreciated, thanks very much in advance. ___
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Re: [gmx-users] forcefield problems - advice needed

[Mark Abraham]

> hi guys,
>
> for quite a long time i am trying to 'create' a forcefield for aliphatic
> alcohols (right now, for ethanol) to use with a water potential we
> employ in our simulations.
>
> there is a problem - the water potential uses combination rule 2, so i
> thought i would just try to use FFGMX and OPLS and change it a bit. it
> didn't seem to work. i also tried the FFAMBER, that uses exactly this
> combination rule. unfortunately, it fails as well.
>
> i'm getting all sorts of errors - segfaults, lincs failures, ... in most
> cases, the whole simulation 'freezes' (kinetic energy of order of 1e-5,
> for example) and nothing happens. i am also quite frequently getting
> close contacts between atoms (within one molecule, or between two
> different molecules).
>
> it seems i am missing something in the forcefield, but i am not able to
> identify what is it... i would be very grateful if anyone of you could
> help me and shed more light in this.

To diagnose the source of this problem, you want to eliminate variables.
Start with a simple system, say methanol in vacuo, and see if you can do a
sensible energy minimization on that. Verify the various parts of the
potential energy by hand in a spreadsheet or something. Once you're happy
that your alcohol internal potentials are all good, then try an isolated
water-methanol complex and repeat. Gradually increase complexity and then
when something explodes you only have a few possible sources of problems.

> also a 'side question' - when using FFAMBER, there are dihedrals defined
> with all atom names specified (e.g., CT CT CT CT), and also dihedrals
> with wildcards (X  CT CT X). for a CT-CT-CT-CT dihedrals, both of these
> would be applicable - are they both used in the simulation, or does the
> latter (X CT CT X) override the former definition (CT CT CT CT)?

I would expect that a specific atom type would override a generic atom
type, although the manual seems to be silent on this issue. You can test
for this in your testing scheme above, of course!

Mark

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[gmx-users] forcefield problems - advice needed

[Lubos Vrbka]

hi guys,

for quite a long time i am trying to 'create' a forcefield for aliphatic 
alcohols (right now, for ethanol) to use with a water potential we 
employ in our simulations.


there is a problem - the water potential uses combination rule 2, so i 
thought i would just try to use FFGMX and OPLS and change it a bit. it 
didn't seem to work. i also tried the FFAMBER, that uses exactly this 
combination rule. unfortunately, it fails as well.


i'm getting all sorts of errors - segfaults, lincs failures, ... in most 
cases, the whole simulation 'freezes' (kinetic energy of order of 1e-5, 
for example) and nothing happens. i am also quite frequently getting 
close contacts between atoms (within one molecule, or between two 
different molecules).


it seems i am missing something in the forcefield, but i am not able to 
identify what is it... i would be very grateful if anyone of you could 
help me and shed more light in this.


if anyone has working alcohol potential (united or all atom type) with 
comb. rule 2, i would be more than happy, if you could share it with me...


also a 'side question' - when using FFAMBER, there are dihedrals defined 
with all atom names specified (e.g., CT CT CT CT), and also dihedrals 
with wildcards (X  CT CT X). for a CT-CT-CT-CT dihedrals, both of these 
would be applicable - are they both used in the simulation, or does the 
latter (X CT CT X) override the former definition (CT CT CT CT)?


once again, i would be very glad if anyone of you could help me. i went 
through the manual many times, but i am becoming more and more confused...


i attach the files for a simulation that is failing for me. it's 2+2 
pentanol molecules in a prismatic simulation box (i have it setup like 
this because we are normally doing slab simulations). all necessary 
files are included.


thanks. with best regards,
lubos


;
; forcefield by Lubos Vrbka for (contaminated) ice simulations
; Lubos Vrbka, 2006
; lubos (@) vrbka (.) net
;
; water parameters - nada/van der eerden
;   implementation by marcelo carignano (cari (@) purdue (.) edu)
; nacl parameters - j. chem. phys. 100, 3757
;   implementation by marcelo carignano (cari (@) purdue (.) edu)
;   used with spc/e - consistency?
; alcohol parameters - AMBER parm99 parameters
;   implementation by lubos vrbka (lubos (@) vrbka (.) net)
;
; changed gen-pairs to yes (consistently with amber FF) - should not affect
; NE6 water potential

#define _FF_ICE

[ defaults ]
; nbfunccomb-rule   gen-pairs   FudgeLJ FudgeQQ
  1 2   yes 0.5 0.8333

; *

[ atomtypes ]
;name  type masscharge  ptype   c6  c12
; original AMBER atom types: CT, H1, HC, OH, HO
; CT sp3 carbon (charge corresponding to CH3!)
; H1 hydrogen bound to C with el. withdrawing substituent
; HC hydrogen bound to C
; HO hydroxyl hydrogen
; OH hydroxyl oxygen 
; name  btype   masscharge  ptype   sigma   epsilon
CT  CT   12.010  0.1116 A   3.39967e-01 4.57730e-01
HC  HC   1.0080  0.0372 A   2.64953e-01 6.56888e-02
H1  H1   1.0080  0.0372 A   2.47135e-01 6.56888e-02
;HO HO   1.0080  0.4215 A   2.47135e-01 6.56888e-02
HO  HO   1.0080  0.4215 A   0.0e+00 0.0e+00
OH  OH  16. -0.6497 A   3.06647e-01 8.80314e-01
; NE6 water model
EP  EP   0.0-0.866  D   0.0E+00 0.0E+00
OW  OW  15.99940 0.000  A   3.11500E-01 0.714850050
HW  HW   1.00800 0.477  A   6.73000E-02 0.115419008
LP  LP   0.0-0.477  D   0.0E+00 0.0E+00

; sections [ types ] contain generic alcohol contaminant params
[ bondtypes ]
; i j   funcb0  kb
HO  OH  1   0.09600 462750.4
CT  OH  1   0.14100 267776.0
CT  CT  1   0.15260 259408.0
CT  H1  1   0.10900 284512.0
CT  HC  1   0.10900 284512.0
  
[ angletypes ]
; i j   k   functh0 cth
CT  OH  HO  1   108.500 460.240
CT  CT  OH  1   109.500 418.400
CT  CT  CT  1   109.500 334.720
CT  CT  HC  1   109.500 418.400
CT  CT  H1  1   109.500 418.400
HC  CT  HC  1   109.500 292.880
H1  CT  H1  1   109.500 292.880
H1  CT  OH  1   109.500 418.400

[ dihedraltypes ]
; i j   k   l   funccoefficients
;CT CT  OH  HO  3   1.71544  0.96232  0.0 -2.67776  
0.0  0.0
;CT CT  CT  OH
;CT CT  CT  CT  3   3.68192  3.09616 -2.09200 -3.01248  
0.0  0.0
;CT CT  CT  HC  3   0.66944  2.00832  0.0 -2.67776  
0.0  0.0
;CT CT  CT  H1  3   0.66944  2.00832  

[gmx-users] Forcefield parameters for Cobalt in gromacs-3.3.1?

[Narayanan V]

Hi,
I was wondering if anyone has used Cobalt(3+) in their work. I am
trying to find the forcefield parameters of cobalt hexamine
[Co(NH3)6]+++

Thanks,
Narayan
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[gmx-users] ForceField for SDPC(sphingomyelin)

[linfu]

Dear Gmx community

I am new to memberane simulation. i want to simulate membrane,
which consists DPPC and SDPC(Sphingomyelin). luckily, i got the
force field and coordinates for DPPC (dppc.itp,dppc.pdb) from
Doctor Peter Tieleman'websites.however,i cannot find the force 
field and coordinates for SDPC. could anyone kindly share with me 
the file above or point me to right website or reference.

Thank you very much

Fu lin


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Re: [gmx-users] forcefield

[Tsjerk Wassenaar]

Dear Hadi,

You also forgot to define "better". What do you want to learn from that
peptide? Do you need all hydrogens for that? Or could you do without?
Also consider that the generality of the question phrased does usually
not trigger people in a way desired for reply. It sounds a bit like
"I've got some homework, but would like you to do it for me". Study the
manual and papers on MD, in particular of small peptides and force
fields. Now there's a bit of homework ;)

Cheers,

TsjerkOn 5/23/06, Mark Abraham <[EMAIL PROTECTED]> wrote:
hadi behzadi wrote:> Hi all of users>> For HHAHHAADAAHHAAD peptide what kinde of force field is better ?I don't know, but I could tell you the answer immediately forHHAHAHADAAHHAAD peptide :-P
General force fields are parameterized to be reasonable over a range ofsystems. The overview of force fields in the GROMACS manual is good, andyou should refer to the papers that describe them for more detail.
Mark___gmx-users mailing listgmx-users@gromacs.org
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.Can't post? Read http://www.gromacs.org/mailing_lists/users.php-- Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)Dept. of Biophysical ChemistryUniversity of GroningenNijenborgh 49747AG Groningen, The Netherlands+31 50 363 4336
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Re: [gmx-users] forcefield

[Mark Abraham]

hadi behzadi wrote:

Hi all of users
 
For HHAHHAADAAHHAAD peptide what kinde of force field is better ?


I don't know, but I could tell you the answer immediately for 
HHAHAHADAAHHAAD peptide :-P


General force fields are parameterized to be reasonable over a range of 
systems. The overview of force fields in the GROMACS manual is good, and 
you should refer to the papers that describe them for more detail.


Mark
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[gmx-users] forcefield

[hadi behzadi]

Hi all of users     For HHAHHAADAAHHAAD peptide what kinde of force field is better ?      
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