Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-09 Thread Justin Lemkul 



On 11/9/13 9:51 PM, Gianluca Interlandi wrote:

On Sat, 9 Nov 2013, Gianluca Interlandi wrote:

Just to chime in. Here is a that paper might be helpful in understanding the
role of cuoffs in the CHARMM force field:

AU STEINBACH, PJ
BROOKS, BR
AF STEINBACH, PJ
BROOKS, BR
TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLECULAR
SIMULATION
SO JOURNAL OF COMPUTATIONAL CHEMISTRY
SN 0192-8651
PD JUL
PY 1994
VL 15
IS 7
BP 667
EP 683
DI 10.1002/jcc.540150702
UT WOS:A1994NU1741


Yes, that's the one I posted several weeks back.  It describes the original 
implementation of cutoff schemes in CHARMM.


-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] Re: CHARMM .mdp settings for GPU

2013-11-09 Thread Gianluca Interlandi 

On Sat, 9 Nov 2013, Gianluca Interlandi wrote:

Just to chime in. Here is a that paper might be helpful in understanding 
the role of cuoffs in the CHARMM force field:


AU STEINBACH, PJ
   BROOKS, BR
AF STEINBACH, PJ
   BROOKS, BR
TI NEW SPHERICAL-CUTOFF METHODS FOR LONG-RANGE FORCES IN MACROMOLECULAR
   SIMULATION
SO JOURNAL OF COMPUTATIONAL CHEMISTRY
SN 0192-8651
PD JUL
PY 1994
VL 15
IS 7
BP 667
EP 683
DI 10.1002/jcc.540150702
UT WOS:A1994NU1741

Gianluca


On Sat, 9 Nov 2013, Justin Lemkul wrote:




On 11/9/13 4:16 PM, rajat desikan wrote:

Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?

cutoff-scheme= Verlet
vdwtype = switch
rlist= 1.2
;rlistlong = 1.4 NOT USED IN GPU...IS THIS
OK?
rvdw   = 1.2
;rvdw-switch= 1.0NOT USED IN GPU...IS THIS OK?
coulombtype   = pme
DispCorr = EnerPres
rcoulomb= 1.2



I have no basis for saying whether or not it will produce correct results. 
I have never tested this force field on GPU with the Verlet scheme.  My 
biggest concern is with the treatment of van der Waals interactions, and I 
have not used the Verlet scheme enough to understand what it is doing and 
how it will treat the interactions that should be switched.  If someone 
else can comment, that would be useful to me, as well!


Test carefully and please report back.  A comparison between CPU and GPU 
would be very valuable.


-Justin



On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012351...@n6.nabble.com> wrote:




On 11/7/13 11:32 PM, Rajat Desikan wrote:


Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html

Is there any reason not to use their .mdp parameters for a

membrane-protein

system? Justin's recommendation is highly valued since I am using his
forcefield. Justin, your comments please



Careful now, it's not "my forcefield."  I derived only a very small part
of it :)


To summarize:
Klauda et al., suggest
rlist  = 1.0
rlistlong= 1.4
rvdw_switch  = 0.8
vdwtype= Switch
coulombtype  = pme
DispCorr= EnerPres ;only usefull with reaction-field
and pme or pppm
rcoulomb   = 1.0
rcoulomb_switch= 0.0
rvdw = 1.2

Justin's recommendation (per mail above)
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2



The differences between these two sets of run parameters are very small,
dealing
mostly with Coulomb and neighbor searching cutoffs.  I would suspect that
any
difference between simulations run with these two settings would be
similarly
small or nonexistent, given that rcoulomb is a bit flexible when using
PME.  The
value of rlist is rarely mentioned in papers, so it is good that the
authors
have provided the actual input file.  Previous interpretation of CHARMM
usage
generally advised setting rcoulomb = 1.2 to remain consistent with the
original
switching/shifting functions.  That setting becomes a bit less stringent
when
using PME.

-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

[hidden email]  |
(410) 706-7441

==
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Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-09 Thread Justin Lemkul 



On 11/9/13 4:16 PM, rajat desikan wrote:

Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?

cutoff-scheme= Verlet
vdwtype = switch
rlist= 1.2
;rlistlong = 1.4 NOT USED IN GPU...IS THIS
OK?
rvdw   = 1.2
;rvdw-switch= 1.0NOT USED IN GPU...IS THIS OK?
coulombtype   = pme
DispCorr = EnerPres
rcoulomb= 1.2



I have no basis for saying whether or not it will produce correct results.  I 
have never tested this force field on GPU with the Verlet scheme.  My biggest 
concern is with the treatment of van der Waals interactions, and I have not used 
the Verlet scheme enough to understand what it is doing and how it will treat 
the interactions that should be switched.  If someone else can comment, that 
would be useful to me, as well!


Test carefully and please report back.  A comparison between CPU and GPU would 
be very valuable.


-Justin



On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012351...@n6.nabble.com> wrote:




On 11/7/13 11:32 PM, Rajat Desikan wrote:


Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html

Is there any reason not to use their .mdp parameters for a

membrane-protein

system? Justin's recommendation is highly valued since I am using his
forcefield. Justin, your comments please



Careful now, it's not "my forcefield."  I derived only a very small part
of it :)


To summarize:
Klauda et al., suggest
rlist  = 1.0
rlistlong= 1.4
rvdw_switch  = 0.8
vdwtype= Switch
coulombtype  = pme
DispCorr= EnerPres ;only usefull with reaction-field
and pme or pppm
rcoulomb   = 1.0
rcoulomb_switch= 0.0
rvdw = 1.2

Justin's recommendation (per mail above)
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2



The differences between these two sets of run parameters are very small,
dealing
mostly with Coulomb and neighbor searching cutoffs.  I would suspect that
any
difference between simulations run with these two settings would be
similarly
small or nonexistent, given that rcoulomb is a bit flexible when using
PME.  The
value of rlist is rarely mentioned in papers, so it is good that the
authors
have provided the actual input file.  Previous interpretation of CHARMM
usage
generally advised setting rcoulomb = 1.2 to remain consistent with the
original
switching/shifting functions.  That setting becomes a bit less stringent
when
using PME.

-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

[hidden email]  |
(410) 706-7441

==
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  To unsubscribe from CHARMM .mdp settings for GPU, click 
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==

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] Re: CHARMM .mdp settings for GPU

2013-11-09 Thread rajat desikan 
Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?

cutoff-scheme= Verlet
vdwtype = switch
rlist= 1.2
;rlistlong = 1.4 NOT USED IN GPU...IS THIS
OK?
rvdw   = 1.2
;rvdw-switch= 1.0NOT USED IN GPU...IS THIS OK?
coulombtype   = pme
DispCorr = EnerPres
rcoulomb= 1.2


On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012351...@n6.nabble.com> wrote:

>
>
> On 11/7/13 11:32 PM, Rajat Desikan wrote:
>
> > Dear All,
> > The setting that I mentioned above are from Klauda et al., for a POPE
> > membrane system. They can be found in charmm_npt.mdp in lipidbook (link
> > below)
> > http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html
> >
> > Is there any reason not to use their .mdp parameters for a
> membrane-protein
> > system? Justin's recommendation is highly valued since I am using his
> > forcefield. Justin, your comments please
> >
>
> Careful now, it's not "my forcefield."  I derived only a very small part
> of it :)
>
> > To summarize:
> > Klauda et al., suggest
> > rlist  = 1.0
> > rlistlong= 1.4
> > rvdw_switch  = 0.8
> > vdwtype= Switch
> > coulombtype  = pme
> > DispCorr= EnerPres ;only usefull with reaction-field
> > and pme or pppm
> > rcoulomb   = 1.0
> > rcoulomb_switch= 0.0
> > rvdw = 1.2
> >
> > Justin's recommendation (per mail above)
> > vdwtype = switch
> > rlist = 1.2
> > rlistlong = 1.4
> > rvdw = 1.2
> > rvdw-switch = 1.0
> > rcoulomb = 1.2
> >
>
> The differences between these two sets of run parameters are very small,
> dealing
> mostly with Coulomb and neighbor searching cutoffs.  I would suspect that
> any
> difference between simulations run with these two settings would be
> similarly
> small or nonexistent, given that rcoulomb is a bit flexible when using
> PME.  The
> value of rlist is rarely mentioned in papers, so it is good that the
> authors
> have provided the actual input file.  Previous interpretation of CHARMM
> usage
> generally advised setting rcoulomb = 1.2 to remain consistent with the
> original
> switching/shifting functions.  That setting becomes a bit less stringent
> when
> using PME.
>
> -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
>
> [hidden email]  |
> (410) 706-7441
>
> ==
> --
> gmx-users mailing list[hidden 
> email]
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
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>
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> http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012351.html
>  To unsubscribe from CHARMM .mdp settings for GPU, click 
> here
> .
> NAML
>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
--
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Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-08 Thread Justin Lemkul 



On 11/7/13 11:32 PM, Rajat Desikan wrote:

Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html

Is there any reason not to use their .mdp parameters for a membrane-protein
system? Justin's recommendation is highly valued since I am using his
forcefield. Justin, your comments please



Careful now, it's not "my forcefield."  I derived only a very small part of it 
:)


To summarize:
Klauda et al., suggest
rlist  = 1.0
rlistlong= 1.4
rvdw_switch  = 0.8
vdwtype= Switch
coulombtype  = pme
DispCorr= EnerPres ;only usefull with reaction-field
and pme or pppm
rcoulomb   = 1.0
rcoulomb_switch= 0.0
rvdw = 1.2

Justin's recommendation (per mail above)
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2



The differences between these two sets of run parameters are very small, dealing 
mostly with Coulomb and neighbor searching cutoffs.  I would suspect that any 
difference between simulations run with these two settings would be similarly 
small or nonexistent, given that rcoulomb is a bit flexible when using PME.  The 
value of rlist is rarely mentioned in papers, so it is good that the authors 
have provided the actual input file.  Previous interpretation of CHARMM usage 
generally advised setting rcoulomb = 1.2 to remain consistent with the original 
switching/shifting functions.  That setting becomes a bit less stringent when 
using PME.


-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] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Rajat Desikan 
Dear All,
The setting that I mentioned above are from Klauda et al., for a POPE
membrane system. They can be found in charmm_npt.mdp in lipidbook (link
below)
http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html

Is there any reason not to use their .mdp parameters for a membrane-protein
system? Justin's recommendation is highly valued since I am using his
forcefield. Justin, your comments please

To summarize:
Klauda et al., suggest
rlist  = 1.0
rlistlong= 1.4
rvdw_switch  = 0.8
vdwtype= Switch
coulombtype  = pme
DispCorr= EnerPres ;only usefull with reaction-field
and pme or pppm
rcoulomb   = 1.0
rcoulomb_switch= 0.0
rvdw = 1.2

Justin's recommendation (per mail above)
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2


On Fri, Nov 8, 2013 at 2:20 AM, Gianluca Interlandi [via GROMACS] <
ml-node+s5086n5012329...@n6.nabble.com> wrote:

> Hi Mark!
>
> I think that this is the paper that you are referring to:
>
> dx.doi.org/10.1021/ct900549r
>
> Also for your reference, these are the settings that Justin recommended
> using with CHARMM in gromacs:
>
> vdwtype = switch
> rlist = 1.2
> rlistlong = 1.4
> rvdw = 1.2
> rvdw-switch = 1.0
> rcoulomb = 1.2
>
> As you mention the switch function in gromacs is different than in CHARMM
> but it appears that the difference is very small.
>
> Gianluca
>
> On Thu, 7 Nov 2013, Mark Abraham wrote:
>
> > Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM
> > switch differs from the GROMACS switch (Justin linked a paper here with
> the
> > CHARMM switch description a month or so back, but I don't have that link
> to
> > hand).
> >
> > Mark
> >
> >
> > On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan <[hidden 
> > email]>wrote:
>
> >
> >> Thank you, Mark. I think that running it on CPUs is a safer choice at
> >> present.
> >>
> >>
> >> On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham <[hidden 
> >> email]
> >>> wrote:
> >>
> >>> Hi,
> >>>
> >>> It's not easy to be explicit. CHARMM wasn't parameterized with PME, so
> >> the
> >>> original paper's coulomb settings can be taken with a grain of salt
> for
> >> use
> >>> with PME - others' success in practice should be a guideline here. The
> >> good
> >>> news is that the default GROMACS PME settings are pretty good for at
> >> least
> >>> some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and
> the
> >> GPU
> >>> auto-tuning of parameters in 4.6 is designed to preserve the right
> sorts
> >> of
> >>> things.
> >>>
> >>> LJ is harder because it would make good sense to preserve the way
> CHARMM
> >>> did it, but IIRC you can't use something equivalent to the CHARMM LJ
> >> shift
> >>> with the Verlet kernels, either natively or with a table. We hope to
> fix
> >>> that in 5.0, but code is not written yet. I would probably use vdwtype
> =
> >>> cut-off, vdw-modifier = potential-shift-verlet and
> >> rcoulomb=rlist=rvdw=1.2,
> >>> but I don't run CHARMM simulations for a living ;-)
> >>>
> >>> Mark
> >>>
> >>>
> >>> On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan <[hidden 
> >>> email]
>  wrote:
> >>>
>  Dear All,
> 
>  Any suggestions?
> 
>  Thank you.
> 
>  --
>  View this message in context:
> 
> >>>
> >>
> http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html
>  Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>  --
>  gmx-users mailing list[hidden 
>  email]
>  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 [hidden 
>  email].
>
>  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> >>> --
> >>> gmx-users mailing list[hidden 
> >>> email]
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> >>> www interface or send it to [hidden 
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>
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >>
> >>
> >>
> >> --
> >> Rajat Desikan (Ph.D Scholar)
> >> Prof. K. Ganapathy Ayappa's Lab (no 13),
> >> Dept. of Chemical Engineering,
> >> Indian Institute of Science, Bangalore
> >> --
> >> gmx-use

Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Gianluca Interlandi 

Hi Mark!

I think that this is the paper that you are referring to:

dx.doi.org/10.1021/ct900549r

Also for your reference, these are the settings that Justin recommended 
using with CHARMM in gromacs:


vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2

As you mention the switch function in gromacs is different than in CHARMM 
but it appears that the difference is very small.


Gianluca

On Thu, 7 Nov 2013, Mark Abraham wrote:


Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM
switch differs from the GROMACS switch (Justin linked a paper here with the
CHARMM switch description a month or so back, but I don't have that link to
hand).

Mark


On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan wrote:


Thank you, Mark. I think that running it on CPUs is a safer choice at
present.


On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham 
wrote:



Hi,

It's not easy to be explicit. CHARMM wasn't parameterized with PME, so

the

original paper's coulomb settings can be taken with a grain of salt for

use

with PME - others' success in practice should be a guideline here. The

good

news is that the default GROMACS PME settings are pretty good for at

least

some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the

GPU

auto-tuning of parameters in 4.6 is designed to preserve the right sorts

of

things.

LJ is harder because it would make good sense to preserve the way CHARMM
did it, but IIRC you can't use something equivalent to the CHARMM LJ

shift

with the Verlet kernels, either natively or with a table. We hope to fix
that in 5.0, but code is not written yet. I would probably use vdwtype =
cut-off, vdw-modifier = potential-shift-verlet and

rcoulomb=rlist=rvdw=1.2,

but I don't run CHARMM simulations for a living ;-)

Mark


On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan 
wrote:



Dear All,

Any suggestions?

Thank you.

--
View this message in context:




http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html

Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Mark Abraham 
Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM
switch differs from the GROMACS switch (Justin linked a paper here with the
CHARMM switch description a month or so back, but I don't have that link to
hand).

Mark


On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan wrote:

> Thank you, Mark. I think that running it on CPUs is a safer choice at
> present.
>
>
> On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham  >wrote:
>
> > Hi,
> >
> > It's not easy to be explicit. CHARMM wasn't parameterized with PME, so
> the
> > original paper's coulomb settings can be taken with a grain of salt for
> use
> > with PME - others' success in practice should be a guideline here. The
> good
> > news is that the default GROMACS PME settings are pretty good for at
> least
> > some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the
> GPU
> > auto-tuning of parameters in 4.6 is designed to preserve the right sorts
> of
> > things.
> >
> > LJ is harder because it would make good sense to preserve the way CHARMM
> > did it, but IIRC you can't use something equivalent to the CHARMM LJ
> shift
> > with the Verlet kernels, either natively or with a table. We hope to fix
> > that in 5.0, but code is not written yet. I would probably use vdwtype =
> > cut-off, vdw-modifier = potential-shift-verlet and
> rcoulomb=rlist=rvdw=1.2,
> > but I don't run CHARMM simulations for a living ;-)
> >
> > Mark
> >
> >
> > On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan  > >wrote:
> >
> > > Dear All,
> > >
> > > Any suggestions?
> > >
> > > Thank you.
> > >
> > > --
> > > View this message in context:
> > >
> >
> http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html
> > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > >
> > --
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> >
>
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread rajat desikan 
Thank you, Mark. I think that running it on CPUs is a safer choice at
present.


On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham wrote:

> Hi,
>
> It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the
> original paper's coulomb settings can be taken with a grain of salt for use
> with PME - others' success in practice should be a guideline here. The good
> news is that the default GROMACS PME settings are pretty good for at least
> some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the GPU
> auto-tuning of parameters in 4.6 is designed to preserve the right sorts of
> things.
>
> LJ is harder because it would make good sense to preserve the way CHARMM
> did it, but IIRC you can't use something equivalent to the CHARMM LJ shift
> with the Verlet kernels, either natively or with a table. We hope to fix
> that in 5.0, but code is not written yet. I would probably use vdwtype =
> cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2,
> but I don't run CHARMM simulations for a living ;-)
>
> Mark
>
>
> On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan  >wrote:
>
> > Dear All,
> >
> > Any suggestions?
> >
> > Thank you.
> >
> > --
> > View this message in context:
> >
> http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
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>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
-- 
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Re: [gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Mark Abraham 
Hi,

It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the
original paper's coulomb settings can be taken with a grain of salt for use
with PME - others' success in practice should be a guideline here. The good
news is that the default GROMACS PME settings are pretty good for at least
some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the GPU
auto-tuning of parameters in 4.6 is designed to preserve the right sorts of
things.

LJ is harder because it would make good sense to preserve the way CHARMM
did it, but IIRC you can't use something equivalent to the CHARMM LJ shift
with the Verlet kernels, either natively or with a table. We hope to fix
that in 5.0, but code is not written yet. I would probably use vdwtype =
cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2,
but I don't run CHARMM simulations for a living ;-)

Mark


On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan wrote:

> Dear All,
>
> Any suggestions?
>
> Thank you.
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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[gmx-users] Re: CHARMM .mdp settings for GPU

2013-11-07 Thread Rajat Desikan 
Dear All,

Any suggestions? 

Thank you.

--
View this message in context: 
http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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