Re: [gmx-users] Lateral Diffusion of Lipids

[Jochen Hub]

Am 8/12/13 5:26 AM, schrieb Kieu Thu Nguyen:
> Dear users,
> 
> I want to use g_msd to measure diffusion coefficients of lipid bilayer. But
> i do not know how to choose the reference atom per lipid for an any type of
> lipid, such as POPC, DOPC,...
> Where i can get these references ?

One suggestion: The two leaflets may move with respect to each other.
Therefore, I recommend to compute D *within* each leaflet first -
otherwise you may get a too large diffusion constant. Btw: g_select can
be used to select the upper / lower phosphates into separate index groups.

Jochen

> 
> Thanks so much for any help !
> 
> ~Thu
> 

-- 
---
Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
---
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Re: [gmx-users] Re: Unkwown Keyword HILLS

[Michael Shirts]

This is

Sent from my iPhone

On Aug 14, 2013, at 1:40, Albert  wrote:

> Does anybody have any idea what's the problem?
> 
> I use the tutorial example and I don't know why it doesn't work.
> 
> THX
> 
> 
> On 08/13/2013 07:19 PM, Albert wrote:
>> Dear:
>> 
>> I am trying to run plumed with gromacs plugin. Here is my plumed.dat file 
>> which I defined two dihedral angels as cvs:
>> 
>> *HILLS HEIGHT 0.3 W_STRIDE 450
>> WELLTEMPERED SIMTEMP 310 BIASFACTOR 1.96
>> TORSION LIST 1 4 65 344 SIGMA 0.12
>> TORSION LIST 2 46 80 656 SIGMA 0.12
>> 
>> ENDMETA*
>> 
>> I am using plumed-1.3+gromacs-4.6.2 with command:
>> 
>> 
>> *mpirun -np 24 mdrun_mpi -s md.tpr -plumed plumed.dat -g md.log -v -x md.xtc 
>> -o md.trr -e md.edr*
>> 
>> 
>> but it failed with messages:
>> 
>> 
>> *starting mdrun 'protein'
>> 1 steps, 20.0 ps.
>> ! PLUMED ERROR: Line 1 Unkwown Keyword HILLS
>> 
>> ! ABORTING RUN
>> ! PLUMED ERROR: Line 1 Unkwown Keyword HILLS
>> 
>> ! ABORTING RUN
>> --*
>> 
>> thank you very much
>> 
>> Albert
> 
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Re: [gmx-users] Re: Unkwown Keyword HILLS

[Michael Shirts]

This is a plumed error, not a gromacs error. Gromacs never handles those 
keywords. 

Sent from my iPhone

On Aug 14, 2013, at 1:40, Albert  wrote:

> Does anybody have any idea what's the problem?
> 
> I use the tutorial example and I don't know why it doesn't work.
> 
> THX
> 
> 
> On 08/13/2013 07:19 PM, Albert wrote:
>> Dear:
>> 
>> I am trying to run plumed with gromacs plugin. Here is my plumed.dat file 
>> which I defined two dihedral angels as cvs:
>> 
>> *HILLS HEIGHT 0.3 W_STRIDE 450
>> WELLTEMPERED SIMTEMP 310 BIASFACTOR 1.96
>> TORSION LIST 1 4 65 344 SIGMA 0.12
>> TORSION LIST 2 46 80 656 SIGMA 0.12
>> 
>> ENDMETA*
>> 
>> I am using plumed-1.3+gromacs-4.6.2 with command:
>> 
>> 
>> *mpirun -np 24 mdrun_mpi -s md.tpr -plumed plumed.dat -g md.log -v -x md.xtc 
>> -o md.trr -e md.edr*
>> 
>> 
>> but it failed with messages:
>> 
>> 
>> *starting mdrun 'protein'
>> 1 steps, 20.0 ps.
>> ! PLUMED ERROR: Line 1 Unkwown Keyword HILLS
>> 
>> ! ABORTING RUN
>> ! PLUMED ERROR: Line 1 Unkwown Keyword HILLS
>> 
>> ! ABORTING RUN
>> --*
>> 
>> thank you very much
>> 
>> Albert
> 
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Re: [gmx-users] Re: Unkwown Keyword HILLS

[Albert]

On 08/14/2013 12:26 PM, Michael Shirts wrote:

This is a plumed error, not a gromacs error. Gromacs never handles those 
keywords.

Sent from my iPhone


IC

THX, it works now. I found some "strange characters" in the plumed.dat 
file. After delete them, it work now

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[gmx-users] how can we control output ?

[Albert]

Hello:

 I am producing MD production with command:

mpirun -np 24 mdrun_mpi -plumed plumed.dat -s md.tpr -v -g md.log -x 
md.xtc -o md.trr -e md.edr


I notice that it generate two additional files:

HILLS COLVAR

the output in this two files are very frequent such as:

#! FIELDS time cv1 cv2 vbias
0. -1.372322679  0.4671409730.0
0.0900 -1.225425363  0.4868991370.02999
0.1800 -1.420091748  0.5462185740.031921782
0.2700 -1.430565715  0.5849254130.057605527
0.3600 -1.193568826  0.5248758790.056731977
0.4500 -1.215992570  0.4391220810.074018419
0.5400 -1.320514202  0.3950026330.059704699
0.6300 -1.247566938  0.4936060310.119831786
0.7200 -1.258976460  0.4036847650.120678633

AND:
 0.090 -1.225425363  0.486899137  0.08697 
0.08697  0.061249998 1.960
 0.180 -1.420091748  0.546218574  0.08697 
0.08697  0.061201861 1.960
 0.270 -1.430565715  0.584925413  0.08697 
0.08697  0.060562217 1.960
 0.360 -1.193568826  0.524875879  0.08697 
0.08697  0.060583858 1.960
 0.450 -1.215992570  0.439122081  0.08697 
0.08697  0.060157006 1.960
 0.540 -1.320514202  0.395002633  0.08697 
0.08697  0.060510237 1.960
 0.630 -1.247566938  0.493606031  0.08697 
0.08697  0.059040397 1.960
 0.720 -1.258976460  0.403684765  0.08697 
0.08697  0.059019958 1.960
 0.810 -1.331293344  0.531644762  0.08697 
0.08697  0.059053400 1.960
 0.900 -1.477816820  0.541284800  0.08697 
0.08697  0.059861982 1.960



I am performing 200 ns MD simulations. The file probably will become too 
big I am just wondering how can we setup the frequency record for 
the HILL and COLVAR file?


THX

Albert
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Re: [gmx-users] Yet another question about what force field to use

[Justin Lemkul]

On 8/13/13 10:26 PM, Pedro Lacerda wrote:

Hi all,

Many questions about how to choose a force field are addressed to this
list, sorry if this one was already answered.

Some argue that proteins are better modeled with ff99sb-ildn or charmm22*
because occur great agreement between NMR experiments and simulations when
using these force fields. But what about organic heteromolecules? One could
say that organic molecules are similar enough to amino acid side chains
concluding that protein force fields are adequate to model these molecules,
but I'm not sure.

What ff would best describe a small ligand bound to protein? What do you
think?



I don't think this question can be asked in the absence of the underlying choice 
of the protein force field.  The ligand parameters are only as good as the 
results of the parameterization of it, within the context of the parent force 
field's criteria.  All force fields can be extended to describe new species, 
though the methods to do so vary.


-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] how can we control output ?

[Justin Lemkul]

On 8/14/13 9:43 AM, Albert wrote:

Hello:

  I am producing MD production with command:

mpirun -np 24 mdrun_mpi -plumed plumed.dat -s md.tpr -v -g md.log -x md.xtc -o
md.trr -e md.edr

I notice that it generate two additional files:

HILLS COLVAR

the output in this two files are very frequent such as:

#! FIELDS time cv1 cv2 vbias
 0. -1.372322679  0.4671409730.0
 0.0900 -1.225425363  0.4868991370.02999
 0.1800 -1.420091748  0.5462185740.031921782
 0.2700 -1.430565715  0.5849254130.057605527
 0.3600 -1.193568826  0.5248758790.056731977
 0.4500 -1.215992570  0.4391220810.074018419
 0.5400 -1.320514202  0.3950026330.059704699
 0.6300 -1.247566938  0.4936060310.119831786
 0.7200 -1.258976460  0.4036847650.120678633

AND:
  0.090 -1.225425363  0.486899137  0.08697 0.08697
0.061249998 1.960
  0.180 -1.420091748  0.546218574  0.08697 0.08697
0.061201861 1.960
  0.270 -1.430565715  0.584925413  0.08697 0.08697
0.060562217 1.960
  0.360 -1.193568826  0.524875879  0.08697 0.08697
0.060583858 1.960
  0.450 -1.215992570  0.439122081  0.08697 0.08697
0.060157006 1.960
  0.540 -1.320514202  0.395002633  0.08697 0.08697
0.060510237 1.960
  0.630 -1.247566938  0.493606031  0.08697 0.08697
0.059040397 1.960
  0.720 -1.258976460  0.403684765  0.08697 0.08697
0.059019958 1.960
  0.810 -1.331293344  0.531644762  0.08697 0.08697
0.059053400 1.960
  0.900 -1.477816820  0.541284800  0.08697 0.08697
0.059861982 1.960


I am performing 200 ns MD simulations. The file probably will become too big
I am just wondering how can we setup the frequency record for the HILL and
COLVAR file?



I would suggest asking PLUMED questions on the PLUMED forum.

-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] plans for mdrun features to deprecate in GROMACS 5.0

[Mark Abraham]

Hi gmx-users and gmx-developers,

There are a number of features of GROMACS that we plan to drop for 5.0
(scheduled for early 2014). We don’t like doing this, but if things
are broken or cause developers pain, then they will go unless there is
manpower to support them. We’d like to keep you informed and hear how
much pain any of this might cause. Some features will be dropped
entirely, and others are likely to be reduced to explicit support only
for some cases. Some discussion has already occurred here
http://redmine.gromacs.org/issues/1292.

Things we plan to drop entirely:
* particle decomposition (see below)
* current QM support (this will be dropped, work on a replacement is
underway, planned for 5.0)
* writing of pair distance and/or time-averaged pair distance to
energy files during simulations with position/orientation restraints
* reaction-field-nec
* Encad-shift
* mdrun -ionize
* GCT
* mdrun -seppot
* mdrun -ffscan
* OpenMM support

There are several algorithms (e.g. fancy kinds of restraints) that
have only ever worked with particle decomposition (if they work at
all...). We plan to support these only in serial.

Things that will likely only work in serial (ie. single-domain DD):
* ensemble- and time-averaged distance restraints
* L-BFGS energy minimization
* Generalized Born

In some cases, “in serial” might mean “in parallel (with DD) with an
extra communication stage that will make it work, but might scale
poorly.” Or “in parallel but if things diffuse too far, the simulation
will crash.” If you have working examples of any of the above in
parallel, we would be most interested to hear from you. We’d like to
construct test cases that show what works now, so that later if we are
able to support some kind of parallelism, we can show that it still
works.

Things that won’t support constraints (because the implementations are
broken or missing):
* L-BFGS energy minimization
* MTTK pressure coupling

As always, what goes into GROMACS depends on people putting the work
in. If something above would affect you, then do speak up.
Contributions of working test cases are particularly valuable, but in
the end you might have to be the one to write the code to make the
test pass. You will have the option of continuing to use old code,
too!

Cheers,

Mark
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[gmx-users] charmm36 proteins

[Dina Mirijanian]

Hello all,
Does anyone know if there is a working version of charmm36 proteins
forcefield converted for gromacs?
Thank you.
-Dina
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[gmx-users] All molecules being coupled for free energy of self solvation simulation

[Brittany Zimmerman]

Dear users,
I am attempting to determine the free energy of self solvation of several
small molecules.
Starting with an equilibrated box of pure fluid (for example, ethanol -
which I am calling thr) I am renaming all of the molecules except for the
first in the .gro file SOL, then updating the .top file [ molecules ]
section.

The free energy section of my .mdp file looks like this (this is mdout.mdp
produced by grompp):

; Free energy variables
free-energy  = yes
couple-moltype   = thr
couple-lambda0   = vdw-q
couple-lambda1   = none
couple-intramol  = no
init-lambda  = -1
init-lambda-state= 15
delta-lambda = 0
nstdhdl  = 200
fep-lambdas  =
mass-lambdas =
coul-lambdas = 0.0 0.3 0.4 0.6 0.8 1.0 1.0 1.0 1.0 1.0 1.0 1.0
1.0 1.0 1.0 1.0
vdw-lambdas  = 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.3 0.5 0.6 0.68
0.76 0.82 0.86 0.92 1.0
bonded-lambdas   =
restraint-lambdas=
temperature-lambdas  =
calc-lambda-neighbors= -1
init-lambda-weights  =
dhdl-print-energy= yes
sc-alpha = 0.001
sc-power = 1
sc-r-power   = 48
sc-sigma = 0.3
sc-coul  = no
separate-dhdl-file   = yes
dhdl-derivatives = yes
dh_hist_size = 0
dh_hist_spacing  = 0.1

The issue is that the simulation appears to be coupling all of the
molecules in the system, rather than just the single molecule named thr.
In the log file produced by mdrun I get this line 'There are 2511 atoms and
2511 charges for free energy perturbation', when I am expecting there to be
9 atoms.

Any ideas as to what could be causing all of my molecules to couple instead
of just a single molecule?

Thank in advance for your assistance!

Brittany
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[gmx-users] Re: All molecules being coupled for free energy of self solvation simulation

[Brittany Zimmerman]

I found the error, I had B states defined for my solvent molecules in the
topology file.


On Wed, Aug 14, 2013 at 2:47 PM, Brittany Zimmerman wrote:

> Dear users,
> I am attempting to determine the free energy of self solvation of several
> small molecules.
> Starting with an equilibrated box of pure fluid (for example, ethanol -
> which I am calling thr) I am renaming all of the molecules except for the
> first in the .gro file SOL, then updating the .top file [ molecules ]
> section.
>
> The free energy section of my .mdp file looks like this (this is mdout.mdp
> produced by grompp):
>
> ; Free energy variables
> free-energy  = yes
> couple-moltype   = thr
> couple-lambda0   = vdw-q
> couple-lambda1   = none
> couple-intramol  = no
> init-lambda  = -1
> init-lambda-state= 15
> delta-lambda = 0
> nstdhdl  = 200
> fep-lambdas  =
> mass-lambdas =
> coul-lambdas = 0.0 0.3 0.4 0.6 0.8 1.0 1.0 1.0 1.0 1.0 1.0 1.0
> 1.0 1.0 1.0 1.0
> vdw-lambdas  = 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.3 0.5 0.6 0.68
> 0.76 0.82 0.86 0.92 1.0
> bonded-lambdas   =
> restraint-lambdas=
> temperature-lambdas  =
> calc-lambda-neighbors= -1
> init-lambda-weights  =
> dhdl-print-energy= yes
> sc-alpha = 0.001
> sc-power = 1
> sc-r-power   = 48
> sc-sigma = 0.3
> sc-coul  = no
> separate-dhdl-file   = yes
> dhdl-derivatives = yes
> dh_hist_size = 0
> dh_hist_spacing  = 0.1
>
> The issue is that the simulation appears to be coupling all of the
> molecules in the system, rather than just the single molecule named thr.
> In the log file produced by mdrun I get this line 'There are 2511 atoms
> and 2511 charges for free energy perturbation', when I am expecting there
> to be 9 atoms.
>
> Any ideas as to what could be causing all of my molecules to couple
> instead of just a single molecule?
>
> Thank in advance for your assistance!
>
> Brittany
>
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Re: [gmx-users] plans for mdrun features to deprecate in GROMACS 5.0

[rajat desikan]

I am interested in Generalized Born. My coding skills are limited, but I
would like to help to whatever extent I can.
I am also interested in helping towards revamping the tutorials if the need
should arise.


On Wed, Aug 14, 2013 at 8:36 PM, Mark Abraham wrote:

> Hi gmx-users and gmx-developers,
>
> There are a number of features of GROMACS that we plan to drop for 5.0
> (scheduled for early 2014). We don’t like doing this, but if things
> are broken or cause developers pain, then they will go unless there is
> manpower to support them. We’d like to keep you informed and hear how
> much pain any of this might cause. Some features will be dropped
> entirely, and others are likely to be reduced to explicit support only
> for some cases. Some discussion has already occurred here
> http://redmine.gromacs.org/issues/1292.
>
> Things we plan to drop entirely:
> * particle decomposition (see below)
> * current QM support (this will be dropped, work on a replacement is
> underway, planned for 5.0)
> * writing of pair distance and/or time-averaged pair distance to
> energy files during simulations with position/orientation restraints
> * reaction-field-nec
> * Encad-shift
> * mdrun -ionize
> * GCT
> * mdrun -seppot
> * mdrun -ffscan
> * OpenMM support
>
> There are several algorithms (e.g. fancy kinds of restraints) that
> have only ever worked with particle decomposition (if they work at
> all...). We plan to support these only in serial.
>
> Things that will likely only work in serial (ie. single-domain DD):
> * ensemble- and time-averaged distance restraints
> * L-BFGS energy minimization
> * Generalized Born
>
> In some cases, “in serial” might mean “in parallel (with DD) with an
> extra communication stage that will make it work, but might scale
> poorly.” Or “in parallel but if things diffuse too far, the simulation
> will crash.” If you have working examples of any of the above in
> parallel, we would be most interested to hear from you. We’d like to
> construct test cases that show what works now, so that later if we are
> able to support some kind of parallelism, we can show that it still
> works.
>
> Things that won’t support constraints (because the implementations are
> broken or missing):
> * L-BFGS energy minimization
> * MTTK pressure coupling
>
> As always, what goes into GROMACS depends on people putting the work
> in. If something above would affect you, then do speak up.
> Contributions of working test cases are particularly valuable, but in
> the end you might have to be the one to write the code to make the
> test pass. You will have the option of continuing to use old code,
> too!
>
> Cheers,
>
> Mark
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Indian Institute of Science, Bangalore
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[gmx-users] VDW switched off in CHARMM tip3p model

[Christopher Neale]

>From my inspection of the force field files included in gromacs-4.6.1, when you
use the charmm ff and the charmm tip3p (tips3p.itp) you get the hydrogen type 
HT,
which does have LJ on the hydrogen atoms, whereas you only get the hydrogen 
type HWT3 when you use the non-charmm tip3p (tip3p.itp).

If I understand Mark's comment to be that there is no good reason to use the 
charmm
tip3p water model with the charmm ff, then I disagree (See below).

I have posted an image ( http://tinypic.com/r/110ak5s/5 ) of the area per lipid 
(APL) 
for a POPC bilayer that I built with charmm-gui (83 lipids/leaflet; 43 
waters/lipid)
and then simulated under the charmm36 lipid parameters for ~ 300 ns many times 
successively with different water models (2 repeats each, starting from 
different 
conformations out of charmm-gui). Note the large difference in the APL for the 
regular tip3p and the charmm tip3p.  In fact, some papers note that you get 
gel-phase bilayers with the charmm36 lipid ff and the non-charmm tip3p model 
when using 
certain cutoff treatments 
(Piggot and Khalid -- http://pubs.acs.org/doi/abs/10.1021/ct3003157 -- is one 
such paper).

Chris.

-- original message --

You could do that, but it's extra cost for no known benefit. See
http://dx.doi.org/10.1021/ct900549r

On Tue, Aug 13, 2013 at 7:15 PM, Weilong Zhao  wrote:
> Hi,
>
> I noticed that for GROMACS versions of 4.5 of later, the force field for
> TIP3P water model in CHARMM27.ff package has a following line included:
>
>  The following atom types are NOT part of the CHARMM distribution
> ..
> .
> HWT31   1.0080000.417   A   0.0 0.0 ; TIP3p H
>
> It seems that VDW interaction of the default hydrogen of water is switched
> off, which makes it not the correct TIP3P ff of CHARMM. However this
> hydrogen type HWT3, is used as default by gromacs as CHARMM water model.
>
> Even though the hydrogen without VDW is the original TIP3P water model, I
> wonder is there any problem to include it in CHARMM ff set? Really
> appreciate if anyone could share some opinion.
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[gmx-users] charmm36 proteins

[Christopher Neale]

What is the charmm36 protein force field? (can you provide a reference to what 
you are referring to).

As far as I know, there is no such thing as "charmm36" proteins. There are 
charmm27+cmap proteins
(implemented in gromacs already) and charmm36 lipids (implemented in gromacs 
already).

-- original message --

Hello all,
Does anyone know if there is a working version of charmm36 proteins
forcefield converted for gromacs?
Thank you.
-Dina

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Re: [gmx-users] charmm36 proteins

[Justin Lemkul]

On 8/14/13 6:22 PM, Christopher Neale wrote:

What is the charmm36 protein force field? (can you provide a reference to what 
you are referring to).

As far as I know, there is no such thing as "charmm36" proteins. There are 
charmm27+cmap proteins
(implemented in gromacs already) and charmm36 lipids (implemented in gromacs 
already).



CHARMM36 protein parameters do exist: dx.doi.org/10.1021/ct300400x.  Whether or 
not they have been implemented in Gromacs, I do not know, but the modifications 
of the CHARMM27 files provided with Gromacs should be straightforward to carry 
out.  For what it's worth, there is no such thing as a CHARMM27 protein force 
field, it's just CHARMM22+CMAP.  The unfortunate naming of the distributed files 
has led to this misconception.


-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] "Sign convention" g_energy total energies

[gg jj]

Hi everybody.
I wonder how the "sign convention" of GROMACS (or better g_energy ) is: Is U(state_i):= _t correct or do i have to choose the other sign U(state_i)= -1.0* _t ?  (<>_t denotes the time average)

 

I need the correct sign for further calculations since i need to add something (-T\Delta S) to the difference of the inner energy of two states: \Delta F=\Delta U -T\Delta S (for T=const)

 

Thank you for your reply

 John

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Re: [gmx-users] "Sign convention" g_energy total energies

[Justin Lemkul]

On 8/14/13 6:42 PM, gg jj wrote:

Hi everybody.
I wonder how the "sign convention" of GROMACS (or better g_energy ) is: Is
U(state_i):= _t correct or do i have to choose the other sign
U(state_i)= -1.0* _t ?  (<>_t denotes the time average)
I need the correct sign for further calculations since i need to add something
(-T\Delta S) to the difference of the inner energy of two states: \Delta
F=\Delta U -T\Delta S (for T=const)


There is no need to manipulate the sign.  It's not even a Gromacs convention, 
it's standard.  Negative energy = net attraction, positive energy = net repulsion.


-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: VDW switched off in CHARMM tip3p model

[qiuxing]

TIP3P and TIPS3P (which I found later is the CHARMM TIP3P) produce slightly
different water bulk density:
0.96 vs. 1.01 when using CHARMM ff set, but TIPS3P is almost two times
slower than original TIP3P. For the benefit of TIPS3P, I think it heavily
depends on applications.

Weilong


Christopher Neale wrote
>>From my inspection of the force field files included in gromacs-4.6.1,
when you
> use the charmm ff and the charmm tip3p (tips3p.itp) you get the hydrogen
> type HT,
> which does have LJ on the hydrogen atoms, whereas you only get the
> hydrogen 
> type HWT3 when you use the non-charmm tip3p (tip3p.itp).
> 
> If I understand Mark's comment to be that there is no good reason to use
> the charmm
> tip3p water model with the charmm ff, then I disagree (See below).
> 
> I have posted an image ( http://tinypic.com/r/110ak5s/5 ) of the area per
> lipid (APL) 
> for a POPC bilayer that I built with charmm-gui (83 lipids/leaflet; 43
> waters/lipid)
> and then simulated under the charmm36 lipid parameters for ~ 300 ns many
> times 
> successively with different water models (2 repeats each, starting from
> different 
> conformations out of charmm-gui). Note the large difference in the APL for
> the 
> regular tip3p and the charmm tip3p.  In fact, some papers note that you
> get 
> gel-phase bilayers with the charmm36 lipid ff and the non-charmm tip3p
> model when using 
> certain cutoff treatments 
> (Piggot and Khalid -- http://pubs.acs.org/doi/abs/10.1021/ct3003157 -- is
> one such paper).
> 
> Chris.
> 
> -- original message --
> 
> You could do that, but it's extra cost for no known benefit. See
> http://dx.doi.org/10.1021/ct900549r
> 
> On Tue, Aug 13, 2013 at 7:15 PM, Weilong Zhao 
> 
>  wrote:
>> Hi,
>>
>> I noticed that for GROMACS versions of 4.5 of later, the force field for
>> TIP3P water model in CHARMM27.ff package has a following line included:
>>
>>  The following atom types are NOT part of the CHARMM distribution
>> ..
>> .
>> HWT31   1.0080000.417   A   0.0 0.0 ; TIP3p H
>>
>> It seems that VDW interaction of the default hydrogen of water is
>> switched
>> off, which makes it not the correct TIP3P ff of CHARMM. However this
>> hydrogen type HWT3, is used as default by gromacs as CHARMM water model.
>>
>> Even though the hydrogen without VDW is the original TIP3P water model, I
>> wonder is there any problem to include it in CHARMM ff set? Really
>> appreciate if anyone could share some opinion.
> --
> gmx-users mailing list

> gmx-users@

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--
View this message in context: 
http://gromacs.5086.x6.nabble.com/VDW-switched-off-in-CHARMM-tip3p-model-tp5010484p5010509.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Re: [gmx-users] charmm36 proteins

[Dina Mirijanian]

Thanks Justin.  I will just modify the existing charmm files for gromacs to
make the charmm36 version.  I just wanted to see if anyone had already done
this, so as not to redo something that's already been done.
-D


On Wed, Aug 14, 2013 at 6:31 PM, Justin Lemkul  wrote:

>
>
> On 8/14/13 6:22 PM, Christopher Neale wrote:
>
>> What is the charmm36 protein force field? (can you provide a reference to
>> what you are referring to).
>>
>> As far as I know, there is no such thing as "charmm36" proteins. There
>> are charmm27+cmap proteins
>> (implemented in gromacs already) and charmm36 lipids (implemented in
>> gromacs already).
>>
>>
> CHARMM36 protein parameters do exist: dx.doi.org/10.1021/ct300400x.
>  Whether or not they have been implemented in Gromacs, I do not know, but
> the modifications of the CHARMM27 files provided with Gromacs should be
> straightforward to carry out.  For what it's worth, there is no such thing
> as a CHARMM27 protein force field, it's just CHARMM22+CMAP.  The
> unfortunate naming of the distributed files has led to this misconception.
>
> -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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