[gmx-users] Polarizable models

[Vitaly V. Chaban]

Hi,

Is there any place to read how gromacs treats polarizable models?
The only thing I found in the official manual is that shells are
denoted as "S" in the topology. What is especially interesting for me
now is a concrete implementation and the ways of use.

Thanks in advance.
Vitaly

--
Vitaly V. Chaban, Ph.D.
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, cell.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===
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[gmx-users] RE: Re: Gromos Parameters for Heme bound Oxygen

[olaniyi yusuff]

Hi,
Thanks for the your reply. I quite know that there is need for expertise to be 
able to derive parameters, that's why i want to know if anyone already have the 
gromos parameters for the oxy- and carbomonoxy- heme.
The references i've seen so far for related works in my literature search used 
the charmm force field parameters and amber but again i had problems when i try 
to use amber, pdb2gmx complain of not finding residue heme in the topology file.
The question now is can i use charmm force field parameters in gromacs and how 
do i go about incorporating charmm ff into gromacs. 
Please i need a guide because i'm relatively new in simulation work, i am from 
experimental background.
thanks.  

> Message: 5
> Date: Tue, 27 Oct 2009 13:36:49 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Gromos Parameters for Heme bound Oxygen
> To: Discussion list for GROMACS users 
> Message-ID: <4ae72fb1.5020...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> Olaniyi Yusuff wrote:
> > Dear gmx users,
> > I would like to know if any one has parameters for oxygen or 
> > carbonmonoxide bound to the heme in hemoglobin.
> > I am running MD simulations on hemoglobin using the gromos force field 
> > G43a1 in gromacs, i had no problem when i used the pdb structure for 
> > pure hemoglobin, but when i try to convert the pdb structure files for 
> > the liganded hemoglobin (both oxy- and carbonmonoxy- ), there was 
> > complain of my oxy and carbomonoxy residue unknown i.e not defined in 
> > the .rtp file.
> > so i would like to know if there is anyone with parameters for these 
> > kind of heme in gromacs or better still another reference of force field 
> > with parameters for them that can be use in gromacs.
> > 
> 
> If it has been published, then perhaps the authors of that particular study 
> will 
> share them with you.  If not, then realize what you are trying to do is 
> certainly an expert topic, one that is not addressed easily:
> 
> http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
> 
> -Justin
> 
> > Thanks


  
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Re: [gmx-users] RE: Re: Gromos Parameters for Heme bound Oxygen

[Erik Marklund]

Hi,

There are HEME entry in the ffG43a1-files that come with gromacs. Wether 
it's oxy- deoxy- or other heme I do not know. At some point I used them 
for a myoglobin simulation, but I don't remember the details.


/Erik

olaniyi yusuff skrev:





Hi,
Thanks for the your reply. I quite know that there is need for 
expertise to be able to derive parameters, that's why i want to know 
if anyone already have the gromos parameters for the oxy- and 
carbomonoxy- heme.
The references i've seen so far for related works in my literature 
search used the charmm force field parameters and amber but again i 
had problems when i try to use amber, pdb2gmx complain of not finding 
residue heme in the topology file.
The question now is can i use charmm force field parameters in gromacs 
and how do i go about incorporating charmm ff into gromacs.
Please i need a guide because i'm relatively new in simulation work, i 
am from experimental background.
thanks. 


> Message: 5
> Date: Tue, 27 Oct 2009 13:36:49 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] Gromos Parameters for Heme bound Oxygen
> To: Discussion list for GROMACS users 
> Message-ID: <4ae72fb1.5020...@vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Olaniyi Yusuff wrote:
> > Dear gmx users,
> > I would like to know if any one has parameters for oxygen or
> > carbonmonoxide bound to the heme in hemoglobin.
> > I am running MD simulations on hemoglobin using the gromos force 
field

> > G43a1 in gromacs, i had no problem when i used the pdb structure for
> > pure hemoglobin, but when i try to convert the pdb structure files 
for

> > the liganded hemoglobin (both oxy- and carbonmonoxy- ), there was
> > complain of my oxy and carbomonoxy residue unknown i.e not defined in
> > the .rtp file.
> > so i would like to know if there is anyone with parameters for these
> > kind of heme in gromacs or better still another reference of force 
field

> > with parameters for them that can be use in gromacs.
> >
>
> If it has been published, then perhaps the authors of that 
particular study will

> share them with you. If not, then realize what you are trying to do is
> certainly an expert topic, one that is not addressed easily:
>
> 
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

>
> -Justin
>
> > Thanks




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--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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Re: [gmx-users] RE: Re: Gromos Parameters for Heme bound Oxygen

[Justin A. Lemkul]

olaniyi yusuff wrote:





Hi,
Thanks for the your reply. I quite know that there is need for expertise 
to be able to derive parameters, that's why i want to know if anyone 
already have the gromos parameters for the oxy- and carbomonoxy- heme.
The references i've seen so far for related works in my literature 
search used the charmm force field parameters and amber but again i had 
problems when i try to use amber, pdb2gmx complain of not finding 
residue heme in the topology file.


If these parameters are already published, the authors of those papers may be 
willing to share them directly by providing a suitable topology.  If you want to 
make your own topology with pdb2gmx, you need to define appropriate .rtp entries 
(see Chapter 5 of the manual).  That would, of course, imply that you have 
parameters already in order to design this .rtp entry.  If you don't have these 
parameters under the given force field, you cannot use pdb2gmx; it is not magic.


The question now is can i use charmm force field parameters in gromacs 
and how do i go about incorporating charmm ff into gromacs.
Please i need a guide because i'm relatively new in simulation work, i 
am from experimental background.


CHARMM is not yet supported, but will be in a future release (4.1).

-Justin

thanks. 


 > Message: 5
 > Date: Tue, 27 Oct 2009 13:36:49 -0400
 > From: "Justin A. Lemkul" 
 > Subject: Re: [gmx-users] Gromos Parameters for Heme bound Oxygen
 > To: Discussion list for GROMACS users 
 > Message-ID: <4ae72fb1.5020...@vt.edu>
 > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
 >
 >
 >
 > Olaniyi Yusuff wrote:
 > > Dear gmx users,
 > > I would like to know if any one has parameters for oxygen or
 > > carbonmonoxide bound to the heme in hemoglobin.
 > > I am running MD simulations on hemoglobin using the gromos force field
 > > G43a1 in gromacs, i had no problem when i used the pdb structure for
 > > pure hemoglobin, but when i try to convert the pdb structure files for
 > > the liganded hemoglobin (both oxy- and carbonmonoxy- ), there was
 > > complain of my oxy and carbomonoxy residue unknown i.e not defined in
 > > the .rtp file.
 > > so i would like to know if there is anyone with parameters for these
 > > kind of heme in gromacs or better still another reference of force 
field

 > > with parameters for them that can be use in gromacs.
 > >
 >
 > If it has been published, then perhaps the authors of that particular 
study will

 > share them with you. If not, then realize what you are trying to do is
 > certainly an expert topic, one that is not addressed easily:
 >
 > 
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

 >
 > -Justin
 >
 > > Thanks




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] LJ scaling and EnerPress correction

[Antonia V .]

Dear all,

I am trying to simulate a two component system, and I would like to ask you the 
two following questions:

1) Is it possible to use a different scaling factor (for the LJ and the 
electrostatics) for each component?

2) Is it possible to use energy and pressure correction only for the one of the 
two components and not for the other?

Thank you in advance for your help,

Antonia
  
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Re: [gmx-users] Polarizable models

[David van der Spoel]

Vitaly V. Chaban wrote:

Hi,

Is there any place to read how gromacs treats polarizable models?
The only thing I found in the official manual is that shells are
denoted as "S" in the topology. What is especially interesting for me
now is a concrete implementation and the ways of use.


Our old SW water model is in the distribution (sw.itp).
The reference to the paper is in there IIRC.



Thanks in advance.
Vitaly

--
Vitaly V. Chaban, Ph.D.
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua,vvcha...@gmail.com
skype: vvchaban, cell.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] % of existence of hydrogen bond

[Moutusi Manna]

Dear all,
    I am dealing with a POPC+PEPTDE+WATER system. Basic residues of the 
peptide make hydrogen bonds with lipid headgroup (as reflected from g_rdf 
analysis) and the number of hydrogen bonds formed can be calculated from 
g_hbond program. Now, i want to calculate the % of trajectory time for which a 
bond between a particular group (say LYS and lipid headgroup po4) exist. -hbm 
gives a .xpm matrix, on solving (using xpm2ps) that i got a .eps file, which is 
a picture file of h_bond existence map, but the data sheet is not given.
Can any one help me to solve this problem?
With regards,
 
Moutusi Manna
 


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Re: [gmx-users] % of existence of hydrogen bond

[Ran Friedman]

Hi,
You can use g_hbond -num and write a small script to calculate the
percentage of h-bond existence per frame by calculating the number of
frames for which a h-bond exists.
Good luck,
Ran.

Moutusi Manna wrote:
>
> Dear all,
>
> I am dealing with a POPC+PEPTDE+WATER system. Basic residues
> of the peptide make hydrogen bonds with lipid headgroup (as reflected
> from g_rdf analysis) and the number of hydrogen bonds formed can be
> calculated from g_hbond program. Now, i want to calculate the % of
> trajectory time for which a bond between a particular group (say LYS
> and lipid headgroup po4) exist. -hbm gives a .xpm matrix, on solving
> (using xpm2ps) that i got a .eps file, which is a picture file of
> h_bond existence map, but the data sheet is not given.
>
> Can any one help me to solve this problem?
>
> With regards,
>
>  
>
> Moutusi Manna
>
>  
>
>
> 
> Add whatever you love to the Yahoo! India homepage. Try now!
> 
> 
>
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Re: [gmx-users] % of existence of hydrogen bond

[Erik Marklund]

Hi,

The xpm-file matches the [ hbonds ] index group in the index file spat 
out by g_hbond. X:th line in the map is the h-bond given by the 4:th 
entry in the index group. Be careful when matching the rows though, 
because in the xpm file the first line of data is the bottom row of the 
matrix if I remember correctly.


/Erik

Moutusi Manna skrev:


Dear all,

I am dealing with a POPC+PEPTDE+WATER system. Basic residues 
of the peptide make hydrogen bonds with lipid headgroup (as reflected 
from g_rdf analysis) and the number of hydrogen bonds formed can be 
calculated from g_hbond program. Now, i want to calculate the % of 
trajectory time for which a bond between a particular group (say LYS 
and lipid headgroup po4) exist. -hbm gives a .xpm matrix, on solving 
(using xpm2ps) that i got a .eps file, which is a picture file of 
h_bond existence map, but the data sheet is not given.


Can any one help me to solve this problem?

With regards,

 


Moutusi Manna

 




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---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
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Re: [gmx-users] Is anyone also using lammps?s

[Peng Yi]

On Wed, 28 Oct 2009, Mark Abraham wrote:


Peng Yi wrote:


I am trying to simulate alkane melt and found out that gromacs and lammps 
gave different results, particularly the bonded interaction energy.

I wonder if anyone has such experience.  Thanks,


Even two installations of the same version of GROMACS can give different 
results. The question is whether when using comparable model physics you 
observe the same ensemble averages.


Mark


Hi, Mark,

Thanks for reply!  The difference is statistically significant.  And I am
wondering if it is caused by the integrator: Leap-frog for Gromacs and
Velocity-verlet for Lammps.  Detail description of the comparison please
see below:

It is an NPT simulation of a melt of 240 n-octane molecules using
united-atom model, i.e., CHx group is considered as one atom.  There are
bond, angle, torsion and LJ interactions.  T=300K and P=1atm.

Lammps uses nose-hoover thermostat and barostat, and Gromacs uses
nose-hoover thermostat and Parranello-Rahman barostat.  Time constants for
thermostat and barostat are 0.02ps and 2.0ps, respectively.

If I use integration time 1fs, Lammps and Gromacs gave consistent results:
Lammps   Gromacs
Ebond(kJ/mol):2092 2146
Eangle:   1757 1760
Etors:2510 2500
Elj+corr:-9238-9350
Volume(nm^3): 66.7 66.5

where energy fluctuation is 100 kJ/mol and volume fluctuation is 1 nm^3,
Elj+corr is the total LJ energy including tail correction.

However, if I use integration time 2fs, Lammps results do not change 
much, but Gromacs results changed a lot:


Lammps   Gromacs
Ebond(kJ/mol):2133 2700 
Eangle:   1799 1640

Etors:2552 2200
Elj+corr:-9292-9886 
Volume:   66.7 64.0


The results given by Lammps is more reasonable because the Ebond should
be equal to the total # of bonds times 1/2k_BT and Eangle should be equal
to the total # of angles times 1/2k_BT.  At T=300K, 1/2k_BT=1.25 kJ/mol.
240 n-octanes have total 1680 bonds and 1440 angles.

The bond and angle interactions are both harmonic functions.  Bond
interaction constant kl=292880 kJ/mol/nm^2, corresponding to a bond
ossilation period 16 fs.

Is there something related to the integrator?

Here I attached my grompp.mdp and topol.top files.

##
grompp.mdp
##

; VARIOUS PREPROCESSING OPTIONS
title= Yo
cpp  = /usr/bin/cpp
include  = 
define   =


; RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.001
nsteps   = 200
init_step= 0
comm-mode= Linear
nstcomm  = 1
comm-grps=

; OUTPUT CONTROL OPTIONS
nstxout  = 5000
nstvout  = 5000
nstfout  = 5000
nstcheckpoint= 1
nstlog   = 1000
nstenergy= 1000
nstxtcout= 5000
xtc-precision= 1000
xtc-grps = 
energygrps   =


; NEIGHBORSEARCHING PARAMETERS
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.0025
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = Cut-off
rcoulomb-switch  = 0
rcoulomb = 1.0025
epsilon-r= 1
vdw-type = Cut-off
rvdw-switch  = 0		; default 
rvdw = 1.0025	; default 1 nm

DispCorr = EnerPres
;table-extension  = 1.5
fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no


; OPTIONS FOR WEAK COUPLING ALGORITHMS
Tcoupl   = nose-hoover
tc-grps  = System
tau_t= 0.02
ref_t= 300.0
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
tau_p= 2.0
compressibility  = 4.5e-5
ref_p= 1.0
andersen_seed= 815131

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = yes
gen_temp = 300
gen_seed = 2009

; OPTIONS FOR BONDS 
constraints  = none

constraint-algorithm = Lincs
unconstrained-start  = no
Shake-SOR= no
shake-tol= 1e-04
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30
morse= no

; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-

Re: [gmx-users] Is anyone also using lammps?s

[aherz]

Hey,

are you running single or double precision gromacs?
Afaik, depending on the circumstances the energy drift in gromacs can be
rather bad for single precision.

Alex


Peng Yi schrieb:
>
> On Wed, 28 Oct 2009, Mark Abraham wrote:
>
>> Peng Yi wrote:
>>>
>>> I am trying to simulate alkane melt and found out that gromacs and
>>> lammps gave different results, particularly the bonded interaction
>>> energy.
>>> I wonder if anyone has such experience.  Thanks,
>>
>> Even two installations of the same version of GROMACS can give
>> different results. The question is whether when using comparable
>> model physics you observe the same ensemble averages.
>>
>> Mark
>
> Hi, Mark,
>
> Thanks for reply!  The difference is statistically significant.  And I am
> wondering if it is caused by the integrator: Leap-frog for Gromacs and
> Velocity-verlet for Lammps.  Detail description of the comparison please
> see below:
>
> It is an NPT simulation of a melt of 240 n-octane molecules using
> united-atom model, i.e., CHx group is considered as one atom.  There are
> bond, angle, torsion and LJ interactions.  T=300K and P=1atm.
>
> Lammps uses nose-hoover thermostat and barostat, and Gromacs uses
> nose-hoover thermostat and Parranello-Rahman barostat.  Time constants
> for
> thermostat and barostat are 0.02ps and 2.0ps, respectively.
>
> If I use integration time 1fs, Lammps and Gromacs gave consistent
> results:
> Lammps   Gromacs
> Ebond(kJ/mol):2092 2146
> Eangle:   1757 1760
> Etors:2510 2500
> Elj+corr:-9238-9350
> Volume(nm^3): 66.7 66.5
>
> where energy fluctuation is 100 kJ/mol and volume fluctuation is 1 nm^3,
> Elj+corr is the total LJ energy including tail correction.
>
> However, if I use integration time 2fs, Lammps results do not change
> much, but Gromacs results changed a lot:
>
> Lammps   Gromacs
> Ebond(kJ/mol):2133 2700 Eangle:  
> 1799 1640
> Etors:2552 2200
> Elj+corr:-9292-9886 Volume:  
> 66.7 64.0
>
> The results given by Lammps is more reasonable because the Ebond should
> be equal to the total # of bonds times 1/2k_BT and Eangle should be equal
> to the total # of angles times 1/2k_BT.  At T=300K, 1/2k_BT=1.25 kJ/mol.
> 240 n-octanes have total 1680 bonds and 1440 angles.
>
> The bond and angle interactions are both harmonic functions.  Bond
> interaction constant kl=292880 kJ/mol/nm^2, corresponding to a bond
> ossilation period 16 fs.
>
> Is there something related to the integrator?
>
> Here I attached my grompp.mdp and topol.top files.
>
> ##
> grompp.mdp
> ##
>
> ; VARIOUS PREPROCESSING OPTIONS
> title= Yo
> cpp  = /usr/bin/cpp
> include  = define   =
>
> ; RUN CONTROL PARAMETERS
> integrator   = md
> tinit= 0
> dt   = 0.001
> nsteps   = 200
> init_step= 0
> comm-mode= Linear
> nstcomm  = 1
> comm-grps=
>
> ; OUTPUT CONTROL OPTIONS
> nstxout  = 5000
> nstvout  = 5000
> nstfout  = 5000
> nstcheckpoint= 1
> nstlog   = 1000
> nstenergy= 1000
> nstxtcout= 5000
> xtc-precision= 1000
> xtc-grps = energygrps   =
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> rlist= 1.0025
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = Cut-off
> rcoulomb-switch  = 0
> rcoulomb = 1.0025
> epsilon-r= 1
> vdw-type = Cut-off
> rvdw-switch  = 0; default rvdw
> = 1.0025; default 1 nm
> DispCorr = EnerPres
> ;table-extension  = 1.5
> fourierspacing   = 0.12
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> pme_order= 4
> ewald_rtol   = 1e-05
> ewald_geometry   = 3d
> epsilon_surface  = 0
> optimize_fft = no
>
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> Tcoupl   = nose-hoover
> tc-grps  = System
> tau_t= 0.02
> ref_t= 300.0
> Pcoupl   = Parrinello-Rahman
> Pcoupltype   = isotropic
> tau_p= 2.0
> compressibility  = 4.5e-5
> ref_p= 1.0
> andersen_seed= 815131
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel   

Re: [gmx-users] Is anyone also using lammps?s

[David van der Spoel]

aherz wrote:

Hey,

are you running single or double precision gromacs?
Afaik, depending on the circumstances the energy drift in gromacs can be
rather bad for single precision.


Please refer to the gromacs 4.0 paper for a discussion of the drift.
If you want to compare energies you need the same density, which you do 
not have, you may need to run NVT for that.


Note that your integration time step is quite large, and the temperature 
coupling constant is very small.


You could try a shifted LJ + dispersion correction, it is not clear to 
me how LAMMPS treats cutoffs, couldn't find it in the manual.




Alex


Peng Yi schrieb:

On Wed, 28 Oct 2009, Mark Abraham wrote:


Peng Yi wrote:

I am trying to simulate alkane melt and found out that gromacs and
lammps gave different results, particularly the bonded interaction
energy.
I wonder if anyone has such experience.  Thanks,

Even two installations of the same version of GROMACS can give
different results. The question is whether when using comparable
model physics you observe the same ensemble averages.

Mark

Hi, Mark,

Thanks for reply!  The difference is statistically significant.  And I am
wondering if it is caused by the integrator: Leap-frog for Gromacs and
Velocity-verlet for Lammps.  Detail description of the comparison please
see below:

It is an NPT simulation of a melt of 240 n-octane molecules using
united-atom model, i.e., CHx group is considered as one atom.  There are
bond, angle, torsion and LJ interactions.  T=300K and P=1atm.

Lammps uses nose-hoover thermostat and barostat, and Gromacs uses
nose-hoover thermostat and Parranello-Rahman barostat.  Time constants
for
thermostat and barostat are 0.02ps and 2.0ps, respectively.

If I use integration time 1fs, Lammps and Gromacs gave consistent
results:
Lammps   Gromacs
Ebond(kJ/mol):2092 2146
Eangle:   1757 1760
Etors:2510 2500
Elj+corr:-9238-9350
Volume(nm^3): 66.7 66.5

where energy fluctuation is 100 kJ/mol and volume fluctuation is 1 nm^3,
Elj+corr is the total LJ energy including tail correction.

However, if I use integration time 2fs, Lammps results do not change
much, but Gromacs results changed a lot:

Lammps   Gromacs
Ebond(kJ/mol):2133 2700 Eangle:  
1799 1640

Etors:2552 2200
Elj+corr:-9292-9886 Volume:  
66.7 64.0


The results given by Lammps is more reasonable because the Ebond should
be equal to the total # of bonds times 1/2k_BT and Eangle should be equal
to the total # of angles times 1/2k_BT.  At T=300K, 1/2k_BT=1.25 kJ/mol.
240 n-octanes have total 1680 bonds and 1440 angles.

The bond and angle interactions are both harmonic functions.  Bond
interaction constant kl=292880 kJ/mol/nm^2, corresponding to a bond
ossilation period 16 fs.

Is there something related to the integrator?

Here I attached my grompp.mdp and topol.top files.

##
grompp.mdp
##

; VARIOUS PREPROCESSING OPTIONS
title= Yo
cpp  = /usr/bin/cpp
include  = define   =

; RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.001
nsteps   = 200
init_step= 0
comm-mode= Linear
nstcomm  = 1
comm-grps=

; OUTPUT CONTROL OPTIONS
nstxout  = 5000
nstvout  = 5000
nstfout  = 5000
nstcheckpoint= 1
nstlog   = 1000
nstenergy= 1000
nstxtcout= 5000
xtc-precision= 1000
xtc-grps = energygrps   =

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.0025
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = Cut-off
rcoulomb-switch  = 0
rcoulomb = 1.0025
epsilon-r= 1
vdw-type = Cut-off
rvdw-switch  = 0; default rvdw
= 1.0025; default 1 nm

DispCorr = EnerPres
;table-extension  = 1.5
fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no


; OPTIONS FOR WEAK COUPLING ALGORITHMS
Tcoupl   = nose-hoover
tc-grps  = System
tau_t= 0.02
ref_t= 300.0
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
t

Re: [gmx-users] Is anyone also using lammps?s

[Ran Friedman]

Hi Peng,

Note that you're not using any bond constraints in Gromacs and a
timestep of 2fs may be too long.
Also, tau_t=0.02 seems too short for me.

With 1fs timescale the agreement seem good enough, but you didn't
include estimated errors so it's hard to tell. Also, I assume you run
GMX in single and LAMMPS in double precision. Did you check for convergence?

Ran

Peng Yi wrote:
>
> On Wed, 28 Oct 2009, Mark Abraham wrote:
>
>> Peng Yi wrote:
>>>
>>> I am trying to simulate alkane melt and found out that gromacs and
>>> lammps gave different results, particularly the bonded interaction
>>> energy.
>>> I wonder if anyone has such experience.  Thanks,
>>
>> Even two installations of the same version of GROMACS can give
>> different results. The question is whether when using comparable
>> model physics you observe the same ensemble averages.
>>
>> Mark
>
> Hi, Mark,
>
> Thanks for reply!  The difference is statistically significant.  And I am
> wondering if it is caused by the integrator: Leap-frog for Gromacs and
> Velocity-verlet for Lammps.  Detail description of the comparison please
> see below:
>
> It is an NPT simulation of a melt of 240 n-octane molecules using
> united-atom model, i.e., CHx group is considered as one atom.  There are
> bond, angle, torsion and LJ interactions.  T=300K and P=1atm.
>
> Lammps uses nose-hoover thermostat and barostat, and Gromacs uses
> nose-hoover thermostat and Parranello-Rahman barostat.  Time constants
> for
> thermostat and barostat are 0.02ps and 2.0ps, respectively.
>
> If I use integration time 1fs, Lammps and Gromacs gave consistent
> results:
> Lammps   Gromacs
> Ebond(kJ/mol):2092 2146
> Eangle:   1757 1760
> Etors:2510 2500
> Elj+corr:-9238-9350
> Volume(nm^3): 66.7 66.5
>
> where energy fluctuation is 100 kJ/mol and volume fluctuation is 1 nm^3,
> Elj+corr is the total LJ energy including tail correction.
>
> However, if I use integration time 2fs, Lammps results do not change
> much, but Gromacs results changed a lot:
>
> Lammps   Gromacs
> Ebond(kJ/mol):2133 2700 Eangle:  
> 1799 1640
> Etors:2552 2200
> Elj+corr:-9292-9886 Volume:  
> 66.7 64.0
>
> The results given by Lammps is more reasonable because the Ebond should
> be equal to the total # of bonds times 1/2k_BT and Eangle should be equal
> to the total # of angles times 1/2k_BT.  At T=300K, 1/2k_BT=1.25 kJ/mol.
> 240 n-octanes have total 1680 bonds and 1440 angles.
>
> The bond and angle interactions are both harmonic functions.  Bond
> interaction constant kl=292880 kJ/mol/nm^2, corresponding to a bond
> ossilation period 16 fs.
>
> Is there something related to the integrator?
>
> Here I attached my grompp.mdp and topol.top files.
>
> ##
> grompp.mdp
> ##
>
> ; VARIOUS PREPROCESSING OPTIONS
> title= Yo
> cpp  = /usr/bin/cpp
> include  = define   =
>
> ; RUN CONTROL PARAMETERS
> integrator   = md
> tinit= 0
> dt   = 0.001
> nsteps   = 200
> init_step= 0
> comm-mode= Linear
> nstcomm  = 1
> comm-grps=
>
> ; OUTPUT CONTROL OPTIONS
> nstxout  = 5000
> nstvout  = 5000
> nstfout  = 5000
> nstcheckpoint= 1
> nstlog   = 1000
> nstenergy= 1000
> nstxtcout= 5000
> xtc-precision= 1000
> xtc-grps = energygrps   =
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist  = 10
> ns_type  = grid
> pbc  = xyz
> rlist= 1.0025
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype  = Cut-off
> rcoulomb-switch  = 0
> rcoulomb = 1.0025
> epsilon-r= 1
> vdw-type = Cut-off
> rvdw-switch  = 0; default rvdw
> = 1.0025; default 1 nm
> DispCorr = EnerPres
> ;table-extension  = 1.5
> fourierspacing   = 0.12
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> pme_order= 4
> ewald_rtol   = 1e-05
> ewald_geometry   = 3d
> epsilon_surface  = 0
> optimize_fft = no
>
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> Tcoupl   = nose-hoover
> tc-grps  = System
> tau_t= 0.02
> ref_t= 300.0
> Pcoupl   = Parrinello-Rahman
> Pcoupltype   = isotropic
> tau

Re: [gmx-users] Is anyone also using lammps?s

[Peng Yi]

Hi, Ran,

I didn't use bond restraints.  I checked that the bond length had a
Gaussian-like distributes, and the length range looked normal.

I estimated the fastest timescale in the system, which is the bond
ossilation period, around 16fs.  Would that require as integration
timestep much smaller than 1fs?

With the parameters I have, could you recommend a set of tau_t and tau_p?
I did mention the fluctuation, 100 kJ/mol for energy and 1 nm^3 for
volume.  And I ran GMX in single.  Not sure about Lammps, should be
double.  All measured physical quantities converged well.  Would you
expect differece if I compile GMX in double?  Would that be much slower?
-Peng

On Thu, 29 Oct 2009, Ran Friedman wrote:


Hi Peng,

Note that you're not using any bond constraints in Gromacs and a
timestep of 2fs may be too long.
Also, tau_t=0.02 seems too short for me.

With 1fs timescale the agreement seem good enough, but you didn't
include estimated errors so it's hard to tell. Also, I assume you run
GMX in single and LAMMPS in double precision. Did you check for convergence?

Ran

Peng Yi wrote:


On Wed, 28 Oct 2009, Mark Abraham wrote:


Peng Yi wrote:


I am trying to simulate alkane melt and found out that gromacs and
lammps gave different results, particularly the bonded interaction
energy.
I wonder if anyone has such experience.  Thanks,


Even two installations of the same version of GROMACS can give
different results. The question is whether when using comparable
model physics you observe the same ensemble averages.

Mark


Hi, Mark,

Thanks for reply!  The difference is statistically significant.  And I am
wondering if it is caused by the integrator: Leap-frog for Gromacs and
Velocity-verlet for Lammps.  Detail description of the comparison please
see below:

It is an NPT simulation of a melt of 240 n-octane molecules using
united-atom model, i.e., CHx group is considered as one atom.  There are
bond, angle, torsion and LJ interactions.  T=300K and P=1atm.

Lammps uses nose-hoover thermostat and barostat, and Gromacs uses
nose-hoover thermostat and Parranello-Rahman barostat.  Time constants
for
thermostat and barostat are 0.02ps and 2.0ps, respectively.

If I use integration time 1fs, Lammps and Gromacs gave consistent
results:
Lammps   Gromacs
Ebond(kJ/mol):2092 2146
Eangle:   1757 1760
Etors:2510 2500
Elj+corr:-9238-9350
Volume(nm^3): 66.7 66.5

where energy fluctuation is 100 kJ/mol and volume fluctuation is 1 nm^3,
Elj+corr is the total LJ energy including tail correction.

However, if I use integration time 2fs, Lammps results do not change
much, but Gromacs results changed a lot:

Lammps   Gromacs
Ebond(kJ/mol):2133 2700 Eangle:
1799 1640
Etors:2552 2200
Elj+corr:-9292-9886 Volume:
66.7 64.0

The results given by Lammps is more reasonable because the Ebond should
be equal to the total # of bonds times 1/2k_BT and Eangle should be equal
to the total # of angles times 1/2k_BT.  At T=300K, 1/2k_BT=1.25 kJ/mol.
240 n-octanes have total 1680 bonds and 1440 angles.

The bond and angle interactions are both harmonic functions.  Bond
interaction constant kl=292880 kJ/mol/nm^2, corresponding to a bond
ossilation period 16 fs.

Is there something related to the integrator?

Here I attached my grompp.mdp and topol.top files.

##
grompp.mdp
##

; VARIOUS PREPROCESSING OPTIONS
title= Yo
cpp  = /usr/bin/cpp
include  = define   =

; RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.001
nsteps   = 200
init_step= 0
comm-mode= Linear
nstcomm  = 1
comm-grps=

; OUTPUT CONTROL OPTIONS
nstxout  = 5000
nstvout  = 5000
nstfout  = 5000
nstcheckpoint= 1
nstlog   = 1000
nstenergy= 1000
nstxtcout= 5000
xtc-precision= 1000
xtc-grps = energygrps   =

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.0025
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = Cut-off
rcoulomb-switch  = 0
rcoulomb = 1.0025
epsilon-r= 1
vdw-type = Cut-off
rvdw-switch  = 0; default rvdw
= 1.0025; default 1 nm
DispCorr = EnerPres
;table-extension  = 1.5
fourierspacing   = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme

Re: [gmx-users] Is anyone also using lammps?s

[Peng Yi]

On Thu, 29 Oct 2009, David van der Spoel wrote:


aherz wrote:

Hey,

are you running single or double precision gromacs?
Afaik, depending on the circumstances the energy drift in gromacs can be
rather bad for single precision.


Please refer to the gromacs 4.0 paper for a discussion of the drift.
If you want to compare energies you need the same density, which you do not 
have, you may need to run NVT for that.


Note that your integration time step is quite large, and the temperature 
coupling constant is very small.


You could try a shifted LJ + dispersion correction, it is not clear to me how 
LAMMPS treats cutoffs, couldn't find it in the manual.




I tried NPT simulation with only LJ interaction.  With tau_t=0.2ps for 
both Gromacs and Lammps, all the other parameters same as I mentioned

before.  At integration time 2fs, Gromacs and Lammps produce same results
and agree with published data. (N=4000, T=2.0, P=0.5 -> rou=0.3).  That's
why I focused my attention to the difference on bonded energy.

I think I used a simple cutoff plus tail correction for energy and
pressure for both Gromacs and Lammps.



Alex


Peng Yi schrieb:

On Wed, 28 Oct 2009, Mark Abraham wrote:


Peng Yi wrote:

I am trying to simulate alkane melt and found out that gromacs and
lammps gave different results, particularly the bonded interaction
energy.
I wonder if anyone has such experience.  Thanks,

Even two installations of the same version of GROMACS can give
different results. The question is whether when using comparable
model physics you observe the same ensemble averages.

Mark

Hi, Mark,

Thanks for reply!  The difference is statistically significant.  And I am
wondering if it is caused by the integrator: Leap-frog for Gromacs and
Velocity-verlet for Lammps.  Detail description of the comparison please
see below:

It is an NPT simulation of a melt of 240 n-octane molecules using
united-atom model, i.e., CHx group is considered as one atom.  There are
bond, angle, torsion and LJ interactions.  T=300K and P=1atm.

Lammps uses nose-hoover thermostat and barostat, and Gromacs uses
nose-hoover thermostat and Parranello-Rahman barostat.  Time constants
for
thermostat and barostat are 0.02ps and 2.0ps, respectively.

If I use integration time 1fs, Lammps and Gromacs gave consistent
results:
Lammps   Gromacs
Ebond(kJ/mol):2092 2146
Eangle:   1757 1760
Etors:2510 2500
Elj+corr:-9238-9350
Volume(nm^3): 66.7 66.5

where energy fluctuation is 100 kJ/mol and volume fluctuation is 1 nm^3,
Elj+corr is the total LJ energy including tail correction.

However, if I use integration time 2fs, Lammps results do not change
much, but Gromacs results changed a lot:

Lammps   Gromacs
Ebond(kJ/mol):2133 2700 Eangle:  1799 
1640

Etors:2552 2200
Elj+corr:-9292-9886 Volume:  66.7 
64.0


The results given by Lammps is more reasonable because the Ebond should
be equal to the total # of bonds times 1/2k_BT and Eangle should be equal
to the total # of angles times 1/2k_BT.  At T=300K, 1/2k_BT=1.25 kJ/mol.
240 n-octanes have total 1680 bonds and 1440 angles.

The bond and angle interactions are both harmonic functions.  Bond
interaction constant kl=292880 kJ/mol/nm^2, corresponding to a bond
ossilation period 16 fs.

Is there something related to the integrator?

Here I attached my grompp.mdp and topol.top files.

##
grompp.mdp
##

; VARIOUS PREPROCESSING OPTIONS
title= Yo
cpp  = /usr/bin/cpp
include  = define   =

; RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.001
nsteps   = 200
init_step= 0
comm-mode= Linear
nstcomm  = 1
comm-grps=

; OUTPUT CONTROL OPTIONS
nstxout  = 5000
nstvout  = 5000
nstfout  = 5000
nstcheckpoint= 1
nstlog   = 1000
nstenergy= 1000
nstxtcout= 5000
xtc-precision= 1000
xtc-grps = energygrps   =

; NEIGHBORSEARCHING PARAMETERS
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.0025
domain-decomposition = no

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype  = Cut-off
rcoulomb-switch  = 0
rcoulomb = 1.0025
epsilon-r= 1
vdw-type = Cut-off
rvdw-switch  = 0; default rvdw= 
1.0025; default 1 nm

DispCorr = EnerPres
;table-extension  = 1.5
fourierspacing   = 0.12
fourier_

Re: [gmx-users] Is anyone also using lammps?s

[Ran Friedman]

Hi Peng,

The time scale should be much shorter than the fastest vibration. A rule
of thumb from the reference below is a factor of ten, but it would
depend on the precision. Running with double precision is shorter but I
didn't make benchmarks (perhaps other users have).

Appropriate values of tau_t and tau_p have also been discussed in this
list (search for references by Berk). I tend to use something like
tau_t=0.2 and tau_p=1.0.

I advise you to follow David's suggestion as well and run with NVT.

Ran.

Reference:
@book{Becker2001,
   Author = {Becker, O. M. and MacKerell, A. D. Jr. and Roux, B.  and
Watanabe, M.},
   Title = {Computational biochemistry and biophysics},
   Publisher = {Dekker, M.},
   Address = {New York},
 Year = {2001} }

Peng Yi wrote:
>
> Hi, Ran,
>
> I didn't use bond restraints.  I checked that the bond length had a
> Gaussian-like distributes, and the length range looked normal.
>
> I estimated the fastest timescale in the system, which is the bond
> ossilation period, around 16fs.  Would that require as integration
> timestep much smaller than 1fs?
>
> With the parameters I have, could you recommend a set of tau_t and tau_p?
> I did mention the fluctuation, 100 kJ/mol for energy and 1 nm^3 for
> volume.  And I ran GMX in single.  Not sure about Lammps, should be
> double.  All measured physical quantities converged well.  Would you
> expect differece if I compile GMX in double?  Would that be much slower?
> -Peng
>
> On Thu, 29 Oct 2009, Ran Friedman wrote:
>
>> Hi Peng,
>>
>> Note that you're not using any bond constraints in Gromacs and a
>> timestep of 2fs may be too long.
>> Also, tau_t=0.02 seems too short for me.
>>
>> With 1fs timescale the agreement seem good enough, but you didn't
>> include estimated errors so it's hard to tell. Also, I assume you run
>> GMX in single and LAMMPS in double precision. Did you check for
>> convergence?
>>
>> Ran
>>
>> Peng Yi wrote:
>>>
>>> On Wed, 28 Oct 2009, Mark Abraham wrote:
>>>
 Peng Yi wrote:
>
> I am trying to simulate alkane melt and found out that gromacs and
> lammps gave different results, particularly the bonded interaction
> energy.
> I wonder if anyone has such experience.  Thanks,

 Even two installations of the same version of GROMACS can give
 different results. The question is whether when using comparable
 model physics you observe the same ensemble averages.

 Mark
>>>
>>> Hi, Mark,
>>>
>>> Thanks for reply!  The difference is statistically significant.  And
>>> I am
>>> wondering if it is caused by the integrator: Leap-frog for Gromacs and
>>> Velocity-verlet for Lammps.  Detail description of the comparison
>>> please
>>> see below:
>>>
>>> It is an NPT simulation of a melt of 240 n-octane molecules using
>>> united-atom model, i.e., CHx group is considered as one atom.  There
>>> are
>>> bond, angle, torsion and LJ interactions.  T=300K and P=1atm.
>>>
>>> Lammps uses nose-hoover thermostat and barostat, and Gromacs uses
>>> nose-hoover thermostat and Parranello-Rahman barostat.  Time constants
>>> for
>>> thermostat and barostat are 0.02ps and 2.0ps, respectively.
>>>
>>> If I use integration time 1fs, Lammps and Gromacs gave consistent
>>> results:
>>> Lammps   Gromacs
>>> Ebond(kJ/mol):2092 2146
>>> Eangle:   1757 1760
>>> Etors:2510 2500
>>> Elj+corr:-9238-9350
>>> Volume(nm^3): 66.7 66.5
>>>
>>> where energy fluctuation is 100 kJ/mol and volume fluctuation is 1
>>> nm^3,
>>> Elj+corr is the total LJ energy including tail correction.
>>>
>>> However, if I use integration time 2fs, Lammps results do not change
>>> much, but Gromacs results changed a lot:
>>>
>>> Lammps   Gromacs
>>> Ebond(kJ/mol):2133 2700 Eangle:
>>> 1799 1640
>>> Etors:2552 2200
>>> Elj+corr:-9292-9886 Volume:
>>> 66.7 64.0
>>>
>>> The results given by Lammps is more reasonable because the Ebond should
>>> be equal to the total # of bonds times 1/2k_BT and Eangle should be
>>> equal
>>> to the total # of angles times 1/2k_BT.  At T=300K, 1/2k_BT=1.25
>>> kJ/mol.
>>> 240 n-octanes have total 1680 bonds and 1440 angles.
>>>
>>> The bond and angle interactions are both harmonic functions.  Bond
>>> interaction constant kl=292880 kJ/mol/nm^2, corresponding to a bond
>>> ossilation period 16 fs.
>>>
>>> Is there something related to the integrator?
>>>
>>> Here I attached my grompp.mdp and topol.top files.
>>>
>>> ##
>>> grompp.mdp
>>> ##
>>>
>>> ; VARIOUS PREPROCESSING OPTIONS
>>> title= Yo
>>> cpp  = /usr/bin/cpp
>>> include  = define   =
>>>
>>> ; RUN CONTROL PARAMETERS
>>> integrator   = md
>>> tinit= 0
>>> dt 

[gmx-users] Adsorption energy of a single molecule

[darrellk]

Dear GROMACS Gurus,
Is it possible to determine the adsorption energy of a single molecule in
a simulation? My simulation has a large number of gas phase molecules
distributed throughout a box with some molecules adsorbed on a graphene
sheet. I would like to compare the adsorption energy of a single
molecule to that reported in research papers.

Thanks.

Darrell
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Re: [gmx-users] Adsorption energy of a single molecule

[Justin A. Lemkul]

darre...@ece.ubc.ca wrote:

Dear GROMACS Gurus,
Is it possible to determine the adsorption energy of a single molecule in
a simulation? My simulation has a large number of gas phase molecules
distributed throughout a box with some molecules adsorbed on a graphene
sheet. I would like to compare the adsorption energy of a single
molecule to that reported in research papers.



You should be able to study interactions between individual molecules by using 
energygrps and an appropriate index file.


-Justin


Thanks.

Darrell
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] PMF in Gromacs 4

[Rebeca García Fandiño]

Hi,
I am trying to calculate the PMF of an ion with Gromacs 4. I have read in the 
Gromacs list that the pull code had been completely rewritten in the new 
version of Gromacs, but I cannot find much information about the new way to use 
this.
Reading the manual (pag 280) I can see: “The options -pi, -po, -pd, -pn are 
used for potential of mean force calculations and umbrella sampling. See 
manual.”
 
So, I prepared a tpr and a .ppa file and tried the calculation and used (for 
example for one window):
 
source /gpfs/apps/GROMACS/gromacs-4.0.2/bin/GMXRC
srun -n 8 mdrun_s -v -stepout 1000 -s NA-0.0250.tpr -pi NA-0.0250.ppa -po 
pullout.ppa -pn NA-0.0250.ndx -pd -deffnm NA-0.0250
gzip NA-0.0250.pdo
 
 
Being NA-0.0250.ppa:
 
verbose   = yes
runtype   = umbrella 
pulldim   = N N Y 
reftype   = com
reference_group = UNK

group_1   = Na_-0.025
K1= 970.86;   ; kJ / (mol nm^2)
Pos1  = 0.000 0.000 -0.025  ; centre of the umbrella potential
 
I don´t get any errors during the calculation, however, I did not get any out 
files such as *.pdo.
 
I only get the *cpt, *trr, *log and *edr files after the calculation, but no 
signal of *pdo.
 
Does anyboy had used Gromacs 4 for calculating PMF? Am I doing something wrong?
 
Thank you very much for your help.
 
Best wishes,
 
Rebeca Garcia.
Santiago de Compostela University
Spain.
 
 
 
  
_
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ordenador. Es fácil y además gratis
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Re: [gmx-users] PMF in Gromacs 4

[Justin A. Lemkul]

Rebeca García Fandiño wrote:

Hi,

I am trying to calculate the PMF of an ion with Gromacs 4. I have read 
in the Gromacs list that the pull code had been completely rewritten in 
the new version of Gromacs, but I cannot find much information about the 
new way to use this.


Reading the manual (pag 280) I can see: “The options -pi, -po, -pd, -pn 
are used for potential of mean force calculations and umbrella sampling. 
See manual.”


 

So, I prepared a tpr and a .ppa file and tried the calculation and used 
(for example for one window):


 


source /gpfs/apps/GROMACS/gromacs-4.0.2/bin/GMXRC

srun -n 8 mdrun_s -v -stepout 1000 -s NA-0.0250.tpr -pi NA-0.0250.ppa 
-po pullout.ppa -pn NA-0.0250.ndx -pd -deffnm NA-0.0250


gzip NA-0.0250.pdo

 

 


Being NA-0.0250.ppa:

 


verbose   = yes

runtype   = umbrella 

pulldim   = N N Y 

reftype   = com

reference_group = UNK   


group_1   = Na_-0.025

K1= 970.86;   ; kJ / (mol nm^2)

Pos1  = 0.000 0.000 -0.025  ; centre of the umbrella potential

 

I don´t get any errors during the calculation, however, I did not get 
any out files such as *.pdo.


 

I only get the *cpt, *trr, *log and *edr files after the calculation, 
but no signal of *pdo.


 

Does anyboy had used Gromacs 4 for calculating PMF? Am I doing something 
wrong?


 


Yes, the pull parameters are all specified in the .mdp file now, so you can't 
supply a .ppa file.  Unfortunately, mdrun does not check for unrecognized flags 
(like -pi, -pn, etc).


Are you reading the right version of the manual?  I can find no mention of these 
old flags in the manual for version 4.


See version 4 manual, section 7.3.21 for COM pulling options.

-Justin



Thank you very much for your help.

 


Best wishes,

 


Rebeca Garcia.

Santiago de Compostela University

Spain.

 

 

 



Entra al Nuevo Canal Motor y descubre por qué los coches más rápidos 
sólo aparcan en MSN. Nuevo diseño, más completo y abierto a tu opinión. 
¡Nuevo Canal Motor! 





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Ph.D. Candidate
ICTAS Doctoral Scholar
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] PMF in Gromacs 4

[Justin A. Lemkul]

Justin A. Lemkul wrote:

Are you reading the right version of the manual?  I can find no mention 
of these old flags in the manual for version 4.


Scratch that, I did find the quoted phrase.  Perhaps the manual can be updated 
to have this erroneous information removed?


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] NAN in g_anaeig -proj

[alexander yakovenko]

Hi all!  
I just wonder if anyone run (know solution) into a problem trying to project a 
trajectory on the eigenvector(s) (with g_anaeig -proj ) from covariace matrix.  
All projections I have calculated are nan. However, the eigenvalues are OK and 
the g_anaeig -comp -v2 -eig2 -over options works OK so eigenvectors seems are 
OK  (but g_anaeig -2d fails to nan too). I am using gromacs-4.0.5 on x86-64 
CentOS5 (compiled with gcc-34).  
Regards,  
Alex.  
P.S. The sequence of commands that reveals the problem is attached bellow:  
  
g_covar_d -f sss_mdsi_1000.trr -s sss_mdsi_1000.tpr -n sss.ndx -o 
sss_1000_eigenval.xvg -xpm sss_1000_covar.xpm -v sss_1000_eigenvec.trr -mwa  -l 
 
...  
Option Filename  Type Description  
  
  -f sss_mdsi_1000.trr  Input    Trajectory: xtc trr trj gro g96 pdb cpt  
  -s sss_mdsi_1000.tpr  Input    Structure+mass(db): tpr tpb tpa gro g96  
   pdb  
  -n    sss.ndx  Input, Opt!  Index file  
  -o sss_1000_eigenval.xvg  Output   xvgr/xmgr file  
  -v sss_1000_eigenvec.trr  Output   Full precision trajectory: trr trj  
   cpt  
 -av    average.pdb  Output   Structure file: gro g96 pdb  
  -l  covar.log  Output   Log file  
-ascii    covar.dat  Output, Opt. Generic data file  
-xpm sss_1000_covar.xpm  Output, Opt! X PixMap compatible matrix file  
-xpma    covara.xpm  Output, Opt. X PixMap compatible matrix file  
  
Option   Type   Value   Description  
--  
-[no]h   bool   no  Print help info and quit  
-nice    int    19  Set the nicelevel  
-b   time   0   First frame (ps) to read from trajectory  
-e   time   0   Last frame (ps) to read from trajectory  
-dt  time   0   Only use frame when t MOD dt = first time (ps)  
-tu  enum   ps  Time unit: ps, fs, ns, us, ms or s  
-[no]xvgr    bool   yes Add specific codes (legends etc.) in the output  
    xvg files for the xmgrace program  
-[no]fit bool   yes Fit to a reference structure  
-[no]ref bool   no  Use the deviation from the conformation in the  
    structure file instead of from the average  
-[no]mwa bool   yes Mass-weighted covariance analysis  
-last    int    -1  Last eigenvector to write away (-1 is till the  
    last)  
-[no]pbc bool   yes Apply corrections for periodic boundary conditions  
  
Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)  
Reading file sss_mdsi_1000.tpr, VERSION 4.0.5 (double precision)  
  
Choose a group for the least squares fit  
Group 0 (  System) has 31748 elements  
...  
Group    20 ( active_site) has    54 elements  
Select a group: 20  
Selected 20: 'active_site'  
  
Choose a group for the covariance analysis  
Group 0 (  System) has 31748 elements  
...  
Group    20 ( active_site) has    54 elements  
Select a group: 20  
Selected 20: 'active_site'  
Calculating the average structure ...  
trn version: GMX_trn_file (double precision)  
Last frame   2000 time 2000.000   
  
Constructing covariance matrix (162x162) ...  
Last frame   2000 time 2000.000   
Read 2001 frames  
  
Trace of the covariance matrix: 6.22756 (u nm^2)  
  
100%  
Diagonalizing ...  
  
Sum of the eigenvalues: 6.22756 (u nm^2)  
  
Writing eigenvalues to sss_1000_eigenval.xvg  
  
Writing reference, average structure & eigenvectors 1--162 to 
sss_1000_eigenvec.trr  
  
Wrote the log to covar.log  
  
gcq#86: "Shake Barrels Of Whisky Down My Throat" (Throwing Muses)  
  
  
  
g_anaeig_d -v sss_1000_eigenvec.trr -eig sss_1000_eigenval.xvg -v2 
sss_1000_eigenvec.trr -eig2 sss_1000_eigenval.xvg -f sss_mdsi_1000.trr -s 
sss_mdsi_1000.tpr -first 1 -last 10 -n sss.ndx -proj -over  
  
...  
  
Option Filename  Type Description  
  
  -v sss_1000_eigenvec.trr  Input    Full precision trajectory: trr trj  
   cpt  
 -v2 sss_1000_eigenvec.trr  Input, Opt!  Full precision trajectory: trr trj  
   cpt  
  -f sss_mdsi_1000.trr  Input, Opt!  Trajectory: xtc trr trj gro g96 pdb cpt  
  -s sss_mdsi_1000.tpr  Input, Opt!  Structure+mass(db): tpr tpb tpa gro g96  
   pdb  
  -n    sss.ndx  Input, Opt!  Index file  
-eig sss_1000_eigenval.xvg  Input, Opt!  xvgr/xmgr file  
-eig2sss_1000_eigenval.xvg  Input, Opt!  xvgr/xmgr file  
-comp   eigcomp.xvg  Output, Opt. xvgr/xmgr file  
-rmsf   eigrmsf.xvg  Output, Opt. xvgr/xmgr file  
-proj  proj.xvg  Output, Opt! xvgr/xmgr file  
 -2d 2dproj.xvg  Output, Opt. xvgr/xmgr file  
 -3d 3dproj.pdb  Output, Opt. Structure file: gro g96 pdb  
-filt  filtered.xtc  Ou

[gmx-users] Re: Inflategro for Coarse Grained

[sunny mishra]

compiled gromacs 4.0.5 on a suse 10.3 x86-64 box
>>> > > after having compiled and installed fftw-3.2.2 and encountered
>>> > > no problems.
>>> > > Now I would like to check whether the installation has
>>> > > worked ok.
>>> > > I downloaded the gmxtest test suite, unpacked it in the gromacs
>>> directory
>>> > > and tried to run it after sourcing GMXRC. However, the test suite
>>> fails.
>>> >
>>> > Don't bother - it's barely a useful test for GROMACS 4. I did some work
>>> > improving it a few months back
>>> > (
>>> http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html
>>> ),
>>> > which is in the git version, but apparently there were too many
>>> > outstanding issues for anybody else to be interested in working towards
>>> > releasing a version that did work reliably for GROMACS 4. It's
>>> > unfortunate that there is all this documentation suggesting using it
>>> and
>>> > it doesn't work. :-(
>>> >
>>> > > The output I get is
>>> > > (~/gromacs-4.0.5): grompp -h
>>> > >  :-)  G  R  O  M  A  C  S  (-:
>>> > >
>>> > > Segmentation fault
>>> > >
>>> > > Has anybody got a clue what I can try to
>>> > > do to get the grompp running or how I can get more information
>>> > > on the possible cause for the segfault?
>>> >
>>> > This failure is not related to the test suite, of course. I'd guess you
>>> > have some problem with dynamic linking of libraries - they were present
>>> > in relevant library paths when you configured, and are not now.
>>> >
>>> > Mark
>>> >
>>> >
>>> > --
>>> >
>>> > Message: 4
>>> > Date: Thu, 29 Oct 2009 02:20:50 +0300
>>> > From: Yuri Garmay 
>>> > Subject: Re: [gmx-users] em ok, md wrong
>>> > To: Discussion list for GROMACS users 
>>> > Message-ID:
>>> >   <3e4d8d8d0910281620o7cef2103nb751716e5541...@mail.gmail.com>
>>> > Content-Type: text/plain; charset="iso-8859-1"
>>> >
>>> > 2009/10/28 Liliya Shamova 
>>> >
>>> > > Hi everybody!
>>> > >
>>> >
>>> > Dihedrals seem be incorrect. Check it. (I don't know what have to be,
>>> is it
>>> > planar molecule or not, it have be known, but it seems to be incorrect,
>>> as
>>> > you say molecule distorted) Additionally, you should use improper
>>> dihedrals
>>> > for making planar parts.
>>> >
>>> > P.S.
>>> >
>>> > 1) I think, this acid is charged in neutral pH. OOC-COO (2-), not
>>> HOOC-COOH
>>> >
>>> > 2) Why not to use topology of charged ASP residue side chaas starting
>>> point?
>>> > -- next part --
>>> > An HTML attachment was scrubbed...
>>> > URL:
>>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20091029/ad96994f/attachment-0001.html
>>> >
>>> > --
>>> >
>>> > Message: 5
>>> > Date: Wed, 28 Oct 2009 20:19:53 -0400
>>> > From: "Justin A. Lemkul" 
>>> > Subject: Re: [gmx-users] em ok, md wrong
>>> > To: Discussion list for GROMACS users 
>>> > Message-ID: <4ae8dfa9.4000...@vt.edu>
>>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>> >
>>> >
>>> >
>>> > Yuri Garmay wrote:
>>> > > 2009/10/28 Liliya Shamova >> lsham...@yahoo.com>>
>>> > >
>>> > > Hi everybody!
>>> > >
>>> > >
>>> > > Dihedrals seem be incorrect. Check it. (I don't know what have to be,
>>> is
>>> > > it planar molecule or not, it have be known, but it seems to be
>>> > > incorrect, as you say molecule distorted) Additionally, you should
>>> use
>>> > > improper dihedrals for making planar parts.
>>> > >
>>> >
>>> > Indeed, the dihedrals don't make much sense.  Based on ASPH, you should
>>> define a
>>> > HO-OH-C-O dihedral for each carboxylic acid group, and I would think
>>> you would
>>> > also need to define an O-C-C-O torsion.  All of this information is in
>>> the
>>> > ffoplsaabon.itp and ffoplsaa.rtp files.  You should definitely define
>>> impropers
>>> > to keep the carboxylic acid groups planar.  Using the ASPH entry in
>>> ffoplsaa.rtp
>>> > is a good start.  If hydrogens are collapsing into neighboring acid
>>> groups, your
>>> > [pairs] directive is probably incorrect.
>>> >
>>> > > P.S.
>>> > >
>>> > > 1) I think, this acid is charged in neutral pH. OOC-COO (2-), not
>>> HOOC-COOH
>>> >
>>> > True, but this is (as described) a vacuum simulation, so we're not
>>> dealing with
>>> > solution pH.
>>> >
>>> > -Justin
>>> >
>>> > >
>>> > > 2) Why not to use topology of charged ASP residue side chaas starting
>>> point?
>>> > >
>>> > >
>>> > >
>>> 
>>> > >
>>> > > ___
>>> > > gmx-users mailing listgmx-users@gromacs.org
>>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> > > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>> >
>>>
>>>
>>
>
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Re: [gmx-users] Re: Inflategro for Coarse Grained

[Justin A. Lemkul]

 > --
 > 
 >
 > Justin A. Lemkul
 > Ph.D. Candidate
 > ICTAS Doctoral Scholar
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 > 
 >
 >
 > --
 >
 > Message: 3
 > Date: Thu, 29 Oct 2009 09:07:58 +1100
 > From: Mark Abraham mailto:mark.abra...@anu.edu.au>>
 > Subject: Re: [gmx-users] grompp segfault
 > To: Discussion list for GROMACS users
mailto:gmx-users@gromacs.org>>
 > Message-ID: <4ae8c0be.8040...@anu.edu.au
<mailto:4ae8c0be.8040...@anu.edu.au>>
 > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
 >
 > Birger Dittrich wrote:
 > > Dear Gromacs users,
 > >
 > > I have compiled gromacs 4.0.5 on a suse 10.3 x86-64 box
 > > after having compiled and installed fftw-3.2.2 and
encountered
 > > no problems.
 > > Now I would like to check whether the installation has
 > > worked ok.
 > > I downloaded the gmxtest test suite, unpacked it in the
gromacs directory
 > > and tried to run it after sourcing GMXRC. However, the
test suite fails.
 >
 > Don't bother - it's barely a useful test for GROMACS 4. I
did some work
 > improving it a few months back
 >

(http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.html),
 > which is in the git version, but apparently there were
too many
 > outstanding issues for anybody else to be interested in
working towards
 > releasing a version that did work reliably for GROMACS 4.
It's
 > unfortunate that there is all this documentation
suggesting using it and
 > it doesn't work. :-(
 >
 > > The output I get is
 > > (~/gromacs-4.0.5): grompp -h
 > >  :-)  G  R  O  M  A  C  S  (-:
 > >
 > > Segmentation fault
 > >
 > > Has anybody got a clue what I can try to
 > > do to get the grompp running or how I can get more
information
 > > on the possible cause for the segfault?
 >
 > This failure is not related to the test suite, of course.
I'd guess you
 > have some problem with dynamic linking of libraries -
they were present
 > in relevant library paths when you configured, and are
not now.
 >
 > Mark
 >
 >
 > --
 >
 > Message: 4
 > Date: Thu, 29 Oct 2009 02:20:50 +0300
 > From: Yuri Garmay mailto:yuri.from@gmail.com>>
 > Subject: Re: [gmx-users] em ok, md wrong
 > To: Discussion list for GROMACS users
mailto:gmx-users@gromacs.org>>
 > Message-ID:
 >  
<3e4d8d8d0910281620o7cef2103nb751716e5541...@mail.gmail.com

<mailto:3e4d8d8d0910281620o7cef2103nb751716e5541...@mail.gmail.com>>
 > Content-Type: text/plain; charset="iso-8859-1"
 >
 > 2009/10/28 Liliya Shamova mailto:lsham...@yahoo.com>>
 >
 > > Hi everybody!
 > >
 >
 > Dihedrals seem be incorrect. Check it. (I don't know what
have to be, is it
 > planar molecule or not, it have be known, but it seems to
be incorrect, as
 > you say molecule distorted) Additionally, you should use
improper dihedrals
 > for making planar parts.
 >
 > P.S.
 >
 > 1) I think, this acid is charged in neutral pH. OOC-COO
(2-), not HOOC-COOH
 >
 > 2) Why not to use topology of charged ASP residue side
chaas starting point?
 

Re: [gmx-users] Re: Inflategro for Coarse Grained

[Justin A. Lemkul]

sunny mishra wrote:
Yes I did the same and when I see my system.gro file it gives me the 
dimensions of the protein box half of the lipid bilayer box so that 
means it should now be set in the center of the lipid bilayer. But after 


I don't understand what you mean.

that when I run the inflategro script and see my output file the protein 
and lipid are separated and I dnt know why?




Can you post the actual commands you're using?

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Different temperatures for different groups, even with Nose-Hoover

[Michael Lerner]

Hi,

I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein in a CG
water box, looking at the diffusion constant of the protein among other
things. I'm using the Nose-Hoover thermostat and Parrinello-Rahman barostat
with tc-grps = System. In CHARMM, a protein-in-water simulation with an
extended ensemble will show equal temperatures for the protein and the
water. However, I'm finding that, with ref_t = 323, I get a SOL (both W and
WF particles) temperature of 323 and a Protein temperature of 295. Is this
what I should expect?

The system has 62.5k particles, the box is 20 x 20 x 20, and the relevant
.mdp parameters I've used are:

tcoupl   = Nose-Hoover
tc-grps  = System
tau_t= 2
ref_t= 323
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
tau_p= 5
compressibility  = 5e-5
ref_p= 1.0

These parameters seem to lead to stable systems for bilayer simulations.
I've included the whole .mdp file at the end in case I've forgotten to
mention something relevant.

I calculated temperatures with

g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5

Thanks,

-Michael

-- begin md2.mdp --

; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
tinit= 0.0
dt   = 0.020
nsteps   = 2550
; mode for center of mass motion removal
comm-mode= linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps= System


; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5
nstvout  = 5
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 2500
nstenergy= 2500
; Output frequency and precision for xtc file =
nstxtcout= 2500
xtc_precision= 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   = System Protein W WF

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 5
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths=
rvdw_switch  = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 10
fourier_ny   = 10
fourier_nz   = 10
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = Nose-Hoover
; Groups to couple separately =
tc-grps  = System
; Time constant (ps) and reference temperature (K) =
tau_t= 2
ref_t= 323
; Pressure coupling  =
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 5
compressibility  = 5e-5
ref_p= 1.0

; SIMULATED ANNEALING CONTROL =
annealing= no

; GENERATE VELOCITIES FOR STARTUP RUN =
continuation  = yes
gen_vel  = no
;gen_temp = 323
;gen_seed = 473529

; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Relative tolerance of shake =
shake_tol= 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs_order  = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle  = 30
; Convert harmonic bonds to morse potentials =
morse= no

; NMR refinement stuff  =
; Distance restraints type: No, Simple or Ensemble =
disre= No
; Force weighting of pairs in one distance restraint: Equal or Con

Re: [gmx-users] Re: Inflategro for Coarse Grained

[sunny mishra]

okk...here are the commands which I am givng...

editconf -f 1SU4_cleancg_trans.gro -o 1SU4_newbox.gro -c -box 13.29820
13.29820 6.59160

I get the 1SU4_newbox.gro which has co-ordinates 13.29820 13.29820 6.59160

cat 1SU4_newbox.gro lipid.gro > system..gro

Now here system.gro also has co-ordinates 13.29820 13.29820 6.59160

now inflategro:

inflategro system.gro 4 DSPC 14 -o inflated_bilayer.gro 5

Now when i visualize my output file in VMD then protein and lipid are
seperated and even after i scale it to .95 they dnt meetthey are still
apart, I was hoping that lipid will be scaled and protein shud have remained
in the center of the lipid but that doesn't happen. I hope you got my
question

On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> Yes I did the same and when I see my system.gro file it gives me the
>> dimensions of the protein box half of the lipid bilayer box so that means it
>> should now be set in the center of the lipid bilayer. But after
>>
>
> I don't understand what you mean.
>
>
>  that when I run the inflategro script and see my output file the protein
>> and lipid are separated and I dnt know why?
>>
>>
> Can you post the actual commands you're using?
>
> -Justin
>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Re: Inflategro for Coarse Grained

[Justin A. Lemkul]

sunny mishra wrote:

okk...here are the commands which I am givng...

editconf -f 1SU4_cleancg_trans.gro -o 1SU4_newbox.gro -c -box 13.29820 
13.29820 6.59160


I get the 1SU4_newbox.gro which has co-ordinates 13.29820 13.29820 6.59160



Have you done the same with lipid.gro?  If the protein and the lipid are in 
different coordinate systems (i.e., lipid.gro centered at the origin and protein 
centered within the box, which has its corner placed at the origin) then you 
will have a problem.


-Justin


cat 1SU4_newbox.gro lipid.gro > system..gro

Now here system.gro also has co-ordinates 13.29820 13.29820 6.59160

now inflategro:

inflategro system.gro 4 DSPC 14 -o inflated_bilayer.gro 5

Now when i visualize my output file in VMD then protein and lipid are 
seperated and even after i scale it to .95 they dnt meetthey are 
still apart, I was hoping that lipid will be scaled and protein shud 
have remained in the center of the lipid but that doesn't happen. I hope 
you got my question


On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul > wrote:




sunny mishra wrote:

Yes I did the same and when I see my system.gro file it gives me
the dimensions of the protein box half of the lipid bilayer box
so that means it should now be set in the center of the lipid
bilayer. But after


I don't understand what you mean.


that when I run the inflategro script and see my output file the
protein and lipid are separated and I dnt know why?


Can you post the actual commands you're using?

-Justin


-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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
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] Re: Inflategro for Coarse Grained

[sunny mishra]

No. But in order to do that with lipid.gro what co-ordinates should I have
to take?

On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> okk...here are the commands which I am givng...
>>
>> editconf -f 1SU4_cleancg_trans.gro -o 1SU4_newbox.gro -c -box 13.29820
>> 13.29820 6.59160
>>
>> I get the 1SU4_newbox.gro which has co-ordinates 13.29820 13.29820 6.59160
>>
>>
> Have you done the same with lipid.gro?  If the protein and the lipid are in
> different coordinate systems (i.e., lipid.gro centered at the origin and
> protein centered within the box, which has its corner placed at the origin)
> then you will have a problem.
>
> -Justin
>
>  cat 1SU4_newbox.gro lipid.gro > system..gro
>>
>> Now here system.gro also has co-ordinates 13.29820 13.29820 6.59160
>>
>> now inflategro:
>>
>> inflategro system.gro 4 DSPC 14 -o inflated_bilayer.gro 5
>>
>> Now when i visualize my output file in VMD then protein and lipid are
>> seperated and even after i scale it to .95 they dnt meetthey are still
>> apart, I was hoping that lipid will be scaled and protein shud have remained
>> in the center of the lipid but that doesn't happen. I hope you got my
>> question
>>
>> On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>sunny mishra wrote:
>>
>>Yes I did the same and when I see my system.gro file it gives me
>>the dimensions of the protein box half of the lipid bilayer box
>>so that means it should now be set in the center of the lipid
>>bilayer. But after
>>
>>
>>I don't understand what you mean.
>>
>>
>>that when I run the inflategro script and see my output file the
>>protein and lipid are separated and I dnt know why?
>>
>>
>>Can you post the actual commands you're using?
>>
>>-Justin
>>
>>
>>--
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>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/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/mailing_lists/users.php
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] Re: Inflategro for Coarse Grained

[Justin A. Lemkul]

sunny mishra wrote:
No. But in order to do that with lipid.gro what co-ordinates should I 
have to take?




I think you need to differentiate between "coordinates" and "box vectors."  You 
should center the molecule in the box (defined by the vectors in the last line 
of the .gro file).  I assumed you were specifying these box vectors with -box.


So, for both the protein and the lipid coordinate files, you need to use

editconf -c -box (x, y, z from .gro file)

-Justin

On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul > wrote:




sunny mishra wrote:

okk...here are the commands which I am givng...

editconf -f 1SU4_cleancg_trans.gro -o 1SU4_newbox.gro -c -box
13.29820 13.29820 6.59160

I get the 1SU4_newbox.gro which has co-ordinates 13.29820
13.29820 6.59160


Have you done the same with lipid.gro?  If the protein and the lipid
are in different coordinate systems (i.e., lipid.gro centered at the
origin and protein centered within the box, which has its corner
placed at the origin) then you will have a problem.

-Justin

cat 1SU4_newbox.gro lipid.gro > system..gro

Now here system.gro also has co-ordinates 13.29820 13.29820 6.59160

now inflategro:

inflategro system.gro 4 DSPC 14 -o inflated_bilayer.gro 5

Now when i visualize my output file in VMD then protein and
lipid are seperated and even after i scale it to .95 they dnt
meetthey are still apart, I was hoping that lipid will be
scaled and protein shud have remained in the center of the lipid
but that doesn't happen. I hope you got my question

On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   sunny mishra wrote:

   Yes I did the same and when I see my system.gro file it
gives me
   the dimensions of the protein box half of the lipid
bilayer box
   so that means it should now be set in the center of the lipid
   bilayer. But after


   I don't understand what you mean.


   that when I run the inflategro script and see my output
file the
   protein and lipid are separated and I dnt know why?


   Can you post the actual commands you're using?

   -Justin


   --

   Justin A. Lemkul
   Ph.D. Candidate
   ICTAS Doctoral Scholar
   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
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   >.

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-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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
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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Please search the arc

[gmx-users] MD fatal error :wrong string length 0 for string buf

[Yanmei Song]

Dear All:

When I submitted the md run, It gives me the following error:

Program mdrun, VERSION 3.3.3
Source code file: gmxfio.c, line: 607

Fatal error:
wrong string length 0 for string buf (source tpxio.c, line 1150)

I run the similar system before using the same md.mdp file. and it was fine.

Any suggestions would be greatly appreciated
Thanks


-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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Re: [gmx-users] MD fatal error :wrong string length 0 for string buf

[David van der Spoel]

Yanmei Song wrote:

Dear All:

When I submitted the md run, It gives me the following error:

Program mdrun, VERSION 3.3.3
Source code file: gmxfio.c, line: 607

Fatal error:
wrong string length 0 for string buf (source tpxio.c, line 1150)

I run the similar system before using the same md.mdp file. and it was 
fine.



what version is the tpr file? The one corresponding to mdrun 3.3.3?

Any suggestions would be greatly appreciated
Thanks


--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University


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Re: [gmx-users] MD fatal error :wrong string length 0 for string buf

[Yanmei Song]

what version is the tpr file? The one corresponding to mdrun 3.3.3?

What do you mean?
I used gromacs-3.3.3 before and now. the same system and I did not have the
problem before.

On Thu, Oct 29, 2009 at 2:06 PM, David van der Spoel
wrote:

> Yanmei Song wrote:
>
>> Dear All:
>>
>> When I submitted the md run, It gives me the following error:
>>
>> Program mdrun, VERSION 3.3.3
>> Source code file: gmxfio.c, line: 607
>>
>> Fatal error:
>> wrong string length 0 for string buf (source tpxio.c, line 1150)
>>
>> I run the similar system before using the same md.mdp file. and it was
>> fine.
>>
>>  what version is the tpr file? The one corresponding to mdrun 3.3.3?
>
>> Any suggestions would be greatly appreciated
>> Thanks
>>
>>
>> --
>> Yanmei Song
>> Ph.D. Candidate
>> Department of Chemical Engineering
>> Arizona State University
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
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>
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-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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Re: [gmx-users] Re: Inflategro for Coarse Grained

[sunny mishra]

Alright. I have done thisI have made another lipid_newbox.gro file and
wrote same box vectors as of lipid.gro file

For LIPID :

editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820 13.29820 6.59160

For Protein :

editconf -f protein.gro -o protein_newbox.gro -c -box 13.29820 13.29820
6.59160

Then cat the system and made system.gro file and did inflategro of the
system.gro file. Do you think this is the correct way and now when I
visualize this in VMD the protein is shifted little upwards but it is at the
center of the lipid.

Sunny


On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> No. But in order to do that with lipid.gro what co-ordinates should I have
>> to take?
>>
>>
> I think you need to differentiate between "coordinates" and "box vectors."
>  You should center the molecule in the box (defined by the vectors in the
> last line of the .gro file).  I assumed you were specifying these box
> vectors with -box.
>
> So, for both the protein and the lipid coordinate files, you need to use
>
> editconf -c -box (x, y, z from .gro file)
>
> -Justin
>
>  On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>sunny mishra wrote:
>>
>>okk...here are the commands which I am givng...
>>
>>editconf -f 1SU4_cleancg_trans.gro -o 1SU4_newbox.gro -c -box
>>13.29820 13.29820 6.59160
>>
>>I get the 1SU4_newbox.gro which has co-ordinates 13.29820
>>13.29820 6.59160
>>
>>
>>Have you done the same with lipid.gro?  If the protein and the lipid
>>are in different coordinate systems (i.e., lipid.gro centered at the
>>origin and protein centered within the box, which has its corner
>>placed at the origin) then you will have a problem.
>>
>>-Justin
>>
>>cat 1SU4_newbox.gro lipid.gro > system..gro
>>
>>Now here system.gro also has co-ordinates 13.29820 13.29820 6.59160
>>
>>now inflategro:
>>
>>inflategro system.gro 4 DSPC 14 -o inflated_bilayer.gro 5
>>
>>Now when i visualize my output file in VMD then protein and
>>lipid are seperated and even after i scale it to .95 they dnt
>>meetthey are still apart, I was hoping that lipid will be
>>scaled and protein shud have remained in the center of the lipid
>>but that doesn't happen. I hope you got my question
>>
>>On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   sunny mishra wrote:
>>
>>   Yes I did the same and when I see my system.gro file it
>>gives me
>>   the dimensions of the protein box half of the lipid
>>bilayer box
>>   so that means it should now be set in the center of the
>> lipid
>>   bilayer. But after
>>
>>
>>   I don't understand what you mean.
>>
>>
>>   that when I run the inflategro script and see my output
>>file the
>>   protein and lipid are separated and I dnt know why?
>>
>>
>>   Can you post the actual commands you're using?
>>
>>   -Justin
>>
>>
>>   --
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   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/searchbefore
>>   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/mailing_lists/users.php
>>
>>
>>
>>--
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>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
>>

Re: [gmx-users] Re: Inflategro for Coarse Grained

[Justin A. Lemkul]

sunny mishra wrote:
Alright. I have done thisI have made another lipid_newbox.gro file 
and wrote same box vectors as of lipid.gro file


For LIPID :

editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820 13.29820 6.59160

For Protein :

editconf -f protein.gro -o protein_newbox.gro -c -box 13.29820 13.29820 
6.59160


Then cat the system and made system.gro file and did inflategro of the 
system.gro file. Do you think this is the correct way and now when I 
visualize this in VMD the protein is shifted little upwards but it is at 
the center of the lipid.




Well, did you get what you expected when you ran InflateGRO?  The protein and 
lipid should have the same center; that's what the editconf commands did, as 
I've told you.  If you need the protein to be placed differently, you must 
specify a different center (providing the coordinates to editconf -center).


-Justin


Sunny
   

On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul > wrote:




sunny mishra wrote:

No. But in order to do that with lipid.gro what co-ordinates
should I have to take?


I think you need to differentiate between "coordinates" and "box
vectors."  You should center the molecule in the box (defined by the
vectors in the last line of the .gro file).  I assumed you were
specifying these box vectors with -box.

So, for both the protein and the lipid coordinate files, you need to use

editconf -c -box (x, y, z from .gro file)

-Justin

On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   sunny mishra wrote:

   okk...here are the commands which I am givng...

   editconf -f 1SU4_cleancg_trans.gro -o 1SU4_newbox.gro -c -box
   13.29820 13.29820 6.59160

   I get the 1SU4_newbox.gro which has co-ordinates 13.29820
   13.29820 6.59160


   Have you done the same with lipid.gro?  If the protein and
the lipid
   are in different coordinate systems (i.e., lipid.gro centered
at the
   origin and protein centered within the box, which has its corner
   placed at the origin) then you will have a problem.

   -Justin

   cat 1SU4_newbox.gro lipid.gro > system..gro

   Now here system.gro also has co-ordinates 13.29820
13.29820 6.59160

   now inflategro:

   inflategro system.gro 4 DSPC 14 -o inflated_bilayer.gro 5

   Now when i visualize my output file in VMD then protein and
   lipid are seperated and even after i scale it to .95 they dnt
   meetthey are still apart, I was hoping that lipid will be
   scaled and protein shud have remained in the center of
the lipid
   but that doesn't happen. I hope you got my question

   On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul
   mailto:jalem...@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/mail

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

[XAvier Periole]

On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote:


Hi,

I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein  
in a CG water box, looking at the diffusion constant of the protein  
among other things. I'm using the Nose-Hoover thermostat and  
Parrinello-Rahman barostat with tc-grps = System. In CHARMM, a  
protein-in-water simulation with an extended ensemble will show  
equal temperatures for the protein and the water. However, I'm  
finding that, with ref_t = 323, I get a SOL (both W and WF  
particles) temperature of 323 and a Protein temperature of 295. Is  
this what I should expect?

No.


The system has 62.5k particles, the box is 20 x 20 x 20, and the  
relevant .mdp parameters I've used are:


tcoupl   = Nose-Hoover
tc-grps  = System
tau_t= 2
ref_t= 323
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
tau_p= 5
compressibility  = 5e-5
ref_p= 1.0

These parameters seem to lead to stable systems for bilayer  
simulations. I've included the whole .mdp file at the end in case  
I've forgotten to mention something relevant.


I calculated temperatures with

g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5
I did not know you could get the temperature throught g_traj ... the - 
ot option is the one

giving you the temperature?

Do you get the same temperature difference with g_energy? Or may be  
the info is not
in there? May be you could rerun you trajectory using a new tpr where  
you define two
different temp coupling groups. And see if you observe the same  
temperature given by

g_energy.


Thanks,

-Michael

-- begin md2.mdp --

; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
tinit= 0.0
dt   = 0.020
nsteps   = 2550
; mode for center of mass motion removal
comm-mode= linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps= System


; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5
nstvout  = 5
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 2500
nstenergy= 2500
; Output frequency and precision for xtc file =
nstxtcout= 2500
xtc_precision= 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   = System Protein W WF

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 5
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths=
rvdw_switch  = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 10
fourier_ny   = 10
fourier_nz   = 10
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = Nose-Hoover
; Groups to couple separately =
tc-grps  = System
; Time constant (ps) and reference temperature (K) =
tau_t= 2
ref_t= 323
; Pressure coupling  =
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 5
compressibility  = 5e-5
ref_p= 1.0

; SIMULATED ANNEALING CONTROL =
annealing= no

; GENERATE VELOCITIES FOR STARTUP RUN =
continuation  = yes
gen_vel  = no
;gen_temp = 323
;gen_seed = 473529

; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Relative tolerance of shake =
shake_tol= 0.0001
; H

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

[Justin A. Lemkul]

Michael Lerner wrote:

Hi,

I'm using GROMACS 4.0.5 to do a MARTINI simulation of a CG protein in a 
CG water box, looking at the diffusion constant of the protein among 
other things. I'm using the Nose-Hoover thermostat and Parrinello-Rahman 
barostat with tc-grps = System. In CHARMM, a protein-in-water simulation 
with an extended ensemble will show equal temperatures for the protein 
and the water. However, I'm finding that, with ref_t = 323, I get a SOL 
(both W and WF particles) temperature of 323 and a Protein temperature 
of 295. Is this what I should expect?


The system has 62.5k particles, the box is 20 x 20 x 20, and the 
relevant .mdp parameters I've used are:


tcoupl   = Nose-Hoover
tc-grps  = System
tau_t= 2
ref_t= 323
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
tau_p= 5
compressibility  = 5e-5
ref_p= 1.0

These parameters seem to lead to stable systems for bilayer simulations. 
I've included the whole .mdp file at the end in case I've forgotten to 
mention something relevant.


I calculated temperatures with

g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5



I see you are using "constraints = none," but are there any constraints defined 
in the topology?  If so, as noted in g_traj -h:


"Option -ot plots the temperature of each group, provided velocities are
present in the trajectory file. No corrections are made for constrained
degrees of freedom! This implies -com."

So you will get an inherently incorrect answer when using g_traj, if there are 
any constraints.


-Justin


Thanks,

-Michael

-- begin md2.mdp --

; RUN CONTROL PARAMETERS =
integrator   = md
; start time and timestep in ps =
tinit= 0.0
dt   = 0.020
nsteps   = 2550
; mode for center of mass motion removal
comm-mode= linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps= System


; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 5
nstvout  = 5
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 2500
nstenergy= 2500
; Output frequency and precision for xtc file =
nstxtcout= 2500
xtc_precision= 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps   = System Protein W WF

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 5
; ns algorithm (simple or grid) =
ns_type  = grid
; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = Shift
rcoulomb_switch  = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r= 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths=
rvdw_switch  = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing   = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 10
fourier_ny   = 10
fourier_nz   = 10
; EWALD/PME/PPPM parameters =
pme_order= 4
ewald_rtol   = 1e-05
epsilon_surface  = 0
optimize_fft = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl   = Nose-Hoover
; Groups to couple separately =
tc-grps  = System
; Time constant (ps) and reference temperature (K) =
tau_t= 2
ref_t= 323
; Pressure coupling  =
Pcoupl   = Parrinello-Rahman
Pcoupltype   = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p= 5
compressibility  = 5e-5
ref_p= 1.0

; SIMULATED ANNEALING CONTROL =
annealing= no

; GENERATE VELOCITIES FOR STARTUP RUN =
continuation  = yes
gen_vel  = no
;gen_temp = 323
;gen_seed = 473529

; OPTIONS FOR BONDS =
constraints  = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Relative tolerance of shake =
shake_tol= 0.0001
; Highest order 

Re: [gmx-users] Re: Inflategro for Coarse Grained

[sunny mishra]

Well yes I guess I am getting the same thing what I expected but now I am
little confused here and I don't know how to explain you this but I will
try.
Initially I aligned my protein using TMDET results and centered that at
ORIGIN and then I centered the lipid at origin using geom_center script
provided in VMD and when I visualized that,  the protein was properly
inserted in the lipid the way MARTINI folks have shown in their website.

After that I followed your tutorial and made the system.gro file by catting
lipid and protein and its visualization gives me the same thing as I was
getting earlier. Now after that when I run the inflategro script for the
system.gro file and scale the lipid by the factor of 4,  the protein goes
apart from lipid (I dnt know why) and after our recent conversation I did
the same thing but now the protein is shifted little upwards but still it is
at the center of lipid. Now I don't know whether this factor will matter a
lot or not? I hope you got my question.

In summary, earlier the upper portion of protein was inserted fully same as
shown in the martini website but after doing the inflategro without running
EM it shifted little upwards but still at the center so I dnt know whether
this will matter a lot or not?



On Thu, Oct 29, 2009 at 5:26 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> Alright. I have done thisI have made another lipid_newbox.gro file and
>> wrote same box vectors as of lipid.gro file
>>
>> For LIPID :
>>
>> editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820 13.29820
>> 6.59160
>>
>> For Protein :
>>
>> editconf -f protein.gro -o protein_newbox.gro -c -box 13.29820 13.29820
>> 6.59160
>>
>> Then cat the system and made system.gro file and did inflategro of the
>> system.gro file. Do you think this is the correct way and now when I
>> visualize this in VMD the protein is shifted little upwards but it is at the
>> center of the lipid.
>>
>>
> Well, did you get what you expected when you ran InflateGRO?  The protein
> and lipid should have the same center; that's what the editconf commands
> did, as I've told you.  If you need the protein to be placed differently,
> you must specify a different center (providing the coordinates to editconf
> -center).
>
> -Justin
>
>  Sunny
>>
>>
>> On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>sunny mishra wrote:
>>
>>No. But in order to do that with lipid.gro what co-ordinates
>>should I have to take?
>>
>>
>>I think you need to differentiate between "coordinates" and "box
>>vectors."  You should center the molecule in the box (defined by the
>>vectors in the last line of the .gro file).  I assumed you were
>>specifying these box vectors with -box.
>>
>>So, for both the protein and the lipid coordinate files, you need to
>> use
>>
>>editconf -c -box (x, y, z from .gro file)
>>
>>-Justin
>>
>>On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   sunny mishra wrote:
>>
>>   okk...here are the commands which I am givng...
>>
>>   editconf -f 1SU4_cleancg_trans.gro -o 1SU4_newbox.gro -c
>> -box
>>   13.29820 13.29820 6.59160
>>
>>   I get the 1SU4_newbox.gro which has co-ordinates 13.29820
>>   13.29820 6.59160
>>
>>
>>   Have you done the same with lipid.gro?  If the protein and
>>the lipid
>>   are in different coordinate systems (i.e., lipid.gro centered
>>at the
>>   origin and protein centered within the box, which has its corner
>>   placed at the origin) then you will have a problem.
>>
>>   -Justin
>>
>>   cat 1SU4_newbox.gro lipid.gro > system..gro
>>
>>   Now here system.gro also has co-ordinates 13.29820
>>13.29820 6.59160
>>
>>   now inflategro:
>>
>>   inflategro system.gro 4 DSPC 14 -o inflated_bilayer.gro 5
>>
>>   Now when i visualize my output file in VMD then protein and
>>   lipid are seperated and even after i scale it to .95 they
>> dnt
>>   meetthey are still apart, I was hoping that lipid will
>> be
>>   scaled and protein shud have remained in the center of
>>the lipid
>>   but that doesn't happen. I hope you got my question
>>
>>   On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul
>>   mailto:jalem...@vt.edu>
>>>
>>   
>>>
>>
>>
>>  sunny mishra wrote:
>>
>>  Yes I did the same and when I see my system.gro
>>file it
>>   gives me
>>  the dimension

Re: [gmx-users] Re: Inflategro for Coarse Grained

[Justin A. Lemkul]

sunny mishra wrote:
Well yes I guess I am getting the same thing what I expected but now I 
am little confused here and I don't know how to explain you this but I 
will try. 
Initially I aligned my protein using TMDET results and centered that at 
ORIGIN and then I centered the lipid at origin using geom_center script 
provided in VMD and when I visualized that,  the protein was properly 
inserted in the lipid the way MARTINI folks have shown in their website.




I am unfamiliar with either of these programs, but I can tell you that if you 
center a molecule at the coordinate origin, that location (0, 0, 0) corresponds 
to the corner of the box, by GROMACS convention.  This is probably the root of 
the problem you were seeing.  I do not know what the VMD script does.  I would 
think them both unnecessary for GROMACS use (at least in this application), 
since all manipulations can easily be done with editconf.


After that I followed your tutorial and made the system.gro file by 
catting lipid and protein and its visualization gives me the same thing 


You can't be guaranteed that different procedures will lead to compatible 
alignment, as you have undoubtedly discovered :)


as I was getting earlier. Now after that when I run the inflategro 
script for the system.gro file and scale the lipid by the factor of 4, 
 the protein goes apart from lipid (I dnt know why) and after our recent 
conversation I did the same thing but now the protein is shifted little 
upwards but still it is at the center of lipid. Now I don't know whether 
this factor will matter a lot or not? I hope you got my question.




I don't know how you define "shifted upwards" - relative to where editconf 
placed it, or relative to where you want it to be?  If it is not too far from 
the center, and the proper positioning is to have the center of the protein 
aligned with the center of the bilayer, it may assume this position after some 
equilibration.


-Justin

In summary, earlier the upper portion of protein was inserted fully same 
as shown in the martini website but after doing the inflategro without 
running EM it shifted little upwards but still at the center so I dnt 
know whether this will matter a lot or not?




On Thu, Oct 29, 2009 at 5:26 PM, Justin A. Lemkul > wrote:




sunny mishra wrote:

Alright. I have done thisI have made another
lipid_newbox.gro file and wrote same box vectors as of lipid.gro
file

For LIPID :

editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820
13.29820 6.59160

For Protein :

editconf -f protein.gro -o protein_newbox.gro -c -box 13.29820
13.29820 6.59160

Then cat the system and made system.gro file and did inflategro
of the system.gro file. Do you think this is the correct way and
now when I visualize this in VMD the protein is shifted little
upwards but it is at the center of the lipid.


Well, did you get what you expected when you ran InflateGRO?  The
protein and lipid should have the same center; that's what the
editconf commands did, as I've told you.  If you need the protein to
be placed differently, you must specify a different center
(providing the coordinates to editconf -center).

-Justin

Sunny

 
On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul

mailto:jalem...@vt.edu>
>> wrote:



   sunny mishra wrote:

   No. But in order to do that with lipid.gro what co-ordinates
   should I have to take?


   I think you need to differentiate between "coordinates" and "box
   vectors."  You should center the molecule in the box (defined
by the
   vectors in the last line of the .gro file).  I assumed you were
   specifying these box vectors with -box.

   So, for both the protein and the lipid coordinate files, you
need to use

   editconf -c -box (x, y, z from .gro file)

   -Justin

   On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>
>
   

[gmx-users] bonds that rotated more than 30 degrees:

[Yanmei Song]

Dear Users:

I used all-bonds for constraints. My MD is dead right after i submit the
task. The error message is :

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 2.084475 (between atoms 23417 and 23431) rms 0.054595
bonds that rotated more than 30 degrees:

Anyone knows what is the problem and how i can fix it?
Thanks


-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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Re: [gmx-users] bonds that rotated more than 30 degrees:

[Justin A. Lemkul]

Yanmei Song wrote:

Dear Users:

I used all-bonds for constraints. My MD is dead right after i submit the 
task. The error message is :


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 2.084475 (between atoms 23417 and 23431) rms 0.054595
bonds that rotated more than 30 degrees:

Anyone knows what is the problem and how i can fix it?


Please see the following:

http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

Beyond that, search the list archive - this error comes up almost daily, and 
there are plenty of solutions to try.  If you still can't find a solution, post 
a detail description of your system, including how you built it, what you've 
done to energy-minimize and/or equilibrate it, and post the contents of any 
relevant .mdp file(s).


-Justin


Thanks
 


--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University




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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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] Re: Inflategro for Coarse Grained

[sunny mishra]

Ok. I guess that makes sense. If you say I can send you my system.gro file
(after catting the system as per our recent conversation) and my protein.gro
and lipid.gro files (In which the protein is inserted before our
conversation) and if you visualize that in VMD you will get more idea of
what I am trying to ask? Can I do that?



On Thu, Oct 29, 2009 at 5:46 PM, Justin A. Lemkul  wrote:

>
>
> sunny mishra wrote:
>
>> Well yes I guess I am getting the same thing what I expected but now I am
>> little confused here and I don't know how to explain you this but I will
>> try. Initially I aligned my protein using TMDET results and centered that at
>> ORIGIN and then I centered the lipid at origin using geom_center script
>> provided in VMD and when I visualized that,  the protein was properly
>> inserted in the lipid the way MARTINI folks have shown in their website.
>>
>>
> I am unfamiliar with either of these programs, but I can tell you that if
> you center a molecule at the coordinate origin, that location (0, 0, 0)
> corresponds to the corner of the box, by GROMACS convention.  This is
> probably the root of the problem you were seeing.  I do not know what the
> VMD script does.  I would think them both unnecessary for GROMACS use (at
> least in this application), since all manipulations can easily be done with
> editconf.
>
>
>  After that I followed your tutorial and made the system.gro file by
>> catting lipid and protein and its visualization gives me the same thing
>>
>
> You can't be guaranteed that different procedures will lead to compatible
> alignment, as you have undoubtedly discovered :)
>
>
>  as I was getting earlier. Now after that when I run the inflategro script
>> for the system.gro file and scale the lipid by the factor of 4,  the protein
>> goes apart from lipid (I dnt know why) and after our recent conversation I
>> did the same thing but now the protein is shifted little upwards but still
>> it is at the center of lipid. Now I don't know whether this factor will
>> matter a lot or not? I hope you got my question.
>>
>>
> I don't know how you define "shifted upwards" - relative to where editconf
> placed it, or relative to where you want it to be?  If it is not too far
> from the center, and the proper positioning is to have the center of the
> protein aligned with the center of the bilayer, it may assume this position
> after some equilibration.
>
> -Justin
>
>  In summary, earlier the upper portion of protein was inserted fully same
>> as shown in the martini website but after doing the inflategro without
>> running EM it shifted little upwards but still at the center so I dnt know
>> whether this will matter a lot or not?
>>
>>
>>
>> On Thu, Oct 29, 2009 at 5:26 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>sunny mishra wrote:
>>
>>Alright. I have done thisI have made another
>>lipid_newbox.gro file and wrote same box vectors as of lipid.gro
>>file
>>
>>For LIPID :
>>
>>editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820
>>13.29820 6.59160
>>
>>For Protein :
>>
>>editconf -f protein.gro -o protein_newbox.gro -c -box 13.29820
>>13.29820 6.59160
>>
>>Then cat the system and made system.gro file and did inflategro
>>of the system.gro file. Do you think this is the correct way and
>>now when I visualize this in VMD the protein is shifted little
>>upwards but it is at the center of the lipid.
>>
>>
>>Well, did you get what you expected when you ran InflateGRO?  The
>>protein and lipid should have the same center; that's what the
>>editconf commands did, as I've told you.  If you need the protein to
>>be placed differently, you must specify a different center
>>(providing the coordinates to editconf -center).
>>
>>-Justin
>>
>>Sunny
>>
>>On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>>> wrote:
>>
>>
>>
>>   sunny mishra wrote:
>>
>>   No. But in order to do that with lipid.gro what co-ordinates
>>   should I have to take?
>>
>>
>>   I think you need to differentiate between "coordinates" and "box
>>   vectors."  You should center the molecule in the box (defined
>>by the
>>   vectors in the last line of the .gro file).  I assumed you were
>>   specifying these box vectors with -box.
>>
>>   So, for both the protein and the lipid coordinate files, you
>>need to use
>>
>>   editconf -c -box (x, y, z from .gro file)
>>
>>   -Justin
>>
>>   On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul
>>   mailto:jalem...@vt.edu>
>>>
>>   
>>

Re: [gmx-users] Re: Inflategro for Coarse Grained

[Justin A. Lemkul]

sunny mishra wrote:
Ok. I guess that makes sense. If you say I can send you my system.gro 
file (after catting the system as per our recent conversation) and my 
protein.gro and lipid.gro files (In which the protein is inserted before 
our conversation) and if you visualize that in VMD you will get more 
idea of what I am trying to ask? Can I do that?




I'm sorry, but no, I don't really have time for extra work right now, nor do I 
know anything about the system you're studying.  That's your job to justify the 
position of the system (and adjust it with editconf -translate, if necessary). 
The position should not simply be an aesthetic observation, it should be based 
on any experimental data available.  And like I said, if it is off slightly from 
center, equilibration may help place it correctly.  With CG, you should be able 
to probe long time frames, over which the system may change quite a bit.


-Justin




On Thu, Oct 29, 2009 at 5:46 PM, Justin A. Lemkul > wrote:




sunny mishra wrote:

Well yes I guess I am getting the same thing what I expected but
now I am little confused here and I don't know how to explain
you this but I will try. Initially I aligned my protein using
TMDET results and centered that at ORIGIN and then I centered
the lipid at origin using geom_center script provided in VMD and
when I visualized that,  the protein was properly inserted in
the lipid the way MARTINI folks have shown in their website.


I am unfamiliar with either of these programs, but I can tell you
that if you center a molecule at the coordinate origin, that
location (0, 0, 0) corresponds to the corner of the box, by GROMACS
convention.  This is probably the root of the problem you were
seeing.  I do not know what the VMD script does.  I would think them
both unnecessary for GROMACS use (at least in this application),
since all manipulations can easily be done with editconf.


After that I followed your tutorial and made the system.gro file
by catting lipid and protein and its visualization gives me the
same thing


You can't be guaranteed that different procedures will lead to
compatible alignment, as you have undoubtedly discovered :)


as I was getting earlier. Now after that when I run the
inflategro script for the system.gro file and scale the lipid by
the factor of 4,  the protein goes apart from lipid (I dnt know
why) and after our recent conversation I did the same thing but
now the protein is shifted little upwards but still it is at the
center of lipid. Now I don't know whether this factor will
matter a lot or not? I hope you got my question.


I don't know how you define "shifted upwards" - relative to where
editconf placed it, or relative to where you want it to be?  If it
is not too far from the center, and the proper positioning is to
have the center of the protein aligned with the center of the
bilayer, it may assume this position after some equilibration.

-Justin

In summary, earlier the upper portion of protein was inserted
fully same as shown in the martini website but after doing the
inflategro without running EM it shifted little upwards but
still at the center so I dnt know whether this will matter a lot
or not?



On Thu, Oct 29, 2009 at 5:26 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   sunny mishra wrote:

   Alright. I have done thisI have made another
   lipid_newbox.gro file and wrote same box vectors as of
lipid.gro
   file

   For LIPID :

   editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820
   13.29820 6.59160

   For Protein :

   editconf -f protein.gro -o protein_newbox.gro -c -box
13.29820
   13.29820 6.59160

   Then cat the system and made system.gro file and did
inflategro
   of the system.gro file. Do you think this is the correct
way and
   now when I visualize this in VMD the protein is shifted
little
   upwards but it is at the center of the lipid.


   Well, did you get what you expected when you ran InflateGRO?  The
   protein and lipid should have the same center; that's what the
   editconf commands did, as I've told you.  If you need the
protein to
   be placed differently, you must specify a different center
   (providing the coordinates to editconf -center).

   -Justin

   Sunny

   On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul
   mailto:jalem...@vt.edu>

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

[Michael Lerner]

On Thu, Oct 29, 2009 at 5:38 PM, Justin A. Lemkul  wrote:

>
> I see you are using "constraints = none," but are there any constraints
> defined in the topology?  If so, as noted in g_traj -h:
>
> "Option -ot plots the temperature of each group, provided velocities are
> present in the trajectory file. No corrections are made for constrained
> degrees of freedom! This implies -com."
>
> So you will get an inherently incorrect answer when using g_traj, if there
> are any constraints.
>
>
Oops! I actually had read some previous messages about that, but I got
confused and thought the problem was with g_energy, not g_traj. I'm not
particularly familiar with the GROMACS source code, but gmx_traj.c has this
function:

static real temp(rvec v[],real mass[],int isize,atom_id index[])
{
  real ekin2=0;
  int  i,j;

  for(i=0; i -Justin
>
>  Thanks,
>>
>> -Michael
>>
>> -- begin md2.mdp --
>>
>> ; RUN CONTROL PARAMETERS =
>> integrator   = md
>> ; start time and timestep in ps =
>> tinit= 0.0
>> dt   = 0.020
>> nsteps   = 2550
>> ; mode for center of mass motion removal
>> comm-mode= linear
>> ; number of steps for center of mass motion removal
>> nstcomm  = 1
>> ; group(s) for center of mass motion removal
>> comm-grps= System
>>
>>
>> ; OUTPUT CONTROL OPTIONS =
>> ; Output frequency for coords (x), velocities (v) and forces (f) =
>> nstxout  = 5
>> nstvout  = 5
>> nstfout  = 0
>> ; Output frequency for energies to log file and energy file =
>> nstlog   = 2500
>> nstenergy= 2500
>> ; Output frequency and precision for xtc file =
>> nstxtcout= 2500
>> xtc_precision= 100
>> ; This selects the subset of atoms for the xtc file. You can =
>> ; select multiple groups. By default all atoms will be written. =
>> xtc-grps =
>> ; Selection of energy groups =
>> energygrps   = System Protein W WF
>>
>> ; NEIGHBORSEARCHING PARAMETERS =
>> ; nblist update frequency =
>> nstlist  = 5
>> ; ns algorithm (simple or grid) =
>> ns_type  = grid
>> ; Periodic boundary conditions: xyz or none =
>> pbc  = xyz
>> ; nblist cut-off =
>> rlist= 1.2
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW =
>> ; Method for doing electrostatics =
>> coulombtype  = Shift
>> rcoulomb_switch  = 0.0
>> rcoulomb = 1.2
>> ; Dielectric constant (DC) for cut-off or DC of reaction field =
>> epsilon_r= 15
>> ; Method for doing Van der Waals =
>> vdw_type = Shift
>> ; cut-off lengths=
>> rvdw_switch  = 0.9
>> rvdw = 1.2
>> ; Apply long range dispersion corrections for Energy and Pressure =
>> DispCorr = No
>> ; Spacing for the PME/PPPM FFT grid =
>> fourierspacing   = 0.12
>> ; FFT grid size, when a value is 0 fourierspacing will be used =
>> fourier_nx   = 10
>> fourier_ny   = 10
>> fourier_nz   = 10
>> ; EWALD/PME/PPPM parameters =
>> pme_order= 4
>> ewald_rtol   = 1e-05
>> epsilon_surface  = 0
>> optimize_fft = no
>>
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
>> ; Temperature coupling   =
>> tcoupl   = Nose-Hoover
>> ; Groups to couple separately =
>> tc-grps  = System
>> ; Time constant (ps) and reference temperature (K) =
>> tau_t= 2
>> ref_t= 323
>> ; Pressure coupling  =
>> Pcoupl   = Parrinello-Rahman
>> Pcoupltype   = isotropic
>> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
>> tau_p= 5
>> compressibility  = 5e-5
>> ref_p= 1.0
>>
>> ; SIMULATED ANNEALING CONTROL =
>> annealing= no
>>
>> ; GENERATE VELOCITIES FOR STARTUP RUN =
>> continuation  = yes
>> gen_vel  = no
>> ;gen_temp = 323
>> ;gen_seed = 473529
>>
>> ; OPTIONS FOR BONDS =
>> constraints  = none
>> ; Type of constraint algorithm =
>> constraint_algorithm = Lincs
>> ; Relative tolerance of shake =
>> shake_tol= 0.0001
>> ; Highest order in the expansion of the constraint coupling matrix =
>> lincs_order  = 4
>> ; Lincs will write a warning to the stderr if in one step a bond =
>> ; rotates over more degrees than =
>> lincs_warnangle  = 30
>> ; Convert harmonic bonds to morse potentials =
>> morse= no
>>
>> ; NMR refinement stuff  =
>> ; Distance restraints type: No, Simple or Ensemble =
>> disre= No
>> ; Force weighting of pairs in one distance restraint: Equal or
>> Conservative =
>> disre_weighting   

Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

[Michael Lerner]

On Thu, Oct 29, 2009 at 5:31 PM, XAvier Periole  wrote:

>
> On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote:
>
>
>> I calculated temperatures with
>>
>> g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5
>>
> I did not know you could get the temperature throught g_traj ... the -ot
> option is the one
> giving you the temperature?
>
>
Yes.


> Do you get the same temperature difference with g_energy? Or may be the
> info is not
> in there? May be you could rerun you trajectory using a new tpr where you
> define two
> different temp coupling groups. And see if you observe the same temperature
> given by
> g_energy.
>

It's possible that I'm doing something wrong, but I couldn't convince
g_energy to give me the temperature of different groups when I used a single
thermostat for the entire system. If I use two temperature coupling groups,
I get the expected results.

As Justin pointed out, it looks like the error was mine for not
understanding the details of g_traj. When I manually correct for the degrees
of freedom, I get temperatures for Protein/Sol that are close enough to each
other (i.e. within a couple of standard deviations).

Thanks,

-Michael


>
>> Thanks,
>>
>> -Michael
>>
>> -- begin md2.mdp --
>>
>> ; RUN CONTROL PARAMETERS =
>> integrator   = md
>> ; start time and timestep in ps =
>> tinit= 0.0
>> dt   = 0.020
>> nsteps   = 2550
>> ; mode for center of mass motion removal
>> comm-mode= linear
>> ; number of steps for center of mass motion removal
>> nstcomm  = 1
>> ; group(s) for center of mass motion removal
>> comm-grps= System
>>
>>
>> ; OUTPUT CONTROL OPTIONS =
>> ; Output frequency for coords (x), velocities (v) and forces (f) =
>> nstxout  = 5
>> nstvout  = 5
>> nstfout  = 0
>> ; Output frequency for energies to log file and energy file =
>> nstlog   = 2500
>> nstenergy= 2500
>> ; Output frequency and precision for xtc file =
>> nstxtcout= 2500
>> xtc_precision= 100
>> ; This selects the subset of atoms for the xtc file. You can =
>> ; select multiple groups. By default all atoms will be written. =
>> xtc-grps =
>> ; Selection of energy groups =
>> energygrps   = System Protein W WF
>>
>> ; NEIGHBORSEARCHING PARAMETERS =
>> ; nblist update frequency =
>> nstlist  = 5
>> ; ns algorithm (simple or grid) =
>> ns_type  = grid
>> ; Periodic boundary conditions: xyz or none =
>> pbc  = xyz
>> ; nblist cut-off =
>> rlist= 1.2
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW =
>> ; Method for doing electrostatics =
>> coulombtype  = Shift
>> rcoulomb_switch  = 0.0
>> rcoulomb = 1.2
>> ; Dielectric constant (DC) for cut-off or DC of reaction field =
>> epsilon_r= 15
>> ; Method for doing Van der Waals =
>> vdw_type = Shift
>> ; cut-off lengths=
>> rvdw_switch  = 0.9
>> rvdw = 1.2
>> ; Apply long range dispersion corrections for Energy and Pressure =
>> DispCorr = No
>> ; Spacing for the PME/PPPM FFT grid =
>> fourierspacing   = 0.12
>> ; FFT grid size, when a value is 0 fourierspacing will be used =
>> fourier_nx   = 10
>> fourier_ny   = 10
>> fourier_nz   = 10
>> ; EWALD/PME/PPPM parameters =
>> pme_order= 4
>> ewald_rtol   = 1e-05
>> epsilon_surface  = 0
>> optimize_fft = no
>>
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
>> ; Temperature coupling   =
>> tcoupl   = Nose-Hoover
>> ; Groups to couple separately =
>> tc-grps  = System
>> ; Time constant (ps) and reference temperature (K) =
>> tau_t= 2
>> ref_t= 323
>> ; Pressure coupling  =
>> Pcoupl   = Parrinello-Rahman
>> Pcoupltype   = isotropic
>> ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
>> tau_p= 5
>> compressibility  = 5e-5
>> ref_p= 1.0
>>
>> ; SIMULATED ANNEALING CONTROL =
>> annealing= no
>>
>> ; GENERATE VELOCITIES FOR STARTUP RUN =
>> continuation  = yes
>> gen_vel  = no
>> ;gen_temp = 323
>> ;gen_seed = 473529
>>
>> ; OPTIONS FOR BONDS =
>> constraints  = none
>> ; Type of constraint algorithm =
>> constraint_algorithm = Lincs
>> ; Relative tolerance of shake =
>> shake_tol= 0.0001
>> ; Highest order in the expansion of the constraint coupling matrix =
>> lincs_order  = 4
>> ; Lincs will write a warning to the stderr if in one step a bond =
>> ; rotates over more degrees than =
>> lincs_warn

Re: [gmx-users] MD fatal error :wrong string length 0 for string buf

[David van der Spoel]

Yanmei Song wrote:

what version is the tpr file? The one corresponding to mdrun 3.3.3?

What do you mean?
I used gromacs-3.3.3 before and now. the same system and I did not 
have the problem before.


Is your disk full?

Is this reproducable?




On Thu, Oct 29, 2009 at 2:06 PM, David van der Spoel 
mailto:sp...@xray.bmc.uu.se>> wrote:


Yanmei Song wrote:

Dear All:

When I submitted the md run, It gives me the following error:

Program mdrun, VERSION 3.3.3
Source code file: gmxfio.c, line: 607

Fatal error:
wrong string length 0 for string buf (source tpxio.c, line 1150)

I run the similar system before using the same md.mdp file.
and it was fine.

what version is the tpr file? The one corresponding to mdrun 3.3.3?

Any suggestions would be greatly appreciated
Thanks


-- 
Yanmei Song

Ph.D. Candidate
Department of Chemical Engineering
Arizona State University


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--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University


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[gmx-users] MVAPICH2 mdrun problem for SD and MD, GROMACS 4.0.5

[Daniel Adriano Silva M]

Dear Gromacs users,

I am experimenting the next problem on an infiniband-cluster (8
intel-cores per node, GROMACS compiled with icc 11.1, all run through
mvapich2):

I have a molecule (protein 498aa, solvated or in vacuum I get the same
problem at any box shape), when I try to SD minimize it with
mvapich2-mdrun, it minimizes well with 1, 2 or 3 cores and reaches
convergence in around 1000steps, however any further combination (4,5,
...n cores) makes it to immediately stop (less than 20 steps) with:

"Steepest Descents converged to machine precision...".

Further if I take "the 1 core minimized structure" and try to make a
solvated-pr dynamics(2fs, MD, NTP, etc.) it also works with 1
processor, but with more cores it begins immediately to bring LINCS
warnings: and dies:

"Too many LINCS warnings" or "Water molecule starting at atom 16221
can not be settled"

For a "long time" I had made another md simulations on this cluster
with the same mdps and other proteic systems, and I only see this
behavior with this particular protein, of course  before send this
mail I re-tested previuos-working tprs.
Finally, the most suspicious is that I have another very similar
8-core box (with the same processors) but with gromacs gcc compiled,
and it actually runs very well the same problematic molecule (even the
same tpr) with mpi and 8-cores.
What do you think??? Please, if you have some tpr to test something send it.

Thanks
Daniel Silva
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Re: [gmx-users] Different temperatures for different groups, even with Nose-Hoover

[TJ Piggot]

To get g_energy to give you the temperature (or any other property) of a 
specific group you need to have defined appropriate energygrps in your mdp 
file. This is independent of the choice of groups you use for the 
temperature coupling.


If you want to calculate these temperatures of the groups after you have 
already ran your simulations you can use the mdrun -rerun option to save 
you a lot of time.


Tom

--On Thursday, October 29, 2009 18:11:53 -0400 Michael Lerner 
 wrote:






On Thu, Oct 29, 2009 at 5:31 PM, XAvier Periole  wrote:



On Oct 29, 2009, at 9:26 PM, Michael Lerner wrote:



I calculated temperatures with

g_traj -f md2.trr -s md2.tpr -n index.ndx -ot -ng 5

I did not know you could get the temperature throught g_traj ... the -ot
option is the one
giving you the temperature?




Yes.
 

Do you get the same temperature difference with g_energy? Or may be the
info is not
in there? May be you could rerun you trajectory using a new tpr where you
define two
different temp coupling groups. And see if you observe the same
temperature given by
g_energy.



It's possible that I'm doing something wrong, but I couldn't convince
g_energy to give me the temperature of different groups when I used a
single thermostat for the entire system. If I use two temperature
coupling groups, I get the expected results.

As Justin pointed out, it looks like the error was mine for not
understanding the details of g_traj. When I manually correct for the
degrees of freedom, I get temperatures for Protein/Sol that are close
enough to each other (i.e. within a couple of standard deviations).

Thanks,

-Michael
 






Thanks,

-Michael

-- begin md2.mdp --

; RUN CONTROL PARAMETERS =
integrator               = md
; start time and timestep in ps =
tinit                    = 0.0
dt                       = 0.020
nsteps                   = 2550
; mode for center of mass motion removal
comm-mode                = linear
; number of steps for center of mass motion removal
nstcomm                  = 1
; group(s) for center of mass motion removal
comm-grps                = System


; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout                  = 5
nstvout                  = 5
nstfout                  = 0
; Output frequency for energies to log file and energy file =
nstlog                   = 2500
nstenergy                = 2500
; Output frequency and precision for xtc file =
nstxtcout                = 2500
xtc_precision            = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps                 =
; Selection of energy groups =
energygrps               = System Protein W WF

; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  = 5
; ns algorithm (simple or grid) =
ns_type                  = grid
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r                = 15
; Method for doing Van der Waals =
vdw_type                 = Shift
; cut-off lengths        =
rvdw_switch              = 0.9
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr                 = No
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 10
fourier_ny               = 10
fourier_nz               = 10
; EWALD/PME/PPPM parameters =
pme_order                = 4
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = no

; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling   =
tcoupl                   = Nose-Hoover
; Groups to couple separately =
tc-grps                  = System
; Time constant (ps) and reference temperature (K) =
tau_t                    = 2
ref_t                    = 323
; Pressure coupling      =
Pcoupl                   = Parrinello-Rahman
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p                    = 5
compressibility          = 5e-5
ref_p                    = 1.0

; SIMULATED ANNEALING CONTROL =
annealing                = no

; GENERATE VELOCITIES FOR STARTUP RUN =
continuation      = yes
gen_vel                  = no
;gen_temp                 = 323
;gen_seed                 = 473529

; OPTIONS FOR BONDS     =
constraints              = none
; Type of constraint algorithm =
constraint_algorithm     = Lincs
; Relative tolerance of shake =
shake_tol                = 0.0001
; Highest order in the expansion of the constraint coupling ma

[gmx-users] Constraints and ligands

[P.R.Anand Narayanan]

Dear users,
I just have 2 queries
1) Is it safe to use "united atoms" constraint for positional restraining and 
md simulation of an enzyme docked to the substrate? if yes, what is the KEYWORD 
to be typed in the mdp file and in what way is it simpler than the "all-bonds" 
constraint?

2) How can a chemical ligand be bonded to a protein ie; with what type of bond 
formation and how are the residues in the protein chosen for the bonding to be 
done with the ligand? 

Regards,
Anand




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[gmx-users] Number of solvent molecules

[P.R.Anand Narayanan]

Dear users,

How is it possible to fix the number of solvent molecules and the size of the 
box used so that I can maintain exactly the same environment for different runs.
For eg, if I have 84000 water solvent molecules and the dimensions of 6.7 6.73 
4.71 nm; how can I use the same system for a different run?? Can I get the 
syntax 

regards,
Anand



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