date:20100914

Hello everybody,

I have many difficulties to reproduce TIP3P simulation results with CHARMM
TIP3P. Regular TIP3P gives systematically a lower density than its CHARMM
counterpart, independantly from the cutoff for non-bonded interactions,
the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
Regular 961,067 +/-0,756 g/L
CHARMM  980,860 +/-0,492 g/L

The Enthalpy of vaporization follows a similar scheme:
regular -39,992 +/-0,021 kJ/mol
CHARMM  -40,665 +/-0,009 kJ/mol

In fact, CHARMM gives results closer to what I should obtain at 300K and 1
bar for TIP3P. I suspect an issue with the bond constraints, but I can't
locate precisely where it is. Settle parameters are exactly the same (as
well as constraints for flexible water). Did someone ever face a similar
problem?

Rgards,
Nicolas

P.S. I My system is just a box of 1728 water molecules pre-equilibrated
for 500 ps at 300 K and 1 bar.

P.S. II I'm using the following simulation parameters:
constraints  = hbonds
constraint_algorithm = LINCS
continuation = no
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30
morse= no
(LINCS or SHAKE should not make any difference since TIP3P is normally
treated by SETTLE).

Other parameters are:
; COUPLING
; Temperature coupling
tcoupl   = Berendsen
nsttcouple   = -1
nh-chain-length  = 10
tc_grps  = System
tau_t= 0.1
ref_t= 300
; Pressure coupling
pcoupl   = Berendsen
pcoupltype   = isotropic
nstpcouple   = -1
tau_p= 1
compressibility  = 4.5e-5
ref_p= 1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.15

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.15
vdwtype  = Cutoff
rvdw = 1.0
fourierspacing   = 0.10
pme_order= 6
ewald_rtol   = 1.0e-6
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 20
comm_mode= Linear
nstcomm  = 1
comm_grps= System


-- 
[ Nicolas Sapay - Post-Doctoral Fellow ]
CERMAV - www.cermav.cnrs.fr
BP53, 38041 Grenoble cedex 9, France
Phone: +33 (0)4 76 03 76 44/53






-- 
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Re: [gmx-users] Regular vs. CHARMM TIP3P water model


On 2010-09-14 10.23, Nicolas SAPAY wrote:

Hello everybody,

I have many difficulties to reproduce TIP3P simulation results with CHARMM
TIP3P. Regular TIP3P gives systematically a lower density than its CHARMM
counterpart, independantly from the cutoff for non-bonded interactions,
the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
Regular 961,067 +/-0,756 g/L
CHARMM  980,860 +/-0,492 g/L

The Enthalpy of vaporization follows a similar scheme:
regular -39,992 +/-0,021 kJ/mol
CHARMM  -40,665 +/-0,009 kJ/mol


How about the dispersion correction?
If that is not turned on densities will be too low (in both cases).



In fact, CHARMM gives results closer to what I should obtain at 300K and 1
bar for TIP3P. I suspect an issue with the bond constraints, but I can't
locate precisely where it is. Settle parameters are exactly the same (as
well as constraints for flexible water). Did someone ever face a similar
problem?

Rgards,
Nicolas

P.S. I My system is just a box of 1728 water molecules pre-equilibrated
for 500 ps at 300 K and 1 bar.

P.S. II I'm using the following simulation parameters:
constraints  = hbonds
constraint_algorithm = LINCS
continuation = no
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30
morse= no
(LINCS or SHAKE should not make any difference since TIP3P is normally
treated by SETTLE).

Other parameters are:
; COUPLING
; Temperature coupling
tcoupl   = Berendsen
nsttcouple   = -1
nh-chain-length  = 10
tc_grps  = System
tau_t= 0.1
ref_t= 300
; Pressure coupling
pcoupl   = Berendsen
pcoupltype   = isotropic
nstpcouple   = -1
tau_p= 1
compressibility  = 4.5e-5
ref_p= 1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.15

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.15
vdwtype  = Cutoff
rvdw = 1.0
fourierspacing   = 0.10
pme_order= 6
ewald_rtol   = 1.0e-6
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = yes

; RUN CONTROL PARAMETERS
integrator   = md
dt   = 0.002
nsteps   = 20
comm_mode= Linear
nstcomm  = 1
comm_grps= System





--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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RE: [gmx-users] Regular vs. CHARMM TIP3P water model


Hi,

I don't understand what exactly you want to reproduce.
Standard tip3p and Charmm tip3p are different models, so the density does not 
have to be identical.
The Gromacs Charmm FF implementation paper:
http://pubs.acs.org/doi/full/10.1021/ct900549r
gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched from 1 
to 1.2 nm).
I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion 
correction.
These numbers are quite different. I'll do some checking.

Berk

> Date: Tue, 14 Sep 2010 11:00:55 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
> 
> On 2010-09-14 10.23, Nicolas SAPAY wrote:
> > Hello everybody,
> >
> > I have many difficulties to reproduce TIP3P simulation results with CHARMM
> > TIP3P. Regular TIP3P gives systematically a lower density than its CHARMM
> > counterpart, independantly from the cutoff for non-bonded interactions,
> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
> > Regular 961,067 +/-0,756 g/L
> > CHARMM  980,860 +/-0,492 g/L
> >
> > The Enthalpy of vaporization follows a similar scheme:
> > regular -39,992 +/-0,021 kJ/mol
> > CHARMM  -40,665 +/-0,009 kJ/mol
> 
> How about the dispersion correction?
> If that is not turned on densities will be too low (in both cases).
> 
> >
> > In fact, CHARMM gives results closer to what I should obtain at 300K and 1
> > bar for TIP3P. I suspect an issue with the bond constraints, but I can't
> > locate precisely where it is. Settle parameters are exactly the same (as
> > well as constraints for flexible water). Did someone ever face a similar
> > problem?
> >
> > Rgards,
> > Nicolas
> >
> > P.S. I My system is just a box of 1728 water molecules pre-equilibrated
> > for 500 ps at 300 K and 1 bar.
> >
> > P.S. II I'm using the following simulation parameters:
> > constraints  = hbonds
> > constraint_algorithm = LINCS
> > continuation = no
> > lincs-order  = 4
> > lincs-iter   = 1
> > lincs-warnangle  = 30
> > morse= no
> > (LINCS or SHAKE should not make any difference since TIP3P is normally
> > treated by SETTLE).
> >
> > Other parameters are:
> > ; COUPLING
> > ; Temperature coupling
> > tcoupl   = Berendsen
> > nsttcouple   = -1
> > nh-chain-length  = 10
> > tc_grps  = System
> > tau_t= 0.1
> > ref_t= 300
> > ; Pressure coupling
> > pcoupl   = Berendsen
> > pcoupltype   = isotropic
> > nstpcouple   = -1
> > tau_p= 1
> > compressibility  = 4.5e-5
> > ref_p= 1
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > ; nblist update frequency
> > nstlist  = 10
> > ns_type  = grid
> > pbc  = xyz
> > rlist= 1.15
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype  = PME
> > rcoulomb-switch  = 0
> > rcoulomb = 1.15
> > vdwtype  = Cutoff
> > rvdw = 1.0
> > fourierspacing   = 0.10
> > pme_order= 6
> > ewald_rtol   = 1.0e-6
> > ewald_geometry   = 3d
> > epsilon_surface  = 0
> > optimize_fft = yes
> >
> > ; RUN CONTROL PARAMETERS
> > integrator   = md
> > dt   = 0.002
> > nsteps   = 20
> > comm_mode= Linear
> > nstcomm  = 1
> > comm_grps= System
> >
> >
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  -- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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RE: [gmx-users] Regular vs. CHARMM TIP3P water model


Hi,

We did some checking.
The value of the density for tip3p reported in the Gromacs Charmm ff 
implementation of 1001.7 is incorrect.
This should have been 985.7. The number of 1014.7 for Charmm tip3p is correct.

I would expect that the difference with your number is mainly due to the 
shorter LJ cut-off you are using.

Berk

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
Date: Tue, 14 Sep 2010 11:33:16 +0200








Hi,

I don't understand what exactly you want to reproduce.
Standard tip3p and Charmm tip3p are different models, so the density does not 
have to be identical.
The Gromacs Charmm FF implementation paper:
http://pubs.acs.org/doi/full/10.1021/ct900549r
gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched from 1 
to 1.2 nm).
I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion 
correction.
These numbers are quite different. I'll do some checking.

Berk

> Date: Tue, 14 Sep 2010 11:00:55 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
> 
> On 2010-09-14 10.23, Nicolas SAPAY wrote:
> > Hello everybody,
> >
> > I have many difficulties to reproduce TIP3P simulation results with CHARMM
> > TIP3P. Regular TIP3P gives systematically a lower density than its CHARMM
> > counterpart, independantly from the cutoff for non-bonded interactions,
> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
> > Regular 961,067 +/-0,756 g/L
> > CHARMM  980,860 +/-0,492 g/L
> >
> > The Enthalpy of vaporization follows a similar scheme:
> > regular -39,992 +/-0,021 kJ/mol
> > CHARMM  -40,665 +/-0,009 kJ/mol
> 
> How about the dispersion correction?
> If that is not turned on densities will be too low (in both cases).
> 
> >
> > In fact, CHARMM gives results closer to what I should obtain at 300K and 1
> > bar for TIP3P. I suspect an issue with the bond constraints, but I can't
> > locate precisely where it is. Settle parameters are exactly the same (as
> > well as constraints for flexible water). Did someone ever face a similar
> > problem?
> >
> > Rgards,
> > Nicolas
> >
> > P.S. I My system is just a box of 1728 water molecules pre-equilibrated
> > for 500 ps at 300 K and 1 bar.
> >
> > P.S. II I'm using the following simulation parameters:
> > constraints  = hbonds
> > constraint_algorithm = LINCS
> > continuation = no
> > lincs-order  = 4
> > lincs-iter   = 1
> > lincs-warnangle  = 30
> > morse= no
> > (LINCS or SHAKE should not make any difference since TIP3P is normally
> > treated by SETTLE).
> >
> > Other parameters are:
> > ; COUPLING
> > ; Temperature coupling
> > tcoupl   = Berendsen
> > nsttcouple   = -1
> > nh-chain-length  = 10
> > tc_grps  = System
> > tau_t= 0.1
> > ref_t= 300
> > ; Pressure coupling
> > pcoupl   = Berendsen
> > pcoupltype   = isotropic
> > nstpcouple   = -1
> > tau_p= 1
> > compressibility  = 4.5e-5
> > ref_p= 1
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > ; nblist update frequency
> > nstlist  = 10
> > ns_type  = grid
> > pbc  = xyz
> > rlist= 1.15
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype  = PME
> > rcoulomb-switch  = 0
> > rcoulomb = 1.15
> > vdwtype  = Cutoff
> > rvdw = 1.0
> > fourierspacing   = 0.10
> > pme_order= 6
> > ewald_rtol   = 1.0e-6
> > ewald_geometry   = 3d
> > epsilon_surface  = 0
> > optimize_fft = yes
> >
> > ; RUN CONTROL PARAMETERS
> > integrator   = md
> > dt   = 0.002
> > nsteps   = 20
> > comm_mode= Linear
> > nstcomm  = 1
> > comm_grps= System
> >
> >
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
  

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
htt

RE: [gmx-users] Regular vs. CHARMM TIP3P water model

Hi,

My last comment was not correct. Sorry, too many numbers in my head.
Both your density numbers are too low, more than can be explained by LJ cut-off 
settings.

How did you determine the density?
g_density does not give the correct number. The number in our paper for tip3p 
(not Charmm tip3p)
is incorrect, because Per used g_density, but g_density normalizes with the 
volume of the last frame
instead of the average volume over the simulation. I just fixed this for the 
next release.
I would always use g_energy to extract the density.

Berk

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
Date: Tue, 14 Sep 2010 11:58:31 +0200

Hi,

We did some checking.
The value of the density for tip3p reported in the Gromacs Charmm ff 
implementation of 1001.7 is incorrect.
This should have been 985.7. The number of 1014.7 for Charmm tip3p is correct.

I would expect that the difference with your number is mainly due to the 
shorter LJ cut-off you are using.

Berk

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
Date: Tue, 14 Sep 2010 11:33:16 +0200

Hi,

I don't understand what exactly you want to reproduce.
Standard tip3p and Charmm tip3p are different models, so the density does not 
have to be identical.
The Gromacs Charmm FF implementation paper:
http://pubs.acs.org/doi/full/10.1021/ct900549r
gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched from 1 
to 1.2 nm).
I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion 
correction.
These numbers are quite different. I'll do some checking.

Berk

> Date: Tue, 14 Sep 2010 11:00:55 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
> 
> On 2010-09-14 10.23, Nicolas SAPAY wrote:
> > Hello everybody,
> >
> > I have many difficulties to reproduce TIP3P simulation results with CHARMM
> > TIP3P. Regular TIP3P gives systematically a lower density than its CHARMM
> > counterpart, independantly from the cutoff for non-bonded interactions,
> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
> > Regular 961,067 +/-0,756 g/L
> > CHARMM  980,860 +/-0,492 g/L
> >
> > The Enthalpy of vaporization follows a similar scheme:
> > regular -39,992 +/-0,021 kJ/mol
> > CHARMM  -40,665 +/-0,009 kJ/mol
> 
> How about the dispersion correction?
> If that is not turned on densities will be too low (in both cases).
> 
> >
> > In fact, CHARMM gives results closer to what I should obtain at 300K and 1
> > bar for TIP3P. I suspect an issue with the bond constraints, but I can't
> > locate precisely where it is. Settle parameters are exactly the same (as
> > well as constraints for flexible water). Did someone ever face a similar
> > problem?
> >
> > Rgards,
> > Nicolas
> >
> > P.S. I My system is just a box of 1728 water molecules pre-equilibrated
> > for 500 ps at 300 K and 1 bar.
> >
> > P.S. II I'm using the following simulation parameters:
> > constraints  = hbonds
> > constraint_algorithm = LINCS
> > continuation = no
> > lincs-order  = 4
> > lincs-iter   = 1
> > lincs-warnangle  = 30
> > morse= no
> > (LINCS or SHAKE should not make any difference since TIP3P is normally
> > treated by SETTLE).
> >
> > Other parameters are:
> > ; COUPLING
> > ; Temperature coupling
> > tcoupl   = Berendsen
> > nsttcouple   = -1
> > nh-chain-length  = 10
> > tc_grps  = System
> > tau_t= 0.1
> > ref_t= 300
> > ; Pressure coupling
> > pcoupl   = Berendsen
> > pcoupltype   = isotropic
> > nstpcouple   = -1
> > tau_p= 1
> > compressibility  = 4.5e-5
> > ref_p= 1
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > ; nblist update frequency
> > nstlist  = 10
> > ns_type  = grid
> > pbc  = xyz
> > rlist= 1.15
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype  = PME
> > rcoulomb-switch  = 0
> > rcoulomb = 1.15
> > vdwtype  = Cutoff
> > rvdw = 1.0
> > fourierspacing   = 0.10
> > pme_order= 6
> > ewald_rtol   = 1.0e-6
> > ewald_geometry   = 3d
> > epsilon_surface  = 0
> > optimize_fft = yes
> >
> > ; RUN CONTROL PARAMETERS
> > integrator   = md
> > dt   = 0.002
> > nsteps   = 20
> > comm_mode= Linear
> > nstcomm  = 1
> > comm_grps= System
> >
> >
> 
> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala

Re: [gmx-users] Correction for the PBC!




tekle...@ualberta.ca wrote:

Dear Justine,

I just checked at the archive list and found out lots of information on 
how to correct for PBC! And if I understood it correctly is this the 
right way to follow...

“If you are trying to correct for periodicity for all species in the system
(protein and water) then a few iterations of trjconv may be necessary, i.e.
-center (on protein), followed by -pbc nojump or -pbc mol -ur compact.  
Using
trjconv is a bit hit-or-miss, and just requires a bit of playing to get 
things working how you want them.”


trjconv –f xxx.xtc –o x_cluster.gro –b 19000 –e 2 –pbc cluster

grompp –f xx.mdp –c x_cluster.gro –o x_cluster.tpr

trjconv –f xxx.xtc –o x_cluster.xtc –b 19000 –e 2 –s xx_cluster.tpr 
–pbc nojump


Then I have to do anaysis on the new .tpr and .xtc.. is that 
correct


Is this the right way to correct for periodicity... I took the idea from 
you and Chris. I have done the RDF and distance measurement but looks a 
bit off my RDF did not converge to 1. They recommend me to do PBC 
correction on my system which is run for 20ns. I am doing the analysis 
on the last 1ns (from 19-20 ns)




Without context, I have no idea if what you've done is right.  The clustering 
algorithm is only really useful for the formation of clustered molecules (i.e. 
micelles), so if you're trying to apply it to something else, I don't know that 
it will work.


-Justin


You suggestion is always helpful!

Rob







Quoting "Justin A. Lemkul" :




tekle...@ualberta.ca wrote:

Dear Gromacs,

I want to correct the periodic boundry condition before analyzing my 
data, how do I perform that?




Please see trjconv -h, as well as any of the thousands of posts in the 
list archive related to this topic.


-Justin


any suggest!

Rob


--


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


--
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Please search the archive at 
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--


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


--
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Please search the archive at 
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RE: [gmx-users] Regular vs. CHARMM TIP3P water model

>
> Hi,
>
> I don't understand what exactly you want to reproduce.
> Standard tip3p and Charmm tip3p are different models, so the density does
> not have to be identical.
> The Gromacs Charmm FF implementation paper:
> http://pubs.acs.org/doi/full/10.1021/ct900549r
> gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched
> from 1 to 1.2 nm).
> I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion
> correction.
> These numbers are quite different. I'll do some checking.
>
> Berk

Actually, TIP3P and CHARMM TIP3P are supposed to give (almost) identical
results as they are not exactly different models but different
implementations of a same model. That is why I'm surprised of the rather
large difference in the density values observed in my simulations or in
the JCTC paper.

In CHARMM, the additionnal Lennard-Jones parameters for the TIP3P hydrogen
are not here to better reproduce water properties but for practical
purpose - normally, the hydrogens are almost entirely included in the
oxygen VDW radius. As far as I understand, those parameters are here to
improve the stability of simulations by limiting artificial close contacts
between a large negative charge and the point charge on the hydrogen
atoms.

In fact, I was wondering if the Settle algorithm is appropriate to CHARMM
TIP3P. In the original CHARMM RTF file, there is a SHAKE constraint on the
H-H distance which is not present in the GROMACS tips3p.itp file. So, a
better use of the CHARMM TIP3P model in GROMACS would be to add this
constraint in tips3p.itp and use Shake instead of Settle, isn't it?

>
>> Date: Tue, 14 Sep 2010 11:00:55 +0200
>> From: sp...@xray.bmc.uu.se
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
>>
>> On 2010-09-14 10.23, Nicolas SAPAY wrote:
>> > Hello everybody,
>> >
>> > I have many difficulties to reproduce TIP3P simulation results with
>> CHARMM
>> > TIP3P. Regular TIP3P gives systematically a lower density than its
>> CHARMM
>> > counterpart, independantly from the cutoff for non-bonded
>> interactions,
>> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
>> > Regular 961,067 +/-0,756 g/L
>> > CHARMM  980,860 +/-0,492 g/L
>> >
>> > The Enthalpy of vaporization follows a similar scheme:
>> > regular -39,992 +/-0,021 kJ/mol
>> > CHARMM  -40,665+/-0,009 kJ/mol
>>
>> How about the dispersion correction?
>> If that is not turned on densities will be too low (in both cases).
>>
>> >
>> > In fact, CHARMM gives results closer to what I should obtain at 300K
>> and 1
>> > bar for TIP3P. I suspect an issue with the bond constraints, but I
>> can't
>> > locate precisely where it is. Settle parameters are exactly the same
>> (as
>> > well as constraints for flexible water). Did someone ever face a
>> similar
>> > problem?
>> >
>> > Rgards,
>> > Nicolas
>> >
>> > P.S. I My system is just a box of 1728 water molecules
>> pre-equilibrated
>> > for 500 ps at 300 K and 1 bar.
>> >
>> > P.S. II I'm using the following simulation parameters:
>> > constraints  = hbonds
>> > constraint_algorithm = LINCS
>> > continuation = no
>> > lincs-order  = 4
>> > lincs-iter   = 1
>> > lincs-warnangle  = 30
>> > morse= no
>> > (LINCS or SHAKE should not make any difference since TIP3P is normally
>> > treated by SETTLE).
>> >
>> > Other parameters are:
>> > ; COUPLING
>> > ; Temperature coupling
>> > tcoupl   = Berendsen
>> > nsttcouple   = -1
>> > nh-chain-length  = 10
>> > tc_grps  = System
>> > tau_t= 0.1
>> > ref_t= 300
>> > ; Pressure coupling
>> > pcoupl   = Berendsen
>> > pcoupltype   = isotropic
>> > nstpcouple   = -1
>> > tau_p= 1
>> > compressibility  = 4.5e-5
>> > ref_p= 1
>> >
>> > ; NEIGHBORSEARCHING PARAMETERS
>> > ; nblist update frequency
>> > nstlist  = 10
>> > ns_type  = grid
>> > pbc  = xyz
>> > rlist= 1.15
>> >
>> > ; OPTIONS FOR ELECTROSTATICS AND VDW
>> > ; Method for doing electrostatics
>> > coulombtype  = PME
>> > rcoulomb-switch  = 0
>> > rcoulomb = 1.15
>> > vdwtype  = Cutoff
>> > rvdw = 1.0
>> > fourierspacing   = 0.10
>> > pme_order= 6
>> > ewald_rtol   = 1.0e-6
>> > ewald_geometry   = 3d
>> > epsilon_surface  = 0
>> > optimize_fft = yes
>> >
>> > ; RUN CONTROL PARAMETERS
>> > integrator   = md
>> > dt   = 0.002
>> > nsteps   = 20
>> > comm_mode= Linear
>> > nstcomm  = 1
>> > comm_grps= System
>> >
>> >
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>>

RE: [gmx-users] Regular vs. CHARMM TIP3P water model


>
> Hi,
>
> My last comment was not correct. Sorry, too many numbers in my head.
> Both your density numbers are too low, more than can be explained by LJ
> cut-off settings.
>
> How did you determine the density?
> g_density does not give the correct number. The number in our paper for
> tip3p (not Charmm tip3p)
> is incorrect, because Per used g_density, but g_density normalizes with
> the volume of the last frame
> instead of the average volume over the simulation. I just fixed this for
> the next release.
> I would always use g_energy to extract the density.

That's a good thing to know, I'll recalculate the density with g_energy.

>
> Berk
>
> From: g...@hotmail.com
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> Date: Tue, 14 Sep 2010 11:58:31 +0200
>
>
>
>
>
>
>
>
> Hi,
>
> We did some checking.
> The value of the density for tip3p reported in the Gromacs Charmm ff
> implementation of 1001.7 is incorrect.
> This should have been 985.7. The number of 1014.7 for Charmm tip3p is
> correct.
>
> I would expect that the difference with your number is mainly due to the
> shorter LJ cut-off you are using.
>
> Berk
>
> From: g...@hotmail.com
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> Date: Tue, 14 Sep 2010 11:33:16 +0200
>
>
>
>
>
>
>
>
> Hi,
>
> I don't understand what exactly you want to reproduce.
> Standard tip3p and Charmm tip3p are different models, so the density does
> not have to be identical.
> The Gromacs Charmm FF implementation paper:
> http://pubs.acs.org/doi/full/10.1021/ct900549r
> gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched
> from 1 to 1.2 nm).
> I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion
> correction.
> These numbers are quite different. I'll do some checking.
>
> Berk
>
>> Date: Tue, 14 Sep 2010 11:00:55 +0200
>> From: sp...@xray.bmc.uu.se
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
>>
>> On 2010-09-14 10.23, Nicolas SAPAY wrote:
>> > Hello everybody,
>> >
>> > I have many difficulties to reproduce TIP3P simulation results with
>> CHARMM
>> > TIP3P. Regular TIP3P gives systematically a lower density than its
>> CHARMM
>> > counterpart, independantly from the cutoff for non-bonded
>> interactions,
>> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
>> > Regular 961,067 +/-0,756 g/L
>> > CHARMM  980,860 +/-0,492 g/L
>> >
>> > The Enthalpy of vaporization follows a similar scheme:
>> > regular -39,992 +/-0,021 kJ/mol
>> > CHARMM  -40,665+/-0,009 kJ/mol
>>
>> How about the dispersion correction?
>> If that is not turned on densities will be too low (in both cases).
>>
>> >
>> > In fact, CHARMM gives results closer to what I should obtain at 300K
>> and 1
>> > bar for TIP3P. I suspect an issue with the bond constraints, but I
>> can't
>> > locate precisely where it is. Settle parameters are exactly the same
>> (as
>> > well as constraints for flexible water). Did someone ever face a
>> similar
>> > problem?
>> >
>> > Rgards,
>> > Nicolas
>> >
>> > P.S. I My system is just a box of 1728 water molecules
>> pre-equilibrated
>> > for 500 ps at 300 K and 1 bar.
>> >
>> > P.S. II I'm using the following simulation parameters:
>> > constraints  = hbonds
>> > constraint_algorithm = LINCS
>> > continuation = no
>> > lincs-order  = 4
>> > lincs-iter   = 1
>> > lincs-warnangle  = 30
>> > morse= no
>> > (LINCS or SHAKE should not make any difference since TIP3P is normally
>> > treated by SETTLE).
>> >
>> > Other parameters are:
>> > ; COUPLING
>> > ; Temperature coupling
>> > tcoupl   = Berendsen
>> > nsttcouple   = -1
>> > nh-chain-length  = 10
>> > tc_grps  = System
>> > tau_t= 0.1
>> > ref_t= 300
>> > ; Pressure coupling
>> > pcoupl   = Berendsen
>> > pcoupltype   = isotropic
>> > nstpcouple   = -1
>> > tau_p= 1
>> > compressibility  = 4.5e-5
>> > ref_p= 1
>> >
>> > ; NEIGHBORSEARCHING PARAMETERS
>> > ; nblist update frequency
>> > nstlist  = 10
>> > ns_type  = grid
>> > pbc  = xyz
>> > rlist= 1.15
>> >
>> > ; OPTIONS FOR ELECTROSTATICS AND VDW
>> > ; Method for doing electrostatics
>> > coulombtype  = PME
>> > rcoulomb-switch  = 0
>> > rcoulomb = 1.15
>> > vdwtype  = Cutoff
>> > rvdw = 1.0
>> > fourierspacing   = 0.10
>> > pme_order= 6
>> > ewald_rtol   = 1.0e-6
>> > ewald_geometry   = 3d
>> > epsilon_surface  = 0
>> > optimize_fft = yes
>> >
>> > ; RUN CONTROL PARAMETERS
>> > integrator   = md
>> > dt

RE: [gmx-users] Regular vs. CHARMM TIP3P water model




> Date: Tue, 14 Sep 2010 13:11:47 +0200
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> From: nicolas.sa...@cermav.cnrs.fr
> To: gmx-users@gromacs.org
> 
> >
> > Hi,
> >
> > I don't understand what exactly you want to reproduce.
> > Standard tip3p and Charmm tip3p are different models, so the density does
> > not have to be identical.
> > The Gromacs Charmm FF implementation paper:
> > http://pubs.acs.org/doi/full/10.1021/ct900549r
> > gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched
> > from 1 to 1.2 nm).
> > I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion
> > correction.
> > These numbers are quite different. I'll do some checking.
> >
> > Berk
> 
> Actually, TIP3P and CHARMM TIP3P are supposed to give (almost) identical
> results as they are not exactly different models but different
> implementations of a same model. That is why I'm surprised of the rather
> large difference in the density values observed in my simulations or in
> the JCTC paper.
> 
> In CHARMM, the additionnal Lennard-Jones parameters for the TIP3P hydrogen
> are not here to better reproduce water properties but for practical
> purpose - normally, the hydrogens are almost entirely included in the
> oxygen VDW radius. As far as I understand, those parameters are here to
> improve the stability of simulations by limiting artificial close contacts
> between a large negative charge and the point charge on the hydrogen
> atoms.

Note that even if the H's are nearly included in the O's LJ, their dispersion 
interaction
still works over larger distances, which would indeed lower the density.

Berk

> 
> In fact, I was wondering if the Settle algorithm is appropriate to CHARMM
> TIP3P. In the original CHARMM RTF file, there is a SHAKE constraint on the
> H-H distance which is not present in the GROMACS tips3p.itp file. So, a
> better use of the CHARMM TIP3P model in GROMACS would be to add this
> constraint in tips3p.itp and use Shake instead of Settle, isn't it?
> 
> >
> >> Date: Tue, 14 Sep 2010 11:00:55 +0200
> >> From: sp...@xray.bmc.uu.se
> >> To: gmx-users@gromacs.org
> >> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
> >>
> >> On 2010-09-14 10.23, Nicolas SAPAY wrote:
> >> > Hello everybody,
> >> >
> >> > I have many difficulties to reproduce TIP3P simulation results with
> >> CHARMM
> >> > TIP3P. Regular TIP3P gives systematically a lower density than its
> >> CHARMM
> >> > counterpart, independantly from the cutoff for non-bonded
> >> interactions,
> >> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
> >> > Regular 961,067 +/-0,756 g/L
> >> > CHARMM  980,860 +/-0,492 g/L
> >> >
> >> > The Enthalpy of vaporization follows a similar scheme:
> >> > regular -39,992 +/-0,021 kJ/mol
> >> > CHARMM  -40,665  +/-0,009 kJ/mol
> >>
> >> How about the dispersion correction?
> >> If that is not turned on densities will be too low (in both cases).
> >>
> >> >
> >> > In fact, CHARMM gives results closer to what I should obtain at 300K
> >> and 1
> >> > bar for TIP3P. I suspect an issue with the bond constraints, but I
> >> can't
> >> > locate precisely where it is. Settle parameters are exactly the same
> >> (as
> >> > well as constraints for flexible water). Did someone ever face a
> >> similar
> >> > problem?
> >> >
> >> > Rgards,
> >> > Nicolas
> >> >
> >> > P.S. I My system is just a box of 1728 water molecules
> >> pre-equilibrated
> >> > for 500 ps at 300 K and 1 bar.
> >> >
> >> > P.S. II I'm using the following simulation parameters:
> >> > constraints  = hbonds
> >> > constraint_algorithm = LINCS
> >> > continuation = no
> >> > lincs-order  = 4
> >> > lincs-iter   = 1
> >> > lincs-warnangle  = 30
> >> > morse= no
> >> > (LINCS or SHAKE should not make any difference since TIP3P is normally
> >> > treated by SETTLE).
> >> >
> >> > Other parameters are:
> >> > ; COUPLING
> >> > ; Temperature coupling
> >> > tcoupl   = Berendsen
> >> > nsttcouple   = -1
> >> > nh-chain-length  = 10
> >> > tc_grps  = System
> >> > tau_t= 0.1
> >> > ref_t= 300
> >> > ; Pressure coupling
> >> > pcoupl   = Berendsen
> >> > pcoupltype   = isotropic
> >> > nstpcouple   = -1
> >> > tau_p= 1
> >> > compressibility  = 4.5e-5
> >> > ref_p= 1
> >> >
> >> > ; NEIGHBORSEARCHING PARAMETERS
> >> > ; nblist update frequency
> >> > nstlist  = 10
> >> > ns_type  = grid
> >> > pbc  = xyz
> >> > rlist= 1.15
> >> >
> >> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> >> > ; Method for doing electrostatics
> >> > coulombtype  = PME
> >> > rcoulomb-switch  = 0
> >> > rcoulomb = 1.15
> >> > vdwtype  = Cutoff

RE: [gmx-users] Regular vs. CHARMM TIP3P water model


Hi,

The choice of constraint algorithm is irrelevant for the results.

As I understood Charmm tip3p has less structure than standard tip3p
and it would not surprise me if the density is different.
But I have never closely looked at Charmm tip3p properties myself.

Berk

> Date: Tue, 14 Sep 2010 13:11:47 +0200
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> From: nicolas.sa...@cermav.cnrs.fr
> To: gmx-users@gromacs.org
> 
> >
> > Hi,
> >
> > I don't understand what exactly you want to reproduce.
> > Standard tip3p and Charmm tip3p are different models, so the density does
> > not have to be identical.
> > The Gromacs Charmm FF implementation paper:
> > http://pubs.acs.org/doi/full/10.1021/ct900549r
> > gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched
> > from 1 to 1.2 nm).
> > I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion
> > correction.
> > These numbers are quite different. I'll do some checking.
> >
> > Berk
> 
> Actually, TIP3P and CHARMM TIP3P are supposed to give (almost) identical
> results as they are not exactly different models but different
> implementations of a same model. That is why I'm surprised of the rather
> large difference in the density values observed in my simulations or in
> the JCTC paper.
> 
> In CHARMM, the additionnal Lennard-Jones parameters for the TIP3P hydrogen
> are not here to better reproduce water properties but for practical
> purpose - normally, the hydrogens are almost entirely included in the
> oxygen VDW radius. As far as I understand, those parameters are here to
> improve the stability of simulations by limiting artificial close contacts
> between a large negative charge and the point charge on the hydrogen
> atoms.
> 
> In fact, I was wondering if the Settle algorithm is appropriate to CHARMM
> TIP3P. In the original CHARMM RTF file, there is a SHAKE constraint on the
> H-H distance which is not present in the GROMACS tips3p.itp file. So, a
> better use of the CHARMM TIP3P model in GROMACS would be to add this
> constraint in tips3p.itp and use Shake instead of Settle, isn't it?
> 
> >
> >> Date: Tue, 14 Sep 2010 11:00:55 +0200
> >> From: sp...@xray.bmc.uu.se
> >> To: gmx-users@gromacs.org
> >> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
> >>
> >> On 2010-09-14 10.23, Nicolas SAPAY wrote:
> >> > Hello everybody,
> >> >
> >> > I have many difficulties to reproduce TIP3P simulation results with
> >> CHARMM
> >> > TIP3P. Regular TIP3P gives systematically a lower density than its
> >> CHARMM
> >> > counterpart, independantly from the cutoff for non-bonded
> >> interactions,
> >> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
> >> > Regular 961,067 +/-0,756 g/L
> >> > CHARMM  980,860 +/-0,492 g/L
> >> >
> >> > The Enthalpy of vaporization follows a similar scheme:
> >> > regular -39,992 +/-0,021 kJ/mol
> >> > CHARMM  -40,665  +/-0,009 kJ/mol
> >>
> >> How about the dispersion correction?
> >> If that is not turned on densities will be too low (in both cases).
> >>
> >> >
> >> > In fact, CHARMM gives results closer to what I should obtain at 300K
> >> and 1
> >> > bar for TIP3P. I suspect an issue with the bond constraints, but I
> >> can't
> >> > locate precisely where it is. Settle parameters are exactly the same
> >> (as
> >> > well as constraints for flexible water). Did someone ever face a
> >> similar
> >> > problem?
> >> >
> >> > Rgards,
> >> > Nicolas
> >> >
> >> > P.S. I My system is just a box of 1728 water molecules
> >> pre-equilibrated
> >> > for 500 ps at 300 K and 1 bar.
> >> >
> >> > P.S. II I'm using the following simulation parameters:
> >> > constraints  = hbonds
> >> > constraint_algorithm = LINCS
> >> > continuation = no
> >> > lincs-order  = 4
> >> > lincs-iter   = 1
> >> > lincs-warnangle  = 30
> >> > morse= no
> >> > (LINCS or SHAKE should not make any difference since TIP3P is normally
> >> > treated by SETTLE).
> >> >
> >> > Other parameters are:
> >> > ; COUPLING
> >> > ; Temperature coupling
> >> > tcoupl   = Berendsen
> >> > nsttcouple   = -1
> >> > nh-chain-length  = 10
> >> > tc_grps  = System
> >> > tau_t= 0.1
> >> > ref_t= 300
> >> > ; Pressure coupling
> >> > pcoupl   = Berendsen
> >> > pcoupltype   = isotropic
> >> > nstpcouple   = -1
> >> > tau_p= 1
> >> > compressibility  = 4.5e-5
> >> > ref_p= 1
> >> >
> >> > ; NEIGHBORSEARCHING PARAMETERS
> >> > ; nblist update frequency
> >> > nstlist  = 10
> >> > ns_type  = grid
> >> > pbc  = xyz
> >> > rlist= 1.15
> >> >
> >> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> >> > ; Method for doing electrostatics
> >> > coulombtype  = PME
> >> > rcoulomb-s

[gmx-users] SWM4-NDP water model in GROMACS

2010-09-14 Thread Mikhail Stukan


Dear gromacs users,

Does anyone have experience in implementation of polarizable SWM4-NDP water 
model by Lamoureux et al. (Chem.Phys.Lett. 418,245 (2006)) in gromacs?
I have performed several simulations with systems of different size (from 1024 
up to 8192 water molecules)  with dispersion correction term and the cut-off 
15A for both Ewald and LJ  (according to the original paper), but on the 
regular basis I have higher density than the one reported in the original 
paper. Namely, average molecular volume (calculated by g_energy) is 29.67 
(density 1008.25) instead of 29.91 (density 1000.18).  Results are  same for 
4.5.1 and 4.0.7 version of gromacs. Other parameters such as dielectric 
constant and surface tension looks fine, though they have much higher error 
bars.

Below are  the .itp and .mdp files  I am using.

Thank you very much in advance.

Mikhail

.itp
--
[ defaults ]
; LJ non-bonded  Lorenz-Berthelot  Generate 1-4 pairs   FudgeLJFudgeQQ
   1 2yes   1.01.0

[ atomtypes ]
;namemass  charge ptype   c6 c12
   WO15.999401.71636e+00A 0.00.0
   WH 1.008000.55733e+00A 0.00.0
   WV0.0   -1.11466e+00V 0.00.0
   WS 0.0   -1.71636e+00S 0.00.0

[ nonbond_params ]
; sigma epsilon
WO  WO  1  0.318395e+00  882.57296e-03

 [ moleculetype ]
; molname nrexcl
SW4   2

[ atoms ]
; id   at type   res nrresidu name   at name  cg nr  
charge
1  WO 1  SW4   OW1   1   1.71636e+00
2  WH 1  SW4   HW2   1  0.55733e+00
3  WH 1  SW4   HW3   1  0.55733e+00
4  WV 1  SW4   VW1  -1.11466e+00
5  WS 1  SW4   SW1  -1.71636e+00

[ polarization ]
; See notes above.   alpha (nm^3)
1  5  1  0.97825e-03

[ settles ]
; dHH = 0.15139 gives HOH agle equal to 104.52 degree
; ifunct  dOHdHH
 1 1  0.09572   0.15139


;[ constraints ]
;1   21   0.09572
;1   31   0.09572
;3   21   0.15139


[ virtual_sites3 ]
; The position of the virtual site is computed as follows:
;
; O
;
; V
;
;  H H
;
;
; Virtual site from funct  a b
4  1  2  3  2  0.50.024034

[ exclusions ]
; iatom excluded from interaction with i
1  2  3  4  5
2  1  3  4  5
3  1  2  4  5
4  1  2  3  5
5  1  2  3  4

.mdp
===
integrator  =  md
dt  =  0.001  ; time step
nsteps  =  100   ; number of steps
comm_mode   =  Linear;Angular; Remove center of mass 
translation and rotation
nstcomm =  1003   ; reset c.o.m. motion
nstxout =  1  ; write coords
nstvout =  1  ; write velocities
nstxtcout   =  2000  ; write coords to xtc-trajectory 
file
nstlog  =  2000   ; print to logfile
nstlist =  20 ; update pairlist
ns_type =  grid ;simple  ; pairlist method
;== Polarizable model parameters ===
emtol =  0.1  ;the convergency criterion for maximum 
force
niter   =  20;maximum number of iterations for the 
shell particle optimization
;=  Cutt off specification =
pbc   = xyz; periodic boundary conditions
optimize_fft=  yes; perform FFT optimization at start
coulombtype =  PME
rcoulomb=  1.5; cut-off for coulomb
rlist   =  1.5; cut-off for ns
vdw-type=  cut-off
rvdw=  1.5; cut-off for vdw
dispcorr=  enerpres
;===
Tcoupl  =  v-rescale ; berendsen;nose-hoover;  ;; 
temperature coupling
tc-grps =  SW4
ref_t =  298.15
tau_t =  0.1
Pcoupl  =  berendsen  ; pressure bath
Pcoupltype  =  isotropic  ; pressure geometry
tau_p   =  0.5; p-coupoling time
compressibility =  4.5e-5 ;
ref_p   =  1.01325
;===
gen_vel =  no ; generate initial velocities
ge

[gmx-users] g_helix problem

2010-09-14 Thread Laercio Pol Fachin

Dear Gromacs Users:

I have a problem when I try to run g_helix in Gromacs 4.0.5.

I have two systems, each one containing a peptide, both with the same number of 
aminoacids; however, in one of them, most of the AA residues are not usual (in 
fact, they are post-translationally modified; thus, to run the MD simulations, 
I modified ffG43a1.rtp - aminoacids.dat - ffG43a1.hdb, to include its 
parameters).

Both simulations worked fine! When I try to run g_helix in the first run (with 
common AAs), everything goes fine:
There are 15 residues
There are 13 complete backbone residues (from 2 to 14)

However, when I do it in the other simulation, it gives me such error:
There are 15 residues
There are 0 complete backbone residues (from 0 to 136679032)

---
Program g_helix, VERSION 4.0.5
Source code file: hxprops.c, line: 389

Fatal error:
rnr==0
---

How can I solve this puzzle?

Thanks in advance,
Laércio Pol-Fachin


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[gmx-users] xpm2ps failure - memory allocation



Hi All,

I'm having a problem with xpm2ps failing in both version 4.5 and the current git 
version (pulled just a few minutes ago).  The program exits with:


xpm2ps(24704) malloc: *** error for object 0x803201: pointer being reallocated 
was not allocated

*** set a breakpoint in malloc_error_break to debug

---
Program xpm2ps, VERSION 4.5.1-2010-09-14 13:11:27 +0200-b953b64
Source code file: smalloc.c, line: 214

Fatal error:
Not enough memory. Failed to realloc 10012 bytes for *line, *line=0x803201
(called from file matio.c, line 197)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Pump Up the Volume Along With the Tempo" (Jazzy Jeff)
: Cannot allocate memory

Version 4.0.7 produces the correct output from the same input files (.xpm and 
.m2p).  Any ideas?


-Justin

--


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


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[gmx-users] an example to test mdrun-gpu x mdrun

2010-09-14 Thread Alan

Hi there,

I am testing on a MBP 17" SL 10.6.4 64 bits and nvidia GeForce 9600M GT

So I got mdrun-gpu compiled and apparently running, but when I try to run
'mdrun' to compare I have a segment fault.

Any other comments to the md.mdp and em.mdp are very welcome too.

# To test mdrun-gpu

cat << EOF >| em.mdp
define   = -DFLEXIBLE
integrator   = cg ; steep
nsteps   = 200
constraints  = none
emtol= 1000.0
nstcgsteep   = 10 ; do a steep every 10 steps of cg
emstep   = 0.01 ; used with steep
nstcomm  = 1
coulombtype  = PME
ns_type  = grid
rlist= 1.0
rcoulomb = 1.0
rvdw = 1.4
Tcoupl   = no
Pcoupl   = no
gen_vel  = no
nstxout  = 0 ; write coords every # step
optimize_fft = yes
EOF

cat << EOF >| md.mdp
integrator   = md-vv
nsteps   = 1000
dt   = 0.002
constraints  = all-bonds
constraint-algorithm = shake
nstcomm  = 1
nstcalcenergy= 1
ns_type  = grid
rlist= 1.3
rcoulomb = 1.3
rvdw = 1.3
vdwtype  = cut-off
coulombtype  = PME
Tcoupl   = Andersen
nsttcouple   = 1
tau_t= 0.1
tc-grps  = system
ref_t= 300
Pcoupl   = mttk
Pcoupltype   = isotropic
nstpcouple   = 1
tau_p= 0.5
compressibility  = 4.5e-5
ref_p= 1.0
gen_vel  = yes
nstxout  = 2 ; write coords every # step
lincs-iter   = 2
DispCorr = EnerPres
optimize_fft = yes
EOF

wget -c "http://www.pdbe.org/download/1brv"; -O 1brv.pdb

pdb2gmx -ff amber99sb -f 1brv.pdb -o Prot.pdb -p Prot.top -water spce -ignh

editconf -bt triclinic -f Prot.pdb -o Prot.pdb -d 1.0

genbox -cp Prot.pdb -o Prot.pdb -p Prot.top -cs

grompp -f em.mdp -c Prot.pdb -p Prot.top -o Prot.tpr

echo 13 | genion -s Prot.tpr -o Prot.pdb -neutral -conc 0.15 -p Prot.top
-norandom

grompp -f em.mdp -c Prot.pdb -p Prot.top -o em.tpr

mdrun -v -deffnm em

grompp -f md.mdp -c em.gro -p Prot.top -o md.tpr

mdrun-gpu -v -deffnm md -device
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes"

[snip]
Reading file md.tpr, VERSION 4.5.1-dev-20100913-9342b (single precision)
Loaded with Money


Back Off! I just backed up md.trr to ./#md.trr.7#

Back Off! I just backed up md.edr to ./#md.edr.7#

WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.


WARNING: OpenMM supports only Monte Carlo barostat for pressure coupling.


WARNING: Non-supported GPU selected (#0, GeForce 9600M GT), forced
continuing.Note, that the simulation can be slow or it migth even crash.


Pre-simulation ~15s memtest in progress...done, no errors detected
starting mdrun 'PROTEIN G in water'
1000 steps,  2.0 ps.
step 900, remaining runtime: 4 s
Writing final coordinates.

step 1000, remaining runtime: 0 s
Post-simulation ~15s memtest in progress...done, no errors detected

OpenMM run - timing based on wallclock.

   NODE (s)   Real (s)  (%)
   Time: 44.556 44.556100.0
   (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:  0.000  0.027  3.882  6.182


But if I try:
mdrun -v -deffnm md -nt 1
[snip]
starting mdrun 'PROTEIN G in water'
1000 steps,  2.0 ps.
[1]75786 segmentation fault  mdrun -v -deffnm md -nt 1

Note: using -nt 1 because SHAKE is not supported with domain decomposition.

If using Tcoupl and Pcoupl = no and then I can compare mdrun x mdrun-gpu,
being my gpu ~2 times slower than only one core. Well, I definitely don't
intended to use mdrun-gpu but I am surprised that it performed that bad (OK,
I am using a low-end GPU, but sander_openmm seems to work fine and very fast
on my mbp).

BTW, in gmx 4.5 manual, there's reference to Andersen thermostat only at
section 6.9 GROMACS on GPUs. Is it supposed to be used only with mdrun-gpu?

Any ideas? Thanks,

Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Re: [gmx-users] xpm2ps failure - memory allocation


On 2010-09-14 15.12, Justin A. Lemkul wrote:


Hi All,

I'm having a problem with xpm2ps failing in both version 4.5 and the
current git version (pulled just a few minutes ago). The program exits
with:

xpm2ps(24704) malloc: *** error for object 0x803201: pointer being
reallocated was not allocated
*** set a breakpoint in malloc_error_break to debug

---
Program xpm2ps, VERSION 4.5.1-2010-09-14 13:11:27 +0200-b953b64
Source code file: smalloc.c, line: 214

Fatal error:
Not enough memory. Failed to realloc 10012 bytes for *line, *line=0x803201
(called from file matio.c, line 197)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"Pump Up the Volume Along With the Tempo" (Jazzy Jeff)
: Cannot allocate memory

Version 4.0.7 produces the correct output from the same input files
(.xpm and .m2p). Any ideas?

-Justin

Please submit a bugzilla, don't forget to specify the machine used, 
since this kind of message is very much dependent on the libc version.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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RE: [gmx-users] xpm2ps failure - memory allocation


Hi,

There were several issues which I fixed.
But my test file/system did not give problems with the buggy code.
Could you test it on your system (use release-4-5-patches)?

Thanks,


> Date: Tue, 14 Sep 2010 09:12:18 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: [gmx-users] xpm2ps failure - memory allocation
> 
> 
> Hi All,
> 
> I'm having a problem with xpm2ps failing in both version 4.5 and the current 
> git 
> version (pulled just a few minutes ago).  The program exits with:
> 
> xpm2ps(24704) malloc: *** error for object 0x803201: pointer being 
> reallocated 
> was not allocated
> *** set a breakpoint in malloc_error_break to debug
> 
> ---
> Program xpm2ps, VERSION 4.5.1-2010-09-14 13:11:27 +0200-b953b64
> Source code file: smalloc.c, line: 214
> 
> Fatal error:
> Not enough memory. Failed to realloc 10012 bytes for *line, *line=0x803201
> (called from file matio.c, line 197)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
> 
> "Pump Up the Volume Along With the Tempo" (Jazzy Jeff)
> : Cannot allocate memory
> 
> Version 4.0.7 produces the correct output from the same input files (.xpm and 
> .m2p).  Any ideas?
> 
> -Justin
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> -- 
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] xpm2ps failure - memory allocation




David van der Spoel wrote:

On 2010-09-14 15.12, Justin A. Lemkul wrote:


Hi All,

I'm having a problem with xpm2ps failing in both version 4.5 and the
current git version (pulled just a few minutes ago). The program exits
with:

xpm2ps(24704) malloc: *** error for object 0x803201: pointer being
reallocated was not allocated
*** set a breakpoint in malloc_error_break to debug

---
Program xpm2ps, VERSION 4.5.1-2010-09-14 13:11:27 +0200-b953b64
Source code file: smalloc.c, line: 214

Fatal error:
Not enough memory. Failed to realloc 10012 bytes for *line, 
*line=0x803201

(called from file matio.c, line 197)
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---

"Pump Up the Volume Along With the Tempo" (Jazzy Jeff)
: Cannot allocate memory

Version 4.0.7 produces the correct output from the same input files
(.xpm and .m2p). Any ideas?

-Justin

Please submit a bugzilla, don't forget to specify the machine used, 
since this kind of message is very much dependent on the libc version.




Berk's fixes seem to have solved the problem.  If it would still be useful to 
sort out any underlying issues, I can certainly file a bugzilla, just let me know.


-Justin

--


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


--
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RE: [gmx-users] Regular vs. CHARMM TIP3P water model


>
> Hi,
>
> We did some checking.
> The value of the density for tip3p reported in the Gromacs Charmm ff
> implementation of 1001.7 is incorrect.
> This should have been 985.7. The number of 1014.7 for Charmm tip3p is
> correct.

I have just done a quick test using dispersion correction
(DispCorr=EnerPres) and the density value extracted from the edr file by
g_energy. I obtain fairly similar results: 984.8 +/-4.5 for TIP3P and
1015.0 +/- 3.6 for Charmm TIP3P.

>
> I would expect that the difference with your number is mainly due to the
> shorter LJ cut-off you are using.
>
> Berk
>
> From: g...@hotmail.com
> To: gmx-users@gromacs.org
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> Date: Tue, 14 Sep 2010 11:33:16 +0200
>
>
>
>
>
>
>
>
> Hi,
>
> I don't understand what exactly you want to reproduce.
> Standard tip3p and Charmm tip3p are different models, so the density does
> not have to be identical.
> The Gromacs Charmm FF implementation paper:
> http://pubs.acs.org/doi/full/10.1021/ct900549r
> gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched
> from 1 to 1.2 nm).
> I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion
> correction.
> These numbers are quite different. I'll do some checking.
>
> Berk
>
>> Date: Tue, 14 Sep 2010 11:00:55 +0200
>> From: sp...@xray.bmc.uu.se
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
>>
>> On 2010-09-14 10.23, Nicolas SAPAY wrote:
>> > Hello everybody,
>> >
>> > I have many difficulties to reproduce TIP3P simulation results with
>> CHARMM
>> > TIP3P. Regular TIP3P gives systematically a lower density than its
>> CHARMM
>> > counterpart, independantly from the cutoff for non-bonded
>> interactions,
>> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
>> > Regular 961,067 +/-0,756 g/L
>> > CHARMM  980,860 +/-0,492 g/L
>> >
>> > The Enthalpy of vaporization follows a similar scheme:
>> > regular -39,992 +/-0,021 kJ/mol
>> > CHARMM  -40,665+/-0,009 kJ/mol
>>
>> How about the dispersion correction?
>> If that is not turned on densities will be too low (in both cases).
>>
>> >
>> > In fact, CHARMM gives results closer to what I should obtain at 300K
>> and 1
>> > bar for TIP3P. I suspect an issue with the bond constraints, but I
>> can't
>> > locate precisely where it is. Settle parameters are exactly the same
>> (as
>> > well as constraints for flexible water). Did someone ever face a
>> similar
>> > problem?
>> >
>> > Rgards,
>> > Nicolas
>> >
>> > P.S. I My system is just a box of 1728 water molecules
>> pre-equilibrated
>> > for 500 ps at 300 K and 1 bar.
>> >
>> > P.S. II I'm using the following simulation parameters:
>> > constraints  = hbonds
>> > constraint_algorithm = LINCS
>> > continuation = no
>> > lincs-order  = 4
>> > lincs-iter   = 1
>> > lincs-warnangle  = 30
>> > morse= no
>> > (LINCS or SHAKE should not make any difference since TIP3P is normally
>> > treated by SETTLE).
>> >
>> > Other parameters are:
>> > ; COUPLING
>> > ; Temperature coupling
>> > tcoupl   = Berendsen
>> > nsttcouple   = -1
>> > nh-chain-length  = 10
>> > tc_grps  = System
>> > tau_t= 0.1
>> > ref_t= 300
>> > ; Pressure coupling
>> > pcoupl   = Berendsen
>> > pcoupltype   = isotropic
>> > nstpcouple   = -1
>> > tau_p= 1
>> > compressibility  = 4.5e-5
>> > ref_p= 1
>> >
>> > ; NEIGHBORSEARCHING PARAMETERS
>> > ; nblist update frequency
>> > nstlist  = 10
>> > ns_type  = grid
>> > pbc  = xyz
>> > rlist= 1.15
>> >
>> > ; OPTIONS FOR ELECTROSTATICS AND VDW
>> > ; Method for doing electrostatics
>> > coulombtype  = PME
>> > rcoulomb-switch  = 0
>> > rcoulomb = 1.15
>> > vdwtype  = Cutoff
>> > rvdw = 1.0
>> > fourierspacing   = 0.10
>> > pme_order= 6
>> > ewald_rtol   = 1.0e-6
>> > ewald_geometry   = 3d
>> > epsilon_surface  = 0
>> > optimize_fft = yes
>> >
>> > ; RUN CONTROL PARAMETERS
>> > integrator   = md
>> > dt   = 0.002
>> > nsteps   = 20
>> > comm_mode= Linear
>> > nstcomm  = 1
>> > comm_grps= System
>> >
>> >
>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:   +46184714205.
>> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org

Re: [gmx-users] Correction for the PBC!

2010-09-14 Thread teklebrh



Dear Justine, 

No, I have 20 surfactants in my system in a pure solvent and try to see the 
aggregation and adsorption properties of these molecules. I have run them for 
20ns. And now start to analyze my data. 

Just in short I want to correct for periodicity! so that to get the accurate 
result for my g_dist and g_rdf. 

trjconv on the xxx.xtc Like 

trjconv -f x_input.xtc -o x_out.xtc -b 19000 -e 2 -s x_input.tpr -pbc 
nojump 

or I have to cluster it first. 

Rob 

Quoting "Justin A. Lemkul" : 

> 
> 
> tekle...@ualberta.ca wrote: 
>> Dear Justine, 
>> 
>> I just checked at the archive list and found out lots of information 
>> on how to correct for PBC! And if I understood it correctly is this 
>> the right way to follow... 
>> "If you are trying to correct for periodicity for all species in the system 
>> (protein and water) then a few iterations of trjconv may be necessary, i.e. 
>> -center (on protein), followed by -pbc nojump or -pbc mol -ur 
>> compact. Using 
>> trjconv is a bit hit-or-miss, and just requires a bit of playing to 
>> get things working how you want them." 
>> 
>> trjconv -f xxx.xtc -o x_cluster.gro -b 19000 -e 2 -pbc cluster 
>> 
>> grompp -f xx.mdp -c x_cluster.gro -o x_cluster.tpr 
>> 
>> trjconv -f xxx.xtc -o x_cluster.xtc -b 19000 -e 2 -s 
>> xx_cluster.tpr -pbc nojump 
>> 
>> Then I have to do anaysis on the new .tpr and .xtc.. is that correct 
>> 
>> Is this the right way to correct for periodicity... I took the idea 
>> from you and Chris. I have done the RDF and distance measurement but 
>> looks a bit off my RDF did not converge to 1. They recommend me to 
>> do PBC correction on my system which is run for 20ns. I am doing the 
>> analysis on the last 1ns (from 19-20 ns) 
>> 
> 
> Without context, I have no idea if what you've done is right. The 
> clustering algorithm is only really useful for the formation of 
> clustered molecules (i.e. micelles), so if you're trying to apply it 
> to something else, I don't know that it will work. 
> 
> -Justin 
> 
>> You suggestion is always helpful! 
>> 
>> Rob 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> Quoting "Justin A. Lemkul" : 
>> 
>>> 
>>> 
>>> tekle...@ualberta.ca wrote: 
 Dear Gromacs, 
 
 I want to correct the periodic boundry condition before analyzing 
 my data, how do I perform that? 
 
>>> 
>>> Please see trjconv -h, as well as any of the thousands of posts in 
>>> the list archive related to this topic. 
>>> 
>>> -Justin 
>>> 
 any suggest! 
 
 Rob 
>>> 
>>> -- 
>>>  
>>> 
>>> Justin A. Lemkul 
>>> Ph.D. Candidate 
>>> ICTAS Doctoral Scholar 
>>> MILES-IGERT Trainee 
>>> Department of Biochemistry 
>>> Virginia Tech 
>>> Blacksburg, VA 
>>> jalemkul[at]vt.edu | (540) 231-9080 
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin[1] 
>>> 
>>>  
>>> -- 
>>> gmx-users mailing list gmx-users@gromacs.org 
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users[2] 
>>> Please search the archive at 
>>> http://www.gromacs.org/Support/Mailing_Lists/Search[3] before posting! 
>>> Please don't post (un)subscribe requests to the list. Use the www 
>>> interface or send it to gmx-users-requ...@gromacs.org. 
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists[4] 
>>> 
>>> 
>> 
> 
> -- 
>  
> 
> Justin A. Lemkul 
> Ph.D. Candidate 
> ICTAS Doctoral Scholar 
> MILES-IGERT Trainee 
> Department of Biochemistry 
> Virginia Tech 
> Blacksburg, VA 
> jalemkul[at]vt.edu | (540) 231-9080 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin[5] 
> 
>  
> -- 
> gmx-users mailing list gmx-users@gromacs.org 
> http://lists.gromacs.org/mailman/listinfo/gmx-users[6] 
> Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/Search[7] before posting! 
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-requ...@gromacs.org. 
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists[8] 
> 
> 



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[5] http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
[6] http://lists.gromacs.org/mailman/listinfo/gmx-users
[7] http://www.gromacs.org/Support/Mailing_Lists/Search
[8] http://www.gromacs.org/Support/Mailing_Lists-- 
gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Correction for the PBC!




tekle...@ualberta.ca wrote:



Dear Justine,

No, I have 20 surfactants in my system in a pure solvent and try to see 
the aggregation and adsorption properties of these molecules. I have run 
them for 20ns. And now start to analyze my data.


Just in short I want to correct for periodicity! so that to get the 
accurate result for my g_dist and g_rdf.


trjconv on the xxx.xtc Like

trjconv -f x_input.xtc -o x_out.xtc -b 19000 -e 2 -s x_input.tpr 
-pbc nojump


or I have to cluster it first.



I'm sorry to say I have no definitive answer, but you should be able to 
determine this for yourself by watching the trajectory.  If a cluster forms, 
then clustering may be useful.  If you try to use -pbc cluster, but not all of 
your molecules are actually aggregating, then trjconv may loop infinitely.


Start with -pbc nojump, and perhaps iterations of -pbc mol and others, until you 
obtain a trajectory you can visualize and easily assess.  For the purposes of 
g_dist and g_rdf, PBC should be handled intrinsically.  There are other tools 
(like g_rms) for which PBC will make a difference, but not likely these two.


-Justin


Rob

Quoting "Justin A. Lemkul" :

 >
 >
 > tekle...@ualberta.ca wrote:
 >> Dear Justine,
 >>
 >> I just checked at the archive list and found out lots of information
 >> on how to correct for PBC! And if I understood it correctly is this
 >> the right way to follow...
 >> "If you are trying to correct for periodicity for all species in the 
system
 >> (protein and water) then a few iterations of trjconv may be 
necessary, i.e.

 >> -center (on protein), followed by -pbc nojump or -pbc mol -ur
 >> compact. Using
 >> trjconv is a bit hit-or-miss, and just requires a bit of playing to
 >> get things working how you want them."
 >>
 >> trjconv -f xxx.xtc -o x_cluster.gro -b 19000 -e 2 -pbc cluster
 >>
 >> grompp -f xx.mdp -c x_cluster.gro -o x_cluster.tpr
 >>
 >> trjconv -f xxx.xtc -o x_cluster.xtc -b 19000 -e 2 -s
 >> xx_cluster.tpr -pbc nojump
 >>
 >> Then I have to do anaysis on the new .tpr and .xtc.. is that 
correct

 >>
 >> Is this the right way to correct for periodicity... I took the idea
 >> from you and Chris. I have done the RDF and distance measurement but
 >> looks a bit off my RDF did not converge to 1. They recommend me to
 >> do PBC correction on my system which is run for 20ns. I am doing the
 >> analysis on the last 1ns (from 19-20 ns)
 >>
 >
 > Without context, I have no idea if what you've done is right. The
 > clustering algorithm is only really useful for the formation of
 > clustered molecules (i.e. micelles), so if you're trying to apply it
 > to something else, I don't know that it will work.
 >
 > -Justin
 >
 >> You suggestion is always helpful!
 >>
 >> Rob
 >>
 >>
 >>
 >>
 >>
 >>
 >>
 >> Quoting "Justin A. Lemkul" :
 >>
 >>>
 >>>
 >>> tekle...@ualberta.ca wrote:
  Dear Gromacs,
 
  I want to correct the periodic boundry condition before analyzing
  my data, how do I perform that?
 
 >>>
 >>> Please see trjconv -h, as well as any of the thousands of posts in
 >>> the list archive related to this topic.
 >>>
 >>> -Justin
 >>>
  any suggest!
 
  Rob
 >>>
 >>> --
 >>> 
 >>>
 >>> Justin A. Lemkul
 >>> Ph.D. Candidate
 >>> ICTAS Doctoral Scholar
 >>> MILES-IGERT Trainee
 >>> Department of Biochemistry
 >>> Virginia Tech
 >>> Blacksburg, VA
 >>> jalemkul[at]vt.edu | (540) 231-9080
 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >>>
 >>> 
 >>> --
 >>> gmx-users mailing list gmx-users@gromacs.org
 >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
 >>> Please search the archive at
 >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 >>> Please don't post (un)subscribe requests to the list. Use the www
 >>> interface or send it to gmx-users-requ...@gromacs.org.
 >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >>>
 >>>
 >>
 >
 > --
 > 
 >
 > Justin A. Lemkul
 > Ph.D. Candidate
 > ICTAS Doctoral Scholar
 > MILES-IGERT Trainee
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 > 
 > --
 > gmx-users mailing list gmx-users@gromacs.org
 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at
 > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 > Please don't post (un)subscribe requests to the list. Use the www
 > interface or send it to gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >
 >



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-908

RE: [gmx-users] Regular vs. CHARMM TIP3P water model


Good.

I just calculated tip3p energies for a Charmm tip3p trajectory.
Standard tip3p gives 1.1 kJ/mol per water molecule higher energies.
Thus the LJ on H's gives significant extra attraction which increases the 
density.

Berk

> Date: Tue, 14 Sep 2010 15:49:03 +0200
> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> From: nicolas.sa...@cermav.cnrs.fr
> To: gmx-users@gromacs.org
> 
> 
> >
> > Hi,
> >
> > We did some checking.
> > The value of the density for tip3p reported in the Gromacs Charmm ff
> > implementation of 1001.7 is incorrect.
> > This should have been 985.7. The number of 1014.7 for Charmm tip3p is
> > correct.
> 
> I have just done a quick test using dispersion correction
> (DispCorr=EnerPres) and the density value extracted from the edr file by
> g_energy. I obtain fairly similar results: 984.8 +/-4.5 for TIP3P and
> 1015.0 +/- 3.6 for Charmm TIP3P.
> 
> >
> > I would expect that the difference with your number is mainly due to the
> > shorter LJ cut-off you are using.
> >
> > Berk
> >
> > From: g...@hotmail.com
> > To: gmx-users@gromacs.org
> > Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
> > Date: Tue, 14 Sep 2010 11:33:16 +0200
> >
> >
> >
> >
> >
> >
> >
> >
> > Hi,
> >
> > I don't understand what exactly you want to reproduce.
> > Standard tip3p and Charmm tip3p are different models, so the density does
> > not have to be identical.
> > The Gromacs Charmm FF implementation paper:
> > http://pubs.acs.org/doi/full/10.1021/ct900549r
> > gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ switched
> > from 1 to 1.2 nm).
> > I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus dispersion
> > correction.
> > These numbers are quite different. I'll do some checking.
> >
> > Berk
> >
> >> Date: Tue, 14 Sep 2010 11:00:55 +0200
> >> From: sp...@xray.bmc.uu.se
> >> To: gmx-users@gromacs.org
> >> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
> >>
> >> On 2010-09-14 10.23, Nicolas SAPAY wrote:
> >> > Hello everybody,
> >> >
> >> > I have many difficulties to reproduce TIP3P simulation results with
> >> CHARMM
> >> > TIP3P. Regular TIP3P gives systematically a lower density than its
> >> CHARMM
> >> > counterpart, independantly from the cutoff for non-bonded
> >> interactions,
> >> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
> >> > Regular 961,067 +/-0,756 g/L
> >> > CHARMM  980,860 +/-0,492 g/L
> >> >
> >> > The Enthalpy of vaporization follows a similar scheme:
> >> > regular -39,992 +/-0,021 kJ/mol
> >> > CHARMM  -40,665  +/-0,009 kJ/mol
> >>
> >> How about the dispersion correction?
> >> If that is not turned on densities will be too low (in both cases).
> >>
> >> >
> >> > In fact, CHARMM gives results closer to what I should obtain at 300K
> >> and 1
> >> > bar for TIP3P. I suspect an issue with the bond constraints, but I
> >> can't
> >> > locate precisely where it is. Settle parameters are exactly the same
> >> (as
> >> > well as constraints for flexible water). Did someone ever face a
> >> similar
> >> > problem?
> >> >
> >> > Rgards,
> >> > Nicolas
> >> >
> >> > P.S. I My system is just a box of 1728 water molecules
> >> pre-equilibrated
> >> > for 500 ps at 300 K and 1 bar.
> >> >
> >> > P.S. II I'm using the following simulation parameters:
> >> > constraints  = hbonds
> >> > constraint_algorithm = LINCS
> >> > continuation = no
> >> > lincs-order  = 4
> >> > lincs-iter   = 1
> >> > lincs-warnangle  = 30
> >> > morse= no
> >> > (LINCS or SHAKE should not make any difference since TIP3P is normally
> >> > treated by SETTLE).
> >> >
> >> > Other parameters are:
> >> > ; COUPLING
> >> > ; Temperature coupling
> >> > tcoupl   = Berendsen
> >> > nsttcouple   = -1
> >> > nh-chain-length  = 10
> >> > tc_grps  = System
> >> > tau_t= 0.1
> >> > ref_t= 300
> >> > ; Pressure coupling
> >> > pcoupl   = Berendsen
> >> > pcoupltype   = isotropic
> >> > nstpcouple   = -1
> >> > tau_p= 1
> >> > compressibility  = 4.5e-5
> >> > ref_p= 1
> >> >
> >> > ; NEIGHBORSEARCHING PARAMETERS
> >> > ; nblist update frequency
> >> > nstlist  = 10
> >> > ns_type  = grid
> >> > pbc  = xyz
> >> > rlist= 1.15
> >> >
> >> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> >> > ; Method for doing electrostatics
> >> > coulombtype  = PME
> >> > rcoulomb-switch  = 0
> >> > rcoulomb = 1.15
> >> > vdwtype  = Cutoff
> >> > rvdw = 1.0
> >> > fourierspacing   = 0.10
> >> > pme_order= 6
> >> > ewald_rtol   = 1.0e-6
> >> > ewald_geometry   = 3d
> >> > epsilon_surface  = 0
> >> > optimize_fft

RE: [gmx-users] Regular vs. CHARMM TIP3P water model


>
> Good.
>
> I just calculated tip3p energies for a Charmm tip3p trajectory.
> Standard tip3p gives 1.1 kJ/mol per water molecule higher energies.
> Thus the LJ on H's gives significant extra attraction which increases the
> density.

Great, I obtain a similar result: -40.0 kJ/mol for regular tip3p vs -41.2
kJ/mol for Charmm tip3p (so a difference of 1.2 kJ/mol in favor of Charmm
tip3p).

By the way, I have noted that the SHAKE force constants are different
between Gromacs and Charmm. In the Gromacs implementation, the constant is
376560 kJ/mol/A^2 for the O-H bond and 460,24 kJ/mol/rad^2 for the H-O-H
angle. In the Charmm parameter file, the force constant is 188280
kJ/mol/A^2 for the bond (2 times lower) and 23012 kJ/mol/rad^2 for the
angle (50 times higher). Is there a justification for that?



>
> Berk
>
>> Date: Tue, 14 Sep 2010 15:49:03 +0200
>> Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
>> From: nicolas.sa...@cermav.cnrs.fr
>> To: gmx-users@gromacs.org
>>
>>
>> >
>> > Hi,
>> >
>> > We did some checking.
>> > The value of the density for tip3p reported in the Gromacs Charmm ff
>> > implementation of 1001.7 is incorrect.
>> > This should have been 985.7. The number of 1014.7 for Charmm tip3p is
>> > correct.
>>
>> I have just done a quick test using dispersion correction
>> (DispCorr=EnerPres) and the density value extracted from the edr file by
>> g_energy. I obtain fairly similar results: 984.8 +/-4.5 for TIP3P and
>> 1015.0 +/- 3.6 for Charmm TIP3P.
>>
>> >
>> > I would expect that the difference with your number is mainly due to
>> the
>> > shorter LJ cut-off you are using.
>> >
>> > Berk
>> >
>> > From: g...@hotmail.com
>> > To: gmx-users@gromacs.org
>> > Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
>> > Date: Tue, 14 Sep 2010 11:33:16 +0200
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > Hi,
>> >
>> > I don't understand what exactly you want to reproduce.
>> > Standard tip3p and Charmm tip3p are different models, so the density
>> does
>> > not have to be identical.
>> > The Gromacs Charmm FF implementation paper:
>> > http://pubs.acs.org/doi/full/10.1021/ct900549r
>> > gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ
>> switched
>> > from 1 to 1.2 nm).
>> > I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus
>> dispersion
>> > correction.
>> > These numbers are quite different. I'll do some checking.
>> >
>> > Berk
>> >
>> >> Date: Tue, 14 Sep 2010 11:00:55 +0200
>> >> From: sp...@xray.bmc.uu.se
>> >> To: gmx-users@gromacs.org
>> >> Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model
>> >>
>> >> On 2010-09-14 10.23, Nicolas SAPAY wrote:
>> >> > Hello everybody,
>> >> >
>> >> > I have many difficulties to reproduce TIP3P simulation results with
>> >> CHARMM
>> >> > TIP3P. Regular TIP3P gives systematically a lower density than its
>> >> CHARMM
>> >> > counterpart, independantly from the cutoff for non-bonded
>> >> interactions,
>> >> > the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
>> >> > Regular 961,067 +/-0,756 g/L
>> >> > CHARMM  980,860 +/-0,492 g/L
>> >> >
>> >> > The Enthalpy of vaporization follows a similar scheme:
>> >> > regular -39,992 +/-0,021 kJ/mol
>> >> > CHARMM  -40,665 +/-0,009 kJ/mol
>> >>
>> >> How about the dispersion correction?
>> >> If that is not turned on densities will be too low (in both cases).
>> >>
>> >> >
>> >> > In fact, CHARMM gives results closer to what I should obtain at
>> 300K
>> >> and 1
>> >> > bar for TIP3P. I suspect an issue with the bond constraints, but I
>> >> can't
>> >> > locate precisely where it is. Settle parameters are exactly the
>> same
>> >> (as
>> >> > well as constraints for flexible water). Did someone ever face a
>> >> similar
>> >> > problem?
>> >> >
>> >> > Rgards,
>> >> > Nicolas
>> >> >
>> >> > P.S. I My system is just a box of 1728 water molecules
>> >> pre-equilibrated
>> >> > for 500 ps at 300 K and 1 bar.
>> >> >
>> >> > P.S. II I'm using the following simulation parameters:
>> >> > constraints  = hbonds
>> >> > constraint_algorithm = LINCS
>> >> > continuation = no
>> >> > lincs-order  = 4
>> >> > lincs-iter   = 1
>> >> > lincs-warnangle  = 30
>> >> > morse= no
>> >> > (LINCS or SHAKE should not make any difference since TIP3P is
>> normally
>> >> > treated by SETTLE).
>> >> >
>> >> > Other parameters are:
>> >> > ; COUPLING
>> >> > ; Temperature coupling
>> >> > tcoupl   = Berendsen
>> >> > nsttcouple   = -1
>> >> > nh-chain-length  = 10
>> >> > tc_grps  = System
>> >> > tau_t= 0.1
>> >> > ref_t= 300
>> >> > ; Pressure coupling
>> >> > pcoupl   = Berendsen
>> >> > pcoupltype   = isotropic
>> >> > nstpcouple   = -1
>> >> > tau_p= 1
>> >> > compressibility  = 4.5e-5
>> >> > ref_p= 1
>

Re: [gmx-users] Regular vs. CHARMM TIP3P water model


On 2010-09-14 17.06, Nicolas SAPAY wrote:




Good.

I just calculated tip3p energies for a Charmm tip3p trajectory.
Standard tip3p gives 1.1 kJ/mol per water molecule higher energies.
Thus the LJ on H's gives significant extra attraction which increases the
density.


Great, I obtain a similar result: -40.0 kJ/mol for regular tip3p vs -41.2
kJ/mol for Charmm tip3p (so a difference of 1.2 kJ/mol in favor of Charmm
tip3p).

By the way, I have noted that the SHAKE force constants are different
between Gromacs and Charmm. In the Gromacs implementation, the constant is
376560 kJ/mol/A^2 for the O-H bond and 460,24 kJ/mol/rad^2 for the H-O-H
angle. In the Charmm parameter file, the force constant is 188280
kJ/mol/A^2 for the bond (2 times lower) and 23012 kJ/mol/rad^2 for the
angle (50 times higher). Is there a justification for that?

Charmm (and amber) probably use a different definition of the harmonic 
potential. Note that this is not used with constraints, only when you 
have flexible models.


Gromacs uses degrees instead of radians in the user input.






Berk


Date: Tue, 14 Sep 2010 15:49:03 +0200
Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
From: nicolas.sa...@cermav.cnrs.fr
To: gmx-users@gromacs.org




Hi,

We did some checking.
The value of the density for tip3p reported in the Gromacs Charmm ff
implementation of 1001.7 is incorrect.
This should have been 985.7. The number of 1014.7 for Charmm tip3p is
correct.


I have just done a quick test using dispersion correction
(DispCorr=EnerPres) and the density value extracted from the edr file by
g_energy. I obtain fairly similar results: 984.8 +/-4.5 for TIP3P and
1015.0 +/- 3.6 for Charmm TIP3P.



I would expect that the difference with your number is mainly due to

the

shorter LJ cut-off you are using.

Berk

From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Regular vs. CHARMM TIP3P water model
Date: Tue, 14 Sep 2010 11:33:16 +0200








Hi,

I don't understand what exactly you want to reproduce.
Standard tip3p and Charmm tip3p are different models, so the density

does

not have to be identical.
The Gromacs Charmm FF implementation paper:
http://pubs.acs.org/doi/full/10.1021/ct900549r
gives 1002 for tip3p and 1015 for charmm tip3p (this is with LJ

switched

from 1 to 1.2 nm).
I have in an old paper 986 for tip3p, with 0.85 nm cut-off plus

dispersion

correction.
These numbers are quite different. I'll do some checking.

Berk


Date: Tue, 14 Sep 2010 11:00:55 +0200
From: sp...@xray.bmc.uu.se
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Regular vs. CHARMM TIP3P water model

On 2010-09-14 10.23, Nicolas SAPAY wrote:

Hello everybody,

I have many difficulties to reproduce TIP3P simulation results with

CHARMM

TIP3P. Regular TIP3P gives systematically a lower density than its

CHARMM

counterpart, independantly from the cutoff for non-bonded

interactions,

the version of GROMACS (4.5.1 or 4.0.7) or the double precision.
Regular 961,067 +/-0,756 g/L
CHARMM  980,860 +/-0,492 g/L

The Enthalpy of vaporization follows a similar scheme:
regular -39,992 +/-0,021 kJ/mol
CHARMM  -40,665 +/-0,009 kJ/mol


How about the dispersion correction?
If that is not turned on densities will be too low (in both cases).



In fact, CHARMM gives results closer to what I should obtain at

300K

and 1

bar for TIP3P. I suspect an issue with the bond constraints, but I

can't

locate precisely where it is. Settle parameters are exactly the

same

(as

well as constraints for flexible water). Did someone ever face a

similar

problem?

Rgards,
Nicolas

P.S. I My system is just a box of 1728 water molecules

pre-equilibrated

for 500 ps at 300 K and 1 bar.

P.S. II I'm using the following simulation parameters:
constraints  = hbonds
constraint_algorithm = LINCS
continuation = no
lincs-order  = 4
lincs-iter   = 1
lincs-warnangle  = 30
morse= no
(LINCS or SHAKE should not make any difference since TIP3P is

normally

treated by SETTLE).

Other parameters are:
; COUPLING
; Temperature coupling
tcoupl   = Berendsen
nsttcouple   = -1
nh-chain-length  = 10
tc_grps  = System
tau_t= 0.1
ref_t= 300
; Pressure coupling
pcoupl   = Berendsen
pcoupltype   = isotropic
nstpcouple   = -1
tau_p= 1
compressibility  = 4.5e-5
ref_p= 1

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
ns_type  = grid
pbc  = xyz
rlist= 1.15

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.15
vdwtype  = Cutoff
rvdw = 1.0
fourierspacing   = 0.10
pme_order

[gmx-users] compilation problem: gromacs 4.5 double precision

2010-09-14 Thread David Parcej


Hi all.
I have a problem building the double (but not single) precision version 
of gromacs 4.5 on an AMD "instanbul" based system.
compiler is gcc3.4, configure line: ./configure 
--prefix=/home/gromacs451 -program-suffix=_d --disable-float --enable-double


and the error:
In file included from nb_kernel400_x86_64_sse2.c:24:
../../../../include/gmx_sse2_double.h: In function `gmx_mm_sincos_pd':
../../../../include/gmx_sse2_double.h:457: warning: implicit declaration 
of function `_mm_castsi128_pd'

../../../../include/gmx_sse2_double.h:457: error: invalid initializer
../../../../include/gmx_sse2_double.h:514: error: incompatible type for 
argument 1 of `_mm_and_pd'
../../../../include/gmx_sse2_double.h:515: error: incompatible type for 
argument 1 of `_mm_andnot_pd'
../../../../include/gmx_sse2_double.h:516: error: incompatible type for 
argument 1 of `_mm_and_pd'
../../../../include/gmx_sse2_double.h:517: error: incompatible type for 
argument 1 of `_mm_andnot_pd'

make[5]: *** [nb_kernel400_x86_64_sse2.lo] Error 1

Any ideas?
cheers
Dave


-

--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Please don't post (un)subscribe requests to the list. Use the 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] compilation problem: gromacs 4.5 double precision

2010-09-14 Thread Szilárd Páll

Hi David,

Are you sure you're using gcc 3.4? Because if you are, I'd strongly
suggest that you switch to 4.x!

Cheers,
--
Szilárd



On Tue, Sep 14, 2010 at 5:21 PM, David Parcej
 wrote:
> Hi all.
> I have a problem building the double (but not single) precision version of
> gromacs 4.5 on an AMD "instanbul" based system.
> compiler is gcc3.4, configure line: ./configure --prefix=/home/gromacs451
> -program-suffix=_d --disable-float --enable-double
>
> and the error:
> In file included from nb_kernel400_x86_64_sse2.c:24:
> ../../../../include/gmx_sse2_double.h: In function `gmx_mm_sincos_pd':
> ../../../../include/gmx_sse2_double.h:457: warning: implicit declaration of
> function `_mm_castsi128_pd'
> ../../../../include/gmx_sse2_double.h:457: error: invalid initializer
> ../../../../include/gmx_sse2_double.h:514: error: incompatible type for
> argument 1 of `_mm_and_pd'
> ../../../../include/gmx_sse2_double.h:515: error: incompatible type for
> argument 1 of `_mm_andnot_pd'
> ../../../../include/gmx_sse2_double.h:516: error: incompatible type for
> argument 1 of `_mm_and_pd'
> ../../../../include/gmx_sse2_double.h:517: error: incompatible type for
> argument 1 of `_mm_andnot_pd'
> make[5]: *** [nb_kernel400_x86_64_sse2.lo] Error 1
>
> Any ideas?
> cheers
> Dave
>
>
> -
>
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Re: [gmx-users] FEP top file setup...

2010-09-14 Thread TJ Mustard

Ok I think I know where you are going with this.

I started a small 2 nucleic acid system. I set RNA_Chain_A as the couple-moltype and couple-lambda0 and couple-lambda1 to vdw-q and none respectively. I then began a steep mdrun and got this error:

Program mdrun, VERSION 4.5
Source code file: topsort.c, line: 112

Fatal error:
Function type Improper Dih. not implemented in ip_pert
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I have searched for this on google and found nothing. Do I need an Improper Dihedral section in my top/itp file?

Any help is much appreciated.

On September 14, 2010 at 4:24 AM Mark Abraham wrote:

- Original Message -
From: TJ Mustard
Date: Tuesday, September 14, 2010 10:54
Subject: [gmx-users] FEP top file setup...
To: "gmx-users@gromacs.org"

> I am tryng to run free energy perturbation (FEP) calculations on several ligands in several proteins. My problem is getting the correct B state atoms and charges for AMBER forcefields. If anyone can point me in the correct direction, that would be great.

I have read the Free Energy Tutorial from the Dill group wiki and found it very informative on how I should set up the top file and the experiment as a whole. But I can't seem to get the jobs to run correctly. I am assuming that the top file is incorrectly setup as the jobs run with lambda = 0.

It sounds to me more like your .mdp might be wrong. Check out the FE section of manual 7.3

Mark

TJ Mustard
Email: musta...@onid.orst.edu

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Re: [gmx-users] Correction for the PBC!

2010-09-14 Thread teklebrh



Dear Justine,

I have tried every thing but the g_rdf of my surfactant molecules 
Surfactant = PAP

PAP-PAP .. RDF looks like this..
  00
 0.002  0
 0.004  0
 0.006  0
 0.008  0
  0.01  0
 0.012  0
 0.014  0
 0.016  0
 0.018  0
  0.02  0
 0.022  0
 0.024  0
 0.026  0
 0.028  0
  0.03  0
 0.032  0
 0.034  0
 0.036  0
 0.038  0
  0.04  0
 0.042  0
 0.044  0
 0.046  0
 0.048  0
  0.05  0
 0.052  0
 0.054  0
 0.056  0
 0.058  0
  0.06  0
 0.062  0
 0.064  0
 0.066  0
 0.068  0
  0.07  0
 0.072  0
 0.074  0
 0.076  0
 0.078  0
  0.08  0
 0.082  0
 0.084  0
 0.086  0
 0.088  0
  0.09  0
 0.092  0
 0.094  0
 0.096  0
 0.098  0
   0.1  0
 0.102  0
 0.104  0
 0.106  0
 0.108  0
  0.11  0
 0.112  0
 0.114  0
 0.116  0
 0.118  0
  0.12  0
 0.122  0
 0.124  0.0386708
 0.126  0
 0.128  0
  0.13  0
 0.132  0
 0.134  0
 0.136  0
 0.138  0.0312225
  0.14  0
 0.142  0.0294884
 0.144  0
 0.146  0
 0.148  0
  0.15  0
 0.152  0
 0.154   0.050144
 0.156  0
 0.158   0.047637
  0.16  0.0464535
 0.162   0.022657
 0.164  0.0221076
 0.166  0.0215781
 0.168  0.0632021
  0.17  0.0617243
 0.172  0.0803955
 0.174  0.0392791
 0.176  0.0767833
 0.178   0.112601
  0.18   0.165168
 0.182  0.0718038
 0.1840.12294
 0.186   0.171872
 0.188   0.117764
  0.19  0.0988267
 0.192  0.0645195
 0.194   0.205385
 0.1960.17026
 0.198   0.121336
   0.2   0.178384
 0.202   0.145723
 0.204   0.257183
 0.206   0.196166
 0.208   0.261133
  0.21   0.350562
 0.212 0.2646
 0.214   0.324599
 0.216   0.382335
 0.218   0.450424
  0.22   0.491411
 0.222   0.591186
 0.224   0.533271
 0.226   0.651932
 0.228   0.834996
  0.231.19148
 0.2321.95537
 0.2342.38904
 0.2363.52306
 0.2384.37741
  0.245.56415
 0.2426.89399
 0.2448.25963
 0.24610.1401
 0.24810.5862
  0.2511.5687
 0.25211.9851
 0.25412.3869
 0.256 11.786
 0.25811.3537
  0.2610.8894
 0.26210.1434
 0.2649.45289
 0.2668.20198
 0.2687.95582
  0.277.26746
 0.2727.00034
 0.2746.43903
 0.2766.16654
 0.2786.10889
  0.286.47701
 0.2826.68453
 0.2847.12153
 0.2867.97467
 0.2888.63126
  0.299.60143
 0.29210.5722
 0.29411.6465
 0.29612.6569
 0.298 14.349
   0.315.1626
 0.30216.1753
 0.30416.5934
 0.30617.2663
 0.30818.0833
  0.3118.3891
 0.31219.2229
 0.31419.0814
 0.31619.8116
 0.31819.5628
  0.3221.2178
 0.32220.5652
 0.32421.5411
 0.32621.5295
 0.32821.4391
  0.3322.2337
 0.33222.1936
 0.33422.6958
 0.33622.5159
 0.33823.9627
  0.3424.1445
 0.34224.5645
 0.34425.3701
 0.34625.3908
 0.34826.6904
  0.3527.0803
 0.35227.5124
 0.35430.0258
 0.35630.3648
 0.35830.5508
  0.3631.3087
 0.36232.5661
 0.36433.0299
 0.36633.3802
 0.36833.9448
  0.3735.4638
 0.37236.3684
 0.37438.6968
 0.37642.1603
 0.37846.8835
  0.3855.6397
 0.38263.6524
 0.38470.6934
 0.38672.4445
 0.38868.5321
  0.3963.1321
 0.39259.9827
 0.39459.5433
 0.39659.5346
 0.39859.6736
   0.460.1412
 0.40263.2898
 0.40468.8691

  -
  -
  -
  -
  -
  -

3.6181.49702
  3.621.49392
 3.6221.49265
 3.6241.47739
 3.6261.48502
 3.6281.49045
  3.631.47957
 3.6321.48315
 3.6341.47226
 3.6361.47088
 3.6381.47169
  3.641.47815
 3.6421.45689
 3.6441.44958
 3.6461.46132
 3.6481.4574

Re: [gmx-users] Correction for the PBC!




tekle...@ualberta.ca wrote:


Dear Justine,

I have tried every thing but the g_rdf of my surfactant molecules 
Surfactant = PAP

PAP-PAP .. RDF looks like this..
  00
 0.002  0
 0.004  0
 0.006  0
 0.008  0
  0.01  0
 0.012  0
 0.014  0
 0.016  0
 0.018  0
  0.02  0
 0.022  0
 0.024  0
 0.026  0
 0.028  0
  0.03  0
 0.032  0
 0.034  0
 0.036  0
 0.038  0
  0.04  0
 0.042  0
 0.044  0
 0.046  0
 0.048  0
  0.05  0
 0.052  0
 0.054  0
 0.056  0
 0.058  0
  0.06  0
 0.062  0
 0.064  0
 0.066  0
 0.068  0
  0.07  0
 0.072  0
 0.074  0
 0.076  0
 0.078  0
  0.08  0
 0.082  0
 0.084  0
 0.086  0
 0.088  0
  0.09  0
 0.092  0
 0.094  0
 0.096  0
 0.098  0
   0.1  0
 0.102  0
 0.104  0
 0.106  0
 0.108  0
  0.11  0
 0.112  0
 0.114  0
 0.116  0
 0.118  0
  0.12  0
 0.122  0
 0.124  0.0386708
 0.126  0
 0.128  0
  0.13  0
 0.132  0
 0.134  0
 0.136  0
 0.138  0.0312225
  0.14  0
 0.142  0.0294884
 0.144  0
 0.146  0
 0.148  0
  0.15  0
 0.152  0
 0.154   0.050144
 0.156  0
 0.158   0.047637
  0.16  0.0464535
 0.162   0.022657
 0.164  0.0221076
 0.166  0.0215781
 0.168  0.0632021
  0.17  0.0617243
 0.172  0.0803955
 0.174  0.0392791
 0.176  0.0767833
 0.178   0.112601
  0.18   0.165168
 0.182  0.0718038
 0.1840.12294
 0.186   0.171872
 0.188   0.117764
  0.19  0.0988267
 0.192  0.0645195
 0.194   0.205385
 0.1960.17026
 0.198   0.121336
   0.2   0.178384
 0.202   0.145723
 0.204   0.257183
 0.206   0.196166
 0.208   0.261133
  0.21   0.350562
 0.212 0.2646
 0.214   0.324599
 0.216   0.382335
 0.218   0.450424
  0.22   0.491411
 0.222   0.591186
 0.224   0.533271
 0.226   0.651932
 0.228   0.834996
  0.231.19148
 0.2321.95537
 0.2342.38904
 0.2363.52306
 0.2384.37741
  0.245.56415
 0.2426.89399
 0.2448.25963
 0.24610.1401
 0.24810.5862
  0.2511.5687
 0.25211.9851
 0.25412.3869
 0.256 11.786
 0.25811.3537
  0.2610.8894
 0.26210.1434
 0.2649.45289
 0.2668.20198
 0.2687.95582
  0.277.26746
 0.2727.00034
 0.2746.43903
 0.2766.16654
 0.2786.10889
  0.286.47701
 0.2826.68453
 0.2847.12153
 0.2867.97467
 0.2888.63126
  0.299.60143
 0.29210.5722
 0.29411.6465
 0.29612.6569
 0.298 14.349
   0.315.1626
 0.30216.1753
 0.30416.5934
 0.30617.2663
 0.30818.0833
  0.3118.3891
 0.31219.2229
 0.31419.0814
 0.31619.8116
 0.31819.5628
  0.3221.2178
 0.32220.5652
 0.32421.5411
 0.32621.5295
 0.32821.4391
  0.3322.2337
 0.33222.1936
 0.33422.6958
 0.33622.5159
 0.33823.9627
  0.3424.1445
 0.34224.5645
 0.34425.3701
 0.34625.3908
 0.34826.6904
  0.3527.0803
 0.35227.5124
 0.35430.0258
 0.35630.3648
 0.35830.5508
  0.3631.3087
 0.36232.5661
 0.36433.0299
 0.36633.3802
 0.36833.9448
  0.3735.4638
 0.37236.3684
 0.37438.6968
 0.37642.1603
 0.37846.8835
  0.3855.6397
 0.38263.6524
 0.38470.6934
 0.38672.4445
 0.38868.5321
  0.3963.1321
 0.39259.9827
 0.39459.5433
 0.39659.5346
 0.39859.6736
   0.460.1412
 0.40263.2898
 0.40468.8691

  -
  -
  -
  -
  -
  -

3.6181.49702
  3.621.49392
 3.6221.49265
 3.6241.47739
 3.6261.48502
 3.6281.49045
  3.631.47957
 3.6321.48315
 3.6341.47226
 3.6361.47088
 3.6381.47169
  3.641.47815
 3.6421.45689
 3.6441.44958
 3.646

Re: [gmx-users] Units of k1 in the pulling code

2010-09-14 Thread XUEMING TANG

Dear Berk:

Thank you so much for the clarification!!! It is so helpful!

Best!
Xueming

On Fri, Aug 13, 2010 at 4:13 AM, Berk Hess  wrote:

>
>
> > Date: Thu, 12 Aug 2010 17:33:09 -0400
> > From: chris.ne...@utoronto.ca
> > To: gmx-users@gromacs.org
> > Subject: [gmx-users] Units of k1 in the pulling code
>
> >
> > Dear Xueming:
> >
> > the word "mol" is short form for "mole"
> >
> > http://en.wikipedia.org/wiki/Mole_%28unit%29
> >
> > In the pull code context, it refers to moles of the pulled group.
> >
> > The force is not "applied" to the COM of a cluster. The magnitude of
> > the force is determined based on the COM distance, and then the force
> > is applied to each atom in the pull groups.
>
> To clarify this, the force on the COM is not simply applied to each atom,
> but each atom receives a fraction of the COM force proportional to the mass
> of the atom divided by the mass of the whole COM group.
>
> Berk
>
>
> >
> > Chris.
> >
> > -- original message --
> >
> > Hi there
> >
> > The units for pull_k1 = $$ kJ/mol/nm. If this force is applied to a
> cluster,
> > the "/mol" in the units of force means per atom in the cluster, or single
> > molecule composed of several atoms? Sorry, I don't know the default value
> of
> > mol in gromacs. Does that mean per molecule? Besides, the force is
> applied
> > to the COM of cluster, but in the real pulling process, the force is
> applied
> > to each of the molecule in the cluster, or each of the atom in the
> cluster?
> >
> > Thanks in advance!
> >
> > Best!
> > Xueming
> >
> >
> > --
> > gmx-users mailing list gmx-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] Units of k1 in the pulling code

2010-09-14 Thread XUEMING TANG

Dear Chris:

Thank you very much for it!

Best!
Xueming

On Thu, Aug 12, 2010 at 5:33 PM,  wrote:

> Dear Xueming:
>
> the word "mol" is short form for "mole"
>
> http://en.wikipedia.org/wiki/Mole_%28unit%29
>
> In the pull code context, it refers to moles of the pulled group.
>
> The force is not "applied" to the COM of a cluster. The magnitude of the
> force is determined based on the COM distance, and then the force is applied
> to each atom in the pull groups.
>
> Chris.
>
> -- original message --
>
> Hi there
>
> The units for pull_k1 = $$ kJ/mol/nm. If this force is applied to a
> cluster,
> the "/mol" in the units of force means per atom in the cluster, or single
> molecule composed of several atoms? Sorry, I don't know the default value
> of
> mol in gromacs. Does that mean per molecule? Besides, the force is applied
> to the COM of cluster, but in the real pulling process, the force is
> applied
> to each of the molecule in the cluster, or each of the atom in the cluster?
>
> Thanks in advance!
>
> Best!
> Xueming
>
>
> --
> 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 thewww 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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[gmx-users] Amb2gmx

2010-09-14 Thread Charlie Forde

Dear all,

Lennard Jones radius parameters are converted between gromacs and amber with 
the conversion factor (2**(5/6))/10 in the amb2gmx script. While I understand 
that the 10 takes care of the Angstrom to nanometers conversion I do not 
understand the origin of the 2 to the power of 5/6. I would like to know how it 
arises?

Thanks

Charile
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[gmx-users] Fw: NO GSL! Can't find and take away ballistic term in ACF without GSL

2010-09-14 Thread Yao Yao



--- On Tue, 9/14/10, Yao Yao  wrote:
Dear Gmxers,

> I met this msg when running g_hbond
> in 4.5-beta version.
> Then it gives "Segmentation Fault" without any time frame
> reading.
> Does anyone know what it means?
> 
> thanks,

 Yao
>       
> 




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Re: [gmx-users] NO GSL! Can't find and take away ballistic term in ACF without GSL




Yao Yao wrote:

I met this msg when running g_hbond in 4.5-beta version.
Then it gives "Segmentation Fault" without any time frame reading.
Does anyone know what it means?




I presume from your subject line that you received an additional error message. 
 It indicates that you did not compile with the GNU Scientific Library and thus 
cannot utilize whatever function you're trying.


There is no real reason to be using a beta - the official 4.5 came out a few 
weeks ago.  From the looks of the code, the block you're trying to access has 
been commented out, but it's hard to assess whether or not you're trying to run 
a legitimate analysis (some features may not yet work, especially if you're 
using a beta).


If you want to try to troubleshoot it, please post the full command line and 
copy and paste any and all error messages.


-Justin

--


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


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[gmx-users] NO GSL! Can't find and take away ballistic term in ACF without GSL

2010-09-14 Thread Yao Yao

I met this msg when running g_hbond in 4.5-beta version.
Then it gives "Segmentation Fault" without any time frame reading.
Does anyone know what it means?


  

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RE: [gmx-users] how to let the grompp finding libraryfromworkingdirectory first.

2010-09-14 Thread Dallas Warren

For future reference, if someone has a similar problem, would be a good
idea to actually state what the issue you had was, and how you fixed it.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 3:52 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding
libraryfromworkingdirectory first.

 

The HO.itp is nothing wrong with this.

I found the answer from last part of this page
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
membrane_protein/02_topology.html).
  
It's a bit trivial and I will test it later.

Thanks again for you time. 

lina



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of Dallas Warren [dallas.war...@monash.edu]
Sent: Tuesday, September 14, 2010 1:35 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library
fromworkingdirectory first.

What is the contents of the HO.itp file?

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 2:53 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library
fromworkingdirectory first.

 

Yes.  

I did it already. But it did not work.
in topol.top file,
;Include topology
#include "HO.itp"

Thanks,

lina



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of Dallas Warren [dallas.war...@monash.edu]
Sent: Tuesday, September 14, 2010 12:48 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] how to let the grompp finding library from
workingdirectory first.

What is the contents of your topol.top and HO.itp file?  Does the
topol.top "include" the HO.itp in it?

 

To have an "included topology file" (.itp) file processed by grompp, it
has to be directed to it.  This is typically done by using a #include
"HO.itp" line within the topol.top file.

 

Catch ya,

Dr. Dallas Warren

Medicinal Chemistry and Drug Action

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu

+61 3 9909 9304
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of #ZHAO LINA#
Sent: Tuesday, 14 September 2010 2:33 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] how to let the grompp finding library from
workingdirectory first.

 

Hi,

The HO atom type was in the working directory .itp file.
How can I let the grompp work from searching the library of the working
directory, not like this:

grompp -v -f minim.mdp -c dummy.pdb -p topol.top -o dummy.tpr


checking input for internal consistency...
processing topology...
Opening library file /usr/share/gromacs/top/ff_dum.itp
Generated 165 of the 1596 non-bonded parameter combinations

---
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/toppush.c, line: 947

Fatal error:
Atomtype HO not found
---

Do I need add something in minim.mdp? Or maybe just some parts wrong I
do not realise.

Thanks and best regards,

lina

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Re: [gmx-users] Solvent Accessible Surface area (SASA) graph label




eyem noob wrote:

Dear all,
 
I am having a doubt that the Solvent Accessible Surface area   (SASA) 
graph is having a mistake on the label of hydrophilic and hydrophobic 
plot? because I get a weird result from the plot...
 


If you want any useful advice, you'll have to do a whole lot better than mention 
a "weird result."  Why is the result unexpected?  What evidence do you have that 
something is wrong?  Have you found an error in the code?


-Justin


g_sas analysis was done by GROMACS v3.3
 
thanks




--


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


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[gmx-users] Solvent Accessible Surface area (SASA) graph label

2010-09-14 Thread eyem noob


Dear all,

 

I am having a doubt that the Solvent Accessible Surface area   (SASA) graph is 
having a mistake on the label of hydrophilic and hydrophobic plot? because I 
get a weird result from the plot...

 

g_sas analysis was done by GROMACS v3.3

 

thanks
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[gmx-users] Having Multiple Chains From One pdb File

2010-09-14 Thread C Johnson


Hi, 

I have a pdb file with a single short peptide chain.  I would like to simulate 
multiple chains, in this case 5.  I've looked at:

http://www.gromacs.org/Documentation/How-tos/Multiple_Chains

but am still a little confused.  Is it possible to get more detail on how to 
simulate multiple chains using a single chain pdb file?

Thanks,
Casey
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[gmx-users] Output per-group kinetic energy

2010-09-14 Thread Anthony Costa

Dear All,

I want to do something very simple: output, say, the kinetic energies
for a subset of my system. For example some energy group of my system.
Is this possible? Creating an index file, and listing each group as an
energy group in my mdp file doesn't get this data into the energy
file, only all the LJ, SR, etc., interactions are listed for each pair
of groups.

Cheers,
Anthony
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Re: [gmx-users] Having Multiple Chains From One pdb File




C Johnson wrote:

Hi,

I have a pdb file with a single short peptide chain.  I would like to 
simulate multiple chains, in this case 5.  I've looked at:


http://www.gromacs.org/Documentation/How-tos/Multiple_Chains

but am still a little confused.  Is it possible to get more detail on 
how to simulate multiple chains using a single chain pdb file?




The fundamental point is that whatever is in your coordinate file must be 
reflected in the topology as well.  Place the 5 copies of the peptide within the 
simulation cell however you need and then in your [molecules] directive, you'll 
have:


Protein 5

-Justin


Thanks,
Casey



--


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


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Re: [gmx-users] Output per-group kinetic energy




Anthony Costa wrote:

Dear All,

I want to do something very simple: output, say, the kinetic energies
for a subset of my system. For example some energy group of my system.
Is this possible? Creating an index file, and listing each group as an
energy group in my mdp file doesn't get this data into the energy
file, only all the LJ, SR, etc., interactions are listed for each pair
of groups.



See g_traj -ekt and/or -ekr.  Note that constraints are not considered, so the 
raw result will not be correct.  Methods for re-calculating proper energies are 
described in the list archive.


-Justin


Cheers,
Anthony


--


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


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[gmx-users] reg grompp error in QM/MM of mopac gromacs

2010-09-14 Thread vidhya sankar

Dear sir/Madam  thanks in Advance
    i wanted to do QM/MM for simple peptide .i have edited 
my topology files as given in the manual i also include the Link atom(LA) under 
[DUMMIES2] secction of my topology  .but when i run the following grompp command
./grompp_d  -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr
I got the error as follows
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.29#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp

---
Program grompp_d, VERSION 4.0.7
Source code file: topdirs.c, line: 99

Fatal error:
Invalid pairs type 0
---
the suggestions are highly appericiated

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[gmx-users] Re: Dear Dr.Van Der Spoel


On 2010-09-14 22.27, mohsen ramezanpour wrote:

Dear Dr.Van Der Spoel
I want to calculate binding fre energy between proteins and drugs.
does Gromacs change protonation state of protein and drug itself when I
fill my simulating box with solute?
Or I need to use some server as PROPKA to predict and determine their
new protonation states in binding,
and using some server to change their protonation state and at the end
using gromacs for Molecular dynamics of my binding problem?
Thanks in advance for your reply
sincrely yours
Mohsen
GROMACS does not change the protonation state of proteins - yet. 
Algorithms are being implemented for allowing that, but that will take 
until version 5.0.


Please ask questions on the gmx-users mailing list.

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] reg grompp error for QM/MM setup

2010-09-14 Thread vidhya sankar

Dear sir/Madam  thanks in Advance 
    i wanted to do QM/MM for simple peptide .i have edited 
my topology files as given in the manual i also include the Link atom(LA) under 
[DUMMIES2] secction of my topology  .but when i run the following grompp 
command 
./grompp_d  -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr 
I got the error as follows
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.29#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp

---
Program grompp_d, VERSION 4.0.7
Source code file: topdirs.c, line: 99

Fatal error:
Invalid pairs type 0
---
the suggestions are highly appericiated



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Re: [gmx-users] reg grompp error in QM/MM of mopac gromacs

2010-09-14 Thread Mark Abraham



- Original Message -
From: vidhya sankar 
Date: Wednesday, September 15, 2010 16:22
Subject: [gmx-users] reg grompp error in QM/MM of mopac  gromacs
To: gmx-users@gromacs.org

---
| > Dear sir/Madam  thanks in Advance
> i wanted to do QM/MM for simple peptide .i have 
> edited my topology files as given in the manual i also include the Link 
> atom(LA) under [DUMMIES2] secction of my topology  .but when i run the 
> following grompp command
> ./grompp_d  -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr
> I got the error as follows
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.29#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp
> 
> ---
> Program grompp_d,  VERSION 4.0.7
> Source code file: topdirs.c, line: 99
> 
> Fatal error:
> Invalid pairs type 0
> ---
> the suggestions are highly appericiated

Something's wrong with your topology. We can't guess what based on this 
information. Reread the instructions and check that your modifications to your 
.top comply.

Mark
 |
---

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Re: [gmx-users] reg grompp error in QM/MM of mopac gromacs