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Today's Topics:
1. Heat of vap (Elisabeth)
2. Re: Heat of vap (David van der Spoel)
3. Re: Heat of vap (Justin A. Lemkul)
4. Help on umbrella sampling (raghu...@bcpindia.org)
5. Re: Help on umbrella sampling (Justin A. Lemkul)
6. the total charge of system is not an integer (ahmet y?ld?r?m)
----------------------------------------------------------------------
Message: 1
Date: Wed, 30 Mar 2011 15:22:56 -0400
From: Elisabeth <katesed...@gmail.com>
Subject: [gmx-users] Heat of vap
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<aanlktin4-pgxw2ntohsqn3gpxfzu+zxpqvy4yj5yx...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear all,
I intend to obtain vaporization heat per volume for a *pure alkane
system*.
Here is the steps I am taking. Please correct me.
1- Obtain total energy of system (kinetic+potential) and divide by number
of
molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol
XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.
My questions is:
in step 2 : what should be the box size? The same size as in 1 or it does
not matter? (step 1 is done for the actual denstiy)
Thanking you all,
Regards,
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Message: 2
Date: Wed, 30 Mar 2011 21:31:22 +0200
From: David van der Spoel <sp...@xray.bmc.uu.se>
Subject: Re: [gmx-users] Heat of vap
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4d93850a.3020...@xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2011-03-30 21.22, Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume for a /pure alkane
system/. Here is the steps I am taking. Please correct me.
1- Obtain total energy of system (kinetic+potential) and divide by
number of molecules to obtain energy per mol of molecules. g_energy -f
*.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.
My questions is:
in step 2 : what should be the box size? The same size as in 1 or it
does not matter? (step 1 is done for the actual denstiy)
do turn off all pbc and cutoff for that one.
Thanking you all,
Regards,
--
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.se http://folding.bmc.uu.se
------------------------------
Message: 3
Date: Wed, 30 Mar 2011 15:30:12 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] Heat of vap
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4d9384c4.2040...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume for a /pure alkane
system/. Here is the steps I am taking. Please correct me.
1- Obtain total energy of system (kinetic+potential) and divide by
number of molecules to obtain energy per mol of molecules. g_energy -f
*.edr -nmol XXX
2- Obtain total energy of a single molecule (use pbc).
3- Subtract step 2 from step 1.
4- Divide by simulation box volume.
My questions is:
in step 2 : what should be the box size? The same size as in 1 or it
does not matter? (step 1 is done for the actual denstiy)
More troubling, how does one define the energy of a molecule? If you use
any
sort of long-range algorithms (especially PME, but also dispersion
correction),
you can't simply decompose the system like this.
In the derivation of recent Gromos96 parameter sets, the heat of
vaporization is
quite simple:
DHvap = <Ugas> - <Uliq> + RT
I have seen this equation used in a number of other studies, as well.
-Justin
Thanking you all,
Regards,
--
========================================
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
========================================
------------------------------
Message: 4
Date: Thu, 31 Mar 2011 02:14:50 +0530
From: raghu...@bcpindia.org
Subject: [gmx-users] Help on umbrella sampling
To: gmx-users@gromacs.org
Message-ID: <20110331021450.tr893fal8cg8k...@www.bcpindia.org>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Dear Users and Developers
I am trying to execute md_pull.mdp {given below} on a small molecule
embedded at the core of lipid bilayer. I have tried to modify the
md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling.
I encounter LINCS warning (1000) after about 100-110 ps of the
simulation resulting in termination of mdrun. This occurs when the
small molecule is near the polar heads. I understand the system is
exploding.
I have minimized the system, followed by anneal to 323K then nvt and
npt after which I perform the md_pull. How can I soften the core {as
mentioned in the errors on www.gromacs.org} or any other alternative
is there adding lincs warning to mdp file {I am not aware}
Following is the md_pull.mdp file as modified;
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
title = Umbrella pulling simulation
define = -DPOSRES_DPPC
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 100000 ; 200 ps
nstcomm = 1
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Nose-Hoover
tc_grps = TPF DPPC SOL
tau_t = 0.1 0.1 0.1
ref_t = 323 323 323
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of x-y box vectors,
independent z
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = DPPC
pull_group1 = TPF
pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Please help me
Thanks N Regards
Raghuvir
------------------------------
Message: 5
Date: Wed, 30 Mar 2011 17:54:02 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] Help on umbrella sampling
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4d93a67a.9010...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
raghu...@bcpindia.org wrote:
Dear Users and Developers
I am trying to execute md_pull.mdp {given below} on a small molecule
embedded at the core of lipid bilayer. I have tried to modify the
md_pull.mdp from the Tutorial by Justin Lemkul on Umbrella sampling. I
encounter LINCS warning (1000) after about 100-110 ps of the simulation
resulting in termination of mdrun. This occurs when the small molecule
is near the polar heads. I understand the system is exploding.
I have minimized the system, followed by anneal to 323K then nvt and npt
after which I perform the md_pull. How can I soften the core {as
mentioned in the errors on www.gromacs.org} or any other alternative is
there adding lincs warning to mdp file {I am not aware}
"Soft core" is a mechanism by which Lennard-Jones interactions are
modified
while doing decoupling/annihilation calculations. This point is not
relevant here.
I see that you're restraining the lipids in some way. Which atoms are
restrained? In which directions? Why are you restraining them? I would
assume
that as a molecule is pulled through your membrane, any artificial forces
that
work against one another would cause instability.
-Justin
Following is the md_pull.mdp file as modified;
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
title = Umbrella pulling simulation
define = -DPOSRES_DPPC
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 100000 ; 200 ps
nstcomm = 1
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout = 500 ; every 1 ps
nstenergy = 500
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in two groups
Tcoupl = Nose-Hoover
tc_grps = TPF DPPC SOL
tau_t = 0.1 0.1 0.1
ref_t = 323 323 323
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = semiisotropic ; uniform scaling of x-y box
vectors, independent z
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 1.0 ; reference pressure, x-y, z
(in bar)
compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility,
bar^-1
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = yes ; define initial COM distance > 0
pull_ngroups = 1
pull_group0 = DPPC
pull_group1 = TPF
pull_rate1 = 0.01 ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000 ; kJ mol^-1 nm^-2
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Please help me
Thanks N Regards
Raghuvir
--
========================================
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
========================================
------------------------------
Message: 6
Date: Thu, 31 Mar 2011 09:18:31 +0300
From: ahmet y?ld?r?m <ahmedo...@gmail.com>
Subject: [gmx-users] the total charge of system is not an integer
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<aanlktinpb72xrj2fd1snojaqu3js9mly8dt3lblva...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Dear users,
Before energy minimization step , I performed the preprosessing step using
grompp .
However, there are two note that :
*NOTE 1 [file topol.top, line 52]:*
System has non-zero total charge: -1.500000e+01
*NOTE 2 [file topol.top]:*
The largest charge group contains 11 atoms.
Since atoms only see each other when the centers of geometry of the
charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
*
PS: *TRS and EDO are not aminoacid*
TRS.itp:*
..
[ moleculetype ]
; Name nrexcl
TRS 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 TRS O1 1 -0.119 15.9994
2 H 1 TRS H13 1 0.032 1.0080
3 CH2 1 TRS C1 1 0.087 14.0270
4 CCl4 1 TRS C 2 0.055 12.0110
5 CH2 1 TRS C3 2 0.049 14.0270
6 OA 1 TRS O3 2 -0.205 15.9994
7 H 1 TRS H33 2 0.019 1.0080
8 NL 1 TRS N 2 0.206 14.0067
9 H 1 TRS H2 2 0.004 1.0080
10 H 1 TRS H3 2 0.004 1.0080
11 H 1 TRS H1 2 0.004 1.0080
12 CH2 1 TRS C2 2 0.050 14.0270
13 OA 1 TRS O2 2 -0.205 15.9994
14 H 1 TRS H23 2 0.019 1.0080
...
*EDO.itp*
...
[ moleculetype ]
; Name nrexcl
EDO 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 EDO OAB 1 -0.111 15.9994
2 H 1 EDO HAE 1 0.031 1.0080
3 CH2 1 EDO CAA 1 0.080 14.0270
4 CH2 1 EDO CAC 1 0.080 14.0270
5 OA 1 EDO OAD 1 -0.111 15.9994
6 H 1 EDO HAF 1 0.031 1.0080
...
*
topol.top:*
..
; Include water topology
#include "gromos43a1.ff/spc.itp"
#include "TRS.itp"
#include "EDO.itp"
..
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
SOL 185
SOL 143
TRS 1
EDO 1
SOL 44125
*
Conf.gro:*
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
5354
2GLN N 1 1.458 -1.158 0.739
2GLN H1 2 1.520 -1.083 0.763
.......
485HOH HW1 5333 0.221 -3.864 -2.291
485HOH HW2 5334 0.303 -3.946 -2.407
1TRS O1 1 -3.812 -0.471 -2.002
1TRS H13 2 -3.865 -0.443 -1.922
1TRS C1 3 -3.672 -0.469 -1.971
1TRS C 4 -3.635 -0.571 -1.863
1TRS C3 5 -3.711 -0.547 -1.731
1TRS O3 6 -3.694 -0.414 -1.679
1TRS H33 7 -3.746 -0.404 -1.594
1TRS N 8 -3.673 -0.705 -1.911
1TRS H2 9 -3.625 -0.725 -1.996
1TRS H3 10 -3.771 -0.707 -1.927
1TRS H1 11 -3.649 -0.774 -1.842
1TRS C2 12 -3.483 -0.573 -1.840
1TRS O2 13 -3.428 -0.445 -1.806
1TRS H23 14 -3.470 -0.412 -1.722
1EDO OAB 1 0.307 -2.792 0.149
1EDO HAE 2 0.390 -2.826 0.104
1EDO CAA 3 0.239 -2.901 0.212
1EDO CAC 4 0.111 -2.851 0.281
1EDO OAD 5 0.144 -2.763 0.388
1EDO HAF 6 0.060 -2.731 0.432
8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550 0.00000
0.00000 0.00000
How can I fixed these notes(note 1 and note 2)?
Thanks in advance
--
Ahmet YILDIRIM
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