Dear Justin

I removed the constrain on the DPPC molecules, however I find still LINCS errors are prominent
Any alterative can I try

Regards
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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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