[gmx-users] Grompp note

[Nilesh Dhumal]

Hello,

I am running a equilibration simulation for ionic liquids  at 400 K.

I am getting following note.

 The sum of the two largest charge group radii (0.213127) is larger than
  rlist (1.00) - rvdw (0.90)

Could you tell what is the problem?  I am using Gromacs VERSION 4.5.5 .


I used the following mdp file.

; RUN CONTROL PARAMETERS =
integrator   = sd
; start time and timestep in ps =
tinit= 0
dt   = 0.001
nsteps   = 20
; number of steps for center of mass motion removal =
nstcomm  = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 0
nstvout  = 0
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 5000
nstenergy= 1000
; Output frequency and precision for xtc file =
nstxtcout= 5000
xtc-precision= 1000
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps  = system
tau_t= 0.1
ref_t= 400
;OPTIONS FOR PRESSURE COUPLING
Pcoupl   = berendsen
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0
; OPTIONS FOR BONDS =
constraints  = hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start  = no
; Relative tolerance of shake =
shake-tol= 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order  = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle  = 30

; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 1.0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = pme
;rcoulomb-switch  = 0
rcoulomb = 1.0
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r= 1
; Method for doing Van der Waals =
vdw-type = switch
; cut-off lengths=
rvdw-switch  = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid =
fourierspacing   = 0.1
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
; Free energy control stuff
free_energy  = no


Nilesh




-- 
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

Re: [gmx-users] Grompp note

[Nilesh Dhumal]

Could you tell how can I get rid of following warning?


WARNING 1 [file test.top, line 263]:
  The bond in molecule-type BMI between atoms 10 C10 and 23 H23 has an
  estimated oscillational period of 1.2e-03 ps, which is less than 5 times
  the time step of 1.0e-03 ps.
  Maybe you forgot to change the constraints mdp option.




 On 10/31/13 10:30 AM, Nilesh Dhumal wrote:
 Hello,

 I am running a equilibration simulation for ionic liquids  at 400 K.

 I am getting following note.

   The sum of the two largest charge group radii (0.213127) is larger
 than
rlist (1.00) - rvdw (0.90)

 Could you tell what is the problem?  I am using Gromacs VERSION 4.5.5 .


 http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb

 Also see the numerous discussions on this topic in the list archive.

 -Justin


 I used the following mdp file.

 ; RUN CONTROL PARAMETERS =
 integrator   = sd
 ; start time and timestep in ps =
 tinit= 0
 dt   = 0.001
 nsteps   = 20
 ; number of steps for center of mass motion removal =
 nstcomm  = 100
 ; OUTPUT CONTROL OPTIONS =
 ; Output frequency for coords (x), velocities (v) and forces (f) =
 nstxout  = 0
 nstvout  = 0
 nstfout  = 0
 ; Output frequency for energies to log file and energy file =
 nstlog   = 5000
 nstenergy= 1000
 ; Output frequency and precision for xtc file =
 nstxtcout= 5000
 xtc-precision= 1000
 ; NEIGHBORSEARCHING PARAMETERS =
 ; nblist update frequency =
 nstlist  = 10
 ; ns algorithm (simple or grid) =
 ns_type  = grid
 ;OPTIONS FOR TEMPERATURE COUPLING
 tc_grps  = system
 tau_t= 0.1
 ref_t= 400
 ;OPTIONS FOR PRESSURE COUPLING
 Pcoupl   = berendsen
 tau_p= 0.5
 compressibility  = 4.5e-05
 ref_p= 1.0
 ; OPTIONS FOR BONDS =
 constraints  = hbonds
 ; Type of constraint algorithm =
 constraint-algorithm = Lincs
 ; Do not constrain the start configuration =
 unconstrained-start  = no
 ; Relative tolerance of shake =
 shake-tol= 0.0001
 ; Highest order in the expansion of the constraint coupling matrix =
 lincs-order  = 12
 ; Lincs will write a warning to the stderr if in one step a bond =
 ; rotates over more degrees than =
 lincs-warnangle  = 30

 ; Periodic boundary conditions: xyz or none =
 pbc  = xyz
 ; nblist cut-off =
 rlist= 1.0
 domain-decomposition = no
 ; OPTIONS FOR ELECTROSTATICS AND VDW =
 ; Method for doing electrostatics =
 coulombtype  = pme
 ;rcoulomb-switch  = 0
 rcoulomb = 1.0
 ; Dielectric constant (DC) for cut-off or DC of reaction field =
 epsilon-r= 1
 ; Method for doing Van der Waals =
 vdw-type = switch
 ; cut-off lengths=
 rvdw-switch  = 0.8
 rvdw = 0.9
 ; Apply long range dispersion corrections for Energy and Pressure =
 DispCorr  = EnerPres
 ; Spacing for the PME/PPPM FFT grid =
 fourierspacing   = 0.1
 ; FFT grid size, when a value is 0 fourierspacing will be used =
 fourier_nx   = 0
 fourier_ny   = 0
 fourier_nz   = 0
 ; EWALD/PME/PPPM parameters =
 pme_order= 6
 ewald_rtol   = 1e-06
 epsilon_surface  = 0
 optimize_fft = no
 ; Free energy control stuff
 free_energy  = no


 Nilesh





 --
 ==

 Justin A. Lemkul, Ph.D.
 Postdoctoral Fellow

 Department of Pharmaceutical Sciences
 School of Pharmacy
 Health Sciences Facility II, Room 601
 University of Maryland, Baltimore
 20 Penn St.
 Baltimore, MD 21201

 jalem...@outerbanks.umaryland.edu | (410) 706-7441

 ==
 --
 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!
* 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] Box size increases in NPT

[Nilesh Dhumal]

Hello,

I am running a NPT simulation for cyclopropylchloride(1) in
50%water(100)+50%ethanol(100) using opls force field parameter .

After equilibration box size increases from 20 A to 70 A.

I used the following mdp file.

; RUN CONTROL PARAMETERS =
integrator   = sd
; start time and timestep in ps =
tinit= 0
dt   = 0.001
nsteps   = 5
; number of steps for center of mass motion removal =
nstcomm  = 100
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout  = 0
nstvout  = 0
nstfout  = 0
; Output frequency for energies to log file and energy file =
nstlog   = 500
nstenergy= 100
; Output frequency and precision for xtc file =
nstxtcout= 5000
xtc-precision= 1000
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist  = 10
; ns algorithm (simple or grid) =
ns_type  = grid
;OPTIONS FOR TEMPERATURE COUPLING
tc_grps  = system
tau_t= 0.1
ref_t= 290;350
;OPTIONS FOR PRESSURE COUPLING
Pcoupl   = berendsen
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0
; OPTIONS FOR BONDS =
constraints  = hbonds
; Type of constraint algorithm =
constraint-algorithm = Lincs
; Do not constrain the start configuration =
unconstrained-start  = no
; Relative tolerance of shake =
shake-tol= 0.0001
; Highest order in the expansion of the constraint coupling matrix =
lincs-order  = 12
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs-warnangle  = 30

; Periodic boundary conditions: xyz or none =
pbc  = xyz
; nblist cut-off =
rlist= 0.9
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype  = pme
;rcoulomb-switch  = 0
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r= 1
; Method for doing Van der Waals =
vdw-type = switch
; cut-off lengths=
rvdw-switch  = 0.8
rvdw = 0.9
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid =
fourierspacing   = 0.1
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
; EWALD/PME/PPPM parameters =
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
optimize_fft = no
; Free energy control stuff
free_energy  = no


Nilesh



-- 
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] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm

[Nilesh Dhumal]

Hello,

I am getting the following error for simulation. I am using Gromacs
VERSION 4.5.5 and running on 24 processors.

Should I reduce the number of processor or the problem is in bonded
parameters. If I use -nt 1 option. I could run the simulation.

Fatal error:
There is no domain decomposition for 16 nodes that is compatible with the
given box and a minimum cell size of 0.826223 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition


Nilesh

-- 
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

Re: [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm

[Nilesh Dhumal]

Thanks for you reply.

I am doing simulation for ionic liquids BMIM + CL. Total number of atoms
are 3328.

Nilesh

 Assuming you're using LINCS, from the manual:
 With domain decomposition, the cell size is limited by the distance
 spanned by *lincs-order*+1 constraints.
 Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance
 for
 5 bonds.

 Which means that you're probably using too many nodes for the size of your
 system.

 Hope that helps. If it doesn't you'll need to provide some information
 about your system.

 -Trayder



 On Thu, Oct 17, 2013 at 1:27 PM, Nilesh Dhumal
 ndhu...@andrew.cmu.eduwrote:

 Hello,

 I am getting the following error for simulation. I am using Gromacs
 VERSION 4.5.5 and running on 24 processors.

 Should I reduce the number of processor or the problem is in bonded
 parameters. If I use -nt 1 option. I could run the simulation.

 Fatal error:
 There is no domain decomposition for 16 nodes that is compatible with
 the
 given box and a minimum cell size of 0.826223 nm
 Change the number of nodes or mdrun option -rdd or -dds
 Look in the log file for details on the domain decomposition


 Nilesh

 --
 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!
 * 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!
* 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] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

[Nilesh Dhumal]

Hello,

I am doing energy minimization for my system.  I am getting following
warnings

Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20)
Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21)
Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22)
Warning: atom name 23 in p2.top and p2.pdb does not match (C4 - O23)
Warning: atom name 24 in p2.top and p2.pdb does not match (N5 - O24)
Warning: atom name 25 in p2.top and p2.pdb does not match (C6 - C25)
Warning: atom name 26 in p2.top and p2.pdb does not match (C7 - C26)
Warning: atom name 27 in p2.top and p2.pdb does not match (C8 - H27)
Warning: atom name 28 in p2.top and p2.pdb does not match (H9 - H28)
Warning: atom name 29 in p2.top and p2.pdb does not match (H10 - H29)
Warning: atom name 30 in p2.top and p2.pdb does not match (H11 - H30)
Warning: atom name 31 in p2.top and p2.pdb does not match (H12 - H31)
Warning: atom name 32 in p2.top and p2.pdb does not match (H13 - C)
Warning: atom name 33 in p2.top and p2.pdb does not match (H14 - C2)
Warning: atom name 34 in p2.top and p2.pdb does not match (H15 - N3)
Warning: atom name 35 in p2.top and p2.pdb does not match (H16 - C4)
Warning: atom name 36 in p2.top and p2.pdb does not match (H17 - N5)
Warning: atom name 37 in p2.top and p2.pdb does not match (H18 - C6)
Warning: atom name 38 in p2.top and p2.pdb does not match (H19 - C7)
Warning: atom name 39 in p2.top and p2.pdb does not match (S20 - C8)


Here is .pdb file

TITLE Protein
REMARKTHIS IS A SIMULATION BOX
CRYST1   34.775   34.775   34.775  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  C   EMI 1   4.659  30.489  15.747  1.00  0.00
ATOM  2  C2  EMI 1   5.238  30.284  14.495  1.00  0.00
ATOM  3  N3  EMI 1   6.415  30.946  14.495  1.00  0.00
ATOM  4  C4  EMI 1   6.627  31.499  15.682  1.00  0.00
ATOM  5  N5  EMI 1   5.595  31.153  16.470  1.00  0.00
ATOM  6  C6  EMI 1   5.462  31.463  17.884  1.00  0.00
ATOM  7  C7  EMI 1   4.501  30.509  18.615  1.00  0.00
ATOM  8  C8  EMI 1   7.321  30.993  13.363  1.00  0.00
ATOM  9  H9  EMI 1   3.672  30.193  16.130  1.00  0.00
ATOM 10  H10 EMI 1   4.839  29.853  13.640  1.00  0.00
ATOM 11  H11 EMI 1   7.514  32.004  16.038  1.00  0.00
ATOM 12  H12 EMI 1   7.951  31.796  13.329  1.00  0.00
ATOM 13  H13 EMI 1   7.967  30.145  13.270  1.00  0.00
ATOM 14  H14 EMI 1   6.890  31.170  12.362  1.00  0.00
ATOM 15  H15 EMI 1   5.214  32.491  18.125  1.00  0.00
ATOM 16  H16 EMI 1   6.495  31.335  18.302  1.00  0.00
ATOM 17  H17 EMI 1   4.834  29.492  18.590  1.00  0.00
ATOM 18  H18 EMI 1   4.337  30.767  19.685  1.00  0.00
ATOM 19  H19 EMI 1   3.486  30.669  18.338  1.00  0.00
ATOM 20  S20 ETS 2  13.817   2.976  33.669  1.00  0.00
ATOM 21  O21 ETS 2  15.031   2.685  34.347  1.00  0.00
ATOM 22  O22 ETS 2  14.005   3.313  32.237  1.00  0.00
ATOM 23  O23 ETS 2  12.775   1.970  33.860  1.00  0.00
ATOM 24  O24 ETS 2  13.303   4.314  34.278  1.00  0.00
ATOM 25  C25 ETS 2  12.361   5.280  33.781  1.00  0.00
ATOM 26  C26 ETS 2  12.277   6.501  34.666  1.00  0.00
ATOM 27  H27 ETS 2  12.582   5.675  32.806  1.00  0.00
ATOM 28  H28 ETS 2  11.377   4.787  33.550  1.00  0.00
ATOM 29  H29 ETS 2  11.686   6.245  35.492  1.00  0.00
ATOM 30  H30 ETS 2  13.256   6.810  34.975  1.00  0.00
ATOM 31  H31 ETS 2  11.856   7.349  34.171  1.00  0.00
ATOM 32  C   EMI 3  25.075  29.706   5.816  1.00  0.00
ATOM 33  C2  EMI 3  24.256  29.876   6.894  1.00  0.00

and .top file is
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
   chargeB  massB
 1   opls_561  1EMI  C  1  -0.13 12.011   ;
qtot -0.13
 2   opls_561  1EMI C2  2  -0.13 12.011   ;
qtot -0.26
 3   opls_557  1EMI N3  3   0.1514.0067   ;
qtot -0.11
 4   opls_558  1EMI C4  4  -0.11 12.011   ;
qtot -0.22
 5   opls_557  1EMI N5  5   0.1514.0067   ;
qtot -0.07
 6   opls_136  1EMI C6  6  -0.05 12.011   ;
qtot -0.12
 7   opls_135  1EMI C7  7  -0.17 12.011   ;
qtot -0.29
 8   opls_135  1EMI C8  8  -0.17 12.011   ;
qtot -0.46
 9   opls_564  1EMI H9  9   0.21  1.008   ;
qtot -0.25
10   opls_564  1EMIH10  9   0.21  1.008   ;
qtot -0.04
11   opls_563  1EMIH11  9   0.21  1.008   ;
qtot 0.17
12   opls_140  1EMIH12 10   0.13  1.008   ;
qtot 0.3
13   opls_140  1EMIH13   

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

[Nilesh Dhumal]

5657 3
   51555658 3
   51555659 3
   55565760 3
   55565761 3
   55565762 3
   58565760 3
   58565761 3
   58565762 3
   59565760 3
   59565761 3
   59565762 3

; Include Position restraint file

; Include water topology
;#include spc.itp


; Include generic topology for ions
;#include ions.itp

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
EMI 2
ETS 2



Nilesh






 On 9/22/13 7:13 PM, Nilesh Dhumal wrote:
 Hello,

 I am doing energy minimization for my system.  I am getting following
 warnings

 Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20)
 Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21)
 Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22)
 Warning: atom name 23 in p2.top and p2.pdb does not match (C4 - O23)
 Warning: atom name 24 in p2.top and p2.pdb does not match (N5 - O24)
 Warning: atom name 25 in p2.top and p2.pdb does not match (C6 - C25)
 Warning: atom name 26 in p2.top and p2.pdb does not match (C7 - C26)
 Warning: atom name 27 in p2.top and p2.pdb does not match (C8 - H27)
 Warning: atom name 28 in p2.top and p2.pdb does not match (H9 - H28)
 Warning: atom name 29 in p2.top and p2.pdb does not match (H10 - H29)
 Warning: atom name 30 in p2.top and p2.pdb does not match (H11 - H30)
 Warning: atom name 31 in p2.top and p2.pdb does not match (H12 - H31)
 Warning: atom name 32 in p2.top and p2.pdb does not match (H13 - C)
 Warning: atom name 33 in p2.top and p2.pdb does not match (H14 - C2)
 Warning: atom name 34 in p2.top and p2.pdb does not match (H15 - N3)
 Warning: atom name 35 in p2.top and p2.pdb does not match (H16 - C4)
 Warning: atom name 36 in p2.top and p2.pdb does not match (H17 - N5)
 Warning: atom name 37 in p2.top and p2.pdb does not match (H18 - C6)
 Warning: atom name 38 in p2.top and p2.pdb does not match (H19 - C7)
 Warning: atom name 39 in p2.top and p2.pdb does not match (S20 - C8)


 Here is .pdb file

 TITLE Protein
 REMARKTHIS IS A SIMULATION BOX
 CRYST1   34.775   34.775   34.775  90.00  90.00  90.00 P 1   1
 MODEL1
 ATOM  1  C   EMI 1   4.659  30.489  15.747  1.00  0.00
 ATOM  2  C2  EMI 1   5.238  30.284  14.495  1.00  0.00
 ATOM  3  N3  EMI 1   6.415  30.946  14.495  1.00  0.00
 ATOM  4  C4  EMI 1   6.627  31.499  15.682  1.00  0.00
 ATOM  5  N5  EMI 1   5.595  31.153  16.470  1.00  0.00
 ATOM  6  C6  EMI 1   5.462  31.463  17.884  1.00  0.00
 ATOM  7  C7  EMI 1   4.501  30.509  18.615  1.00  0.00
 ATOM  8  C8  EMI 1   7.321  30.993  13.363  1.00  0.00
 ATOM  9  H9  EMI 1   3.672  30.193  16.130  1.00  0.00
 ATOM 10  H10 EMI 1   4.839  29.853  13.640  1.00  0.00
 ATOM 11  H11 EMI 1   7.514  32.004  16.038  1.00  0.00
 ATOM 12  H12 EMI 1   7.951  31.796  13.329  1.00  0.00
 ATOM 13  H13 EMI 1   7.967  30.145  13.270  1.00  0.00
 ATOM 14  H14 EMI 1   6.890  31.170  12.362  1.00  0.00
 ATOM 15  H15 EMI 1   5.214  32.491  18.125  1.00  0.00
 ATOM 16  H16 EMI 1   6.495  31.335  18.302  1.00  0.00
 ATOM 17  H17 EMI 1   4.834  29.492  18.590  1.00  0.00
 ATOM 18  H18 EMI 1   4.337  30.767  19.685  1.00  0.00
 ATOM 19  H19 EMI 1   3.486  30.669  18.338  1.00  0.00
 ATOM 20  S20 ETS 2  13.817   2.976  33.669  1.00  0.00
 ATOM 21  O21 ETS 2  15.031   2.685  34.347  1.00  0.00
 ATOM 22  O22 ETS 2  14.005   3.313  32.237  1.00  0.00
 ATOM 23  O23 ETS 2  12.775   1.970  33.860  1.00  0.00
 ATOM 24  O24 ETS 2  13.303   4.314  34.278  1.00  0.00
 ATOM 25  C25 ETS 2  12.361   5.280  33.781  1.00  0.00
 ATOM 26  C26 ETS 2  12.277   6.501  34.666  1.00  0.00
 ATOM 27  H27 ETS 2  12.582   5.675  32.806  1.00  0.00
 ATOM 28  H28 ETS 2  11.377   4.787  33.550  1.00  0.00
 ATOM 29  H29 ETS 2  11.686   6.245  35.492  1.00  0.00
 ATOM 30  H30 ETS 2  13.256   6.810  34.975  1.00  0.00
 ATOM 31  H31 ETS 2  11.856   7.349  34.171  1.00  0.00
 ATOM 32  C   EMI 3  25.075  29.706   5.816  1.00  0.00
 ATOM 33  C2  EMI 3  24.256  29.876   6.894  1.00  0.00

 and .top file is
 [ atoms ]
 ;   nr   type  resnr residue  atom   cgnr charge   mass
 typeB
 chargeB  massB
   1   opls_561  1EMI  C  1  -0.13 12.011   ;
 qtot -0.13
   2   opls_561  1EMI C2  2  -0.13 12.011   ;
 qtot -0.26
   3   opls_557  1EMI N3  3   0.1514.0067   ;
 qtot -0.11
   4   opls_558  1EMI C4  4  -0.11

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

[Nilesh Dhumal]

Thanks.

I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI
and 2 ETS.

How can I define for 128 EMI and 128 ETS ?

Nilesh

 On 9/22/13 9:18 PM, Nilesh Dhumal wrote:
 Sorry to paste big files here. (.pdb file and processed.top )


 pdb file.

 TITLE Protein
 REMARKTHIS IS A SIMULATION BOX
 CRYST1   34.775   34.775   34.775  90.00  90.00  90.00 P 1   1
 MODEL1
 ATOM  1  C   EMI 1   4.659  30.489  15.747  1.00  0.00
 ATOM  2  C2  EMI 1   5.238  30.284  14.495  1.00  0.00
 ATOM  3  N3  EMI 1   6.415  30.946  14.495  1.00  0.00
 ATOM  4  C4  EMI 1   6.627  31.499  15.682  1.00  0.00
 ATOM  5  N5  EMI 1   5.595  31.153  16.470  1.00  0.00
 ATOM  6  C6  EMI 1   5.462  31.463  17.884  1.00  0.00
 ATOM  7  C7  EMI 1   4.501  30.509  18.615  1.00  0.00
 ATOM  8  C8  EMI 1   7.321  30.993  13.363  1.00  0.00
 ATOM  9  H9  EMI 1   3.672  30.193  16.130  1.00  0.00
 ATOM 10  H10 EMI 1   4.839  29.853  13.640  1.00  0.00
 ATOM 11  H11 EMI 1   7.514  32.004  16.038  1.00  0.00
 ATOM 12  H12 EMI 1   7.951  31.796  13.329  1.00  0.00
 ATOM 13  H13 EMI 1   7.967  30.145  13.270  1.00  0.00
 ATOM 14  H14 EMI 1   6.890  31.170  12.362  1.00  0.00
 ATOM 15  H15 EMI 1   5.214  32.491  18.125  1.00  0.00
 ATOM 16  H16 EMI 1   6.495  31.335  18.302  1.00  0.00
 ATOM 17  H17 EMI 1   4.834  29.492  18.590  1.00  0.00
 ATOM 18  H18 EMI 1   4.337  30.767  19.685  1.00  0.00
 ATOM 19  H19 EMI 1   3.486  30.669  18.338  1.00  0.00
 ATOM 20  S20 ETS 2  13.817   2.976  33.669  1.00  0.00
 ATOM 21  O21 ETS 2  15.031   2.685  34.347  1.00  0.00
 ATOM 22  O22 ETS 2  14.005   3.313  32.237  1.00  0.00
 ATOM 23  O23 ETS 2  12.775   1.970  33.860  1.00  0.00
 ATOM 24  O24 ETS 2  13.303   4.314  34.278  1.00  0.00
 ATOM 25  C25 ETS 2  12.361   5.280  33.781  1.00  0.00
 ATOM 26  C26 ETS 2  12.277   6.501  34.666  1.00  0.00
 ATOM 27  H27 ETS 2  12.582   5.675  32.806  1.00  0.00
 ATOM 28  H28 ETS 2  11.377   4.787  33.550  1.00  0.00
 ATOM 29  H29 ETS 2  11.686   6.245  35.492  1.00  0.00
 ATOM 30  H30 ETS 2  13.256   6.810  34.975  1.00  0.00
 ATOM 31  H31 ETS 2  11.856   7.349  34.171  1.00  0.00
 ATOM 32  C   EMI 3  25.075  29.706   5.816  1.00  0.00
 ATOM 33  C2  EMI 3  24.256  29.876   6.894  1.00  0.00
 ATOM 34  N3  EMI 3  25.074  30.288   7.940  1.00  0.00
 ATOM 35  C4  EMI 3  26.335  30.336   7.464  1.00  0.00
 ATOM 36  N5  EMI 3  26.369  29.867   6.216  1.00  0.00
 ATOM 37  C6  EMI 3  27.586  29.761   5.460  1.00  0.00
 ATOM 38  C7  EMI 3  27.397  29.088   4.106  1.00  0.00
 ATOM 39  C8  EMI 3  24.601  30.404   9.351  1.00  0.00
 ATOM 40  H9  EMI 3  24.815  29.446   4.790  1.00  0.00
 ATOM 41  H10 EMI 3  23.203  29.817   6.920  1.00  0.00
 ATOM 42  H11 EMI 3  27.238  30.558   8.074  1.00  0.00
 ATOM 43  H12 EMI 3  24.321  29.435   9.759  1.00  0.00
 ATOM 44  H13 EMI 3  25.411  30.876   9.880  1.00  0.00
 ATOM 45  H14 EMI 3  23.735  31.092   9.515  1.00  0.00
 ATOM 46  H15 EMI 3  28.216  29.130   6.169  1.00  0.00
 ATOM 47  H16 EMI 3  28.027  30.763   5.434  1.00  0.00
 ATOM 48  H17 EMI 3  26.886  29.695   3.344  1.00  0.00
 ATOM 49  H18 EMI 3  28.366  28.886   3.715  1.00  0.00
 ATOM 50  H19 EMI 3  26.842  28.200   3.880  1.00  0.00
 ATOM 51  S20 ETS 4  26.876  17.203   7.791  1.00  0.00
 ATOM 52  O21 ETS 4  28.030  16.750   7.061  1.00  0.00
 ATOM 53  O22 ETS 4  25.656  16.428   7.528  1.00  0.00
 ATOM 54  O23 ETS 4  27.112  17.470   9.202  1.00  0.00
 ATOM 55  O24 ETS 4  26.578  18.733   7.129  1.00  0.00
 ATOM 56  C25 ETS 4  26.215  18.995   5.843  1.00  0.00
 ATOM 57  C26 ETS 4  27.436  19.133   4.921  1.00  0.00
 ATOM 58  H27 ETS 4  25.607  18.170   5.486  1.00  0.00
 ATOM 59  H28 ETS 4  25.530  19.872   5.774  1.00  0.00
 ATOM 60  H29 ETS 4  28.107  19.910   5.179  1.00  0.00
 ATOM 61  H30 ETS 4  27.944  18.247   4.832  1.00  0.00
 ATOM 62  H31 ETS 4  27.138  19.330   3.927  1.00  0.00
 TER
 ENDMDL

 snip

 [ molecules ]
 ; Compound#mols
 EMI 2
 ETS 2


 As I suspected, your molecules are simply out of order.  Your topology
 specifies
 EMI-EMI-ETS-ETS, but the coordinate file lists the molecules as
 EMI-ETS-EMI-ETS,
 hence the mismatch.  The Protein [moleculetype] seems superfluous, but
 would
 be the appropriate

RE: [gmx-users] g_current

[Nilesh Dhumal]

Did you get chance to take look at the g_current?

why it is -inf  (infinity)  at the end with -mc option (mc.xvg).


 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
 boun...@gromacs.org] On Behalf Of Nilesh Dhumal
 Sent: Tuesday, July 09, 2013 5:06 AM
 To: Discussion list for GROMACS users
 Subject: RE: [gmx-users] g_current

 Thanks for reply.

 Still I have a question why it is -inf  (infinity)  at the end.

 This is a good question. At the moment, the only thing I can imagine is a
 faulty normalization, because the value of the integral at t=0 equals
 always
 zero. However, if you integrate the first row with another tool, such as
 g_analyze for example, the same values as in the second row show appear.

 As soon as I have some time left, I will take a look at the code and
 report
 back.

 /Flo


 Nilesh

  Hi,
 
   I would say the problem is too less statistics. In the paper where
 the
  tool
  was introduced, a simulation of 100ns has been performed in order to
  achieved sufficient sampling.
 
  The order of magnitude is given due to the units.
 
  Simulate for a longer time to get rid of the noise. Calculating these
 kind
  of correlations functions is really not a simple task.
 
  Schroeder et al. have published an article about fitting of dielectric
  spectra for ionic liquids, where this problem is discussed in detail.
 
  Cheers,
  Flo
 
  -Original Message-
  From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
  boun...@gromacs.org] On Behalf Of Nilesh Dhumal
  Sent: Monday, July 08, 2013 10:32 PM
  To: gmx-users@gromacs.org
  Subject: [gmx-users] g_current
 
  Hello,
  I am calculating the correlation of rotational and translation dipole
  moment of ionic liquids. I run the 1 ns simulation and saved the
  trajectory at 1 fs.
 
  g_current -f md.trr -s md.tpr -n index.ndx -mc
 
  I selected system group.
 
  Here I pasted the initial j(t) vales and the final value is infinity.
 
  # This file was created Sun Jul  7 20:51:59 2013
  # by the following command:
  # g_current -f md.trr -s md.tpr -e 10.0 -mc
  #
  # g_current is part of G R O M A C S:
  #
  # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  #
  @title M\sD\N - current  autocorrelation function
  @xaxis  label Time (ps)
  @yaxis  label  M\sD\N (0)\c7\CJ(t)   (e nm/ps)\S2
  @TYPE xy
  # time   M_D(0) J(t) acf Integral acf
  0.000   -5.20584e-15 0
  0.001   -6.97466e-15-1.42702e-17
  0.002   -6.97511e-15-5.25081e-17
  0.003   -6.97474e-15-9.07484e-17
  0.004   -6.97391e-15-1.28987e-16
 
 
 
  Why final value is infinity? If I do autocorrelation function of
 these
  values, I get all values 0.
 
  Why J(t)values are in range of e-15?
 
  Nilesh
 
 
 
  --
  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!
  * 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!
 * 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!
 * 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!
* 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] fluctuation of energy in rerun

[Nilesh Dhumal]

Hello

I am running a simulation with charge and without charge for 128 pairs of
bmim-tf2n ioinc liquids.
This is the command for the original run without charge
mdrun -s gs.tpr -o gs.trr -c 0.pdb -e gs.edr -g gs.log -pd -nt 8
This is the command for the rerun with charge
mdrun -s es.tpr -o es.trr -c 0.pdb -e es.edr -g es.log -rerun gs.trr -pd
-nt 8

In the original trajectory, the energy of the system fluctuates around 5000
kJ/mol. In the rerun trajectory, the energy of the system also mostly
fluctuates around 5000 kJ/mol, but sometimes it jumps to 10^13 or 10^-13.
In the most recent run (20 ns), 16 data points out of 200 were
extremely large.

Checking the trajectory files, it seems like caused by molecule stretching
across the pbc.

Nilesh

-- 
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] qm-mm calculation

[Nilesh Dhumal]

Hello,
I am trying to run the qm-mm gas phase calculations for my system.

 I am using following in md.mdp file.

title   =  cpeptide MD
cpp =  /usr/bin/cpp
integrator  =  md
dt  =  0.001; ps !
nsteps  =  500 ; total 5 ps.
nstcomm =  1
nstxout =  1
nstvout =  1
nstfout =  1
nstlist =  1
ns_type = simple
rlist   =  0.0
rcoulomb=  0.0
rvdw=  0.0
coulombtype = cut-off
vdwtype = cut-off
pbc = no
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
Tcoupl = nose-hoover
tau_t = 0.1
tc-grps  =system
ref_t =   350
; Pressure coupling is  on
Pcoupl  = no ;Parrinello-Rahman
pcoupltype  = isotropic
tau_p   =  2.0
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  350.0
gen_seed=  173529
QMMM = yes
QMMM-grps= System
QMmethod = RHF
QMbasis  = 3-21G
QMcharge = 0
QMmult   = 1


I could run the grompp and for mdrun I am getting following error.

Back Off! I just backed up md.log to ./#md.log.2#
Reading file 1.tpr, VERSION 4.0.7 (single precision)
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 32
QMlevel: RHF/3-21G

number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
[c63:25888] *** Process received signal ***
[c63:25888] Signal: Segmentation fault (11)
[c63:25888] Signal code: Address not mapped (1)
[c63:25888] Failing at address: (nil)
[c63:25888] [ 0] /lib64/libpthread.so.0 [0x2b2d89ac1a90]
[c63:25888] [ 1] /lib64/libc.so.6(strlen+0x40) [0x2b2d89d4b590]
[c63:25888] [ 2] /lib64/libc.so.6(fputs+0x1e) [0x2b2d89d33dde]
[c63:25888] [ 3] mdrun(init_gaussian+0x4c3) [0x51e993]
[c63:25888] [ 4] mdrun(init_QMMMrec+0xef8) [0x517578]
[c63:25888] [ 5] mdrun(mdrunner+0x1019) [0x42e109]
[c63:25888] [ 6] mdrun(main+0x3c5) [0x434b95]
[c63:25888] [ 7] /lib64/libc.so.6(__libc_start_main+0xe6) [0x2b2d89ced586]
[c63:25888] [ 8] mdrun [0x415cb9]
[c63:25888] *** End of error message ***
Segmentation fault

Could you tell what is the problem.

Nilesh




-- 
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] qm-mm calculation

[Nilesh Dhumal]

Hello,
I am trying to run the qm-mm gas phase calculations for my system.

 I am using following in md.mdp file.

title   =  cpeptide MD
cpp =  /usr/bin/cpp
integrator  =  md
dt  =  0.001; ps !
nsteps  =  500 ; total 5 ps.
nstcomm =  1
nstxout =  1
nstvout =  1
nstfout =  1
nstlist =  1
ns_type = simple
rlist   =  0.0
rcoulomb=  0.0
rvdw=  0.0
coulombtype = cut-off
vdwtype = cut-off
pbc = no
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
Tcoupl = nose-hoover
tau_t = 0.1
tc-grps  =system
ref_t =   350
; Pressure coupling is  on
Pcoupl  = no ;Parrinello-Rahman
pcoupltype  = isotropic
tau_p   =  2.0
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  350.0
gen_seed=  173529
QMMM = yes
QMMM-grps= System
QMmethod = RHF
QMbasis  = 3-21G
QMcharge = 0
QMmult   = 1


I could run the grompp and for mdrun I am getting following error.

Back Off! I just backed up md.log to ./#md.log.2#
Reading file 1.tpr, VERSION 4.0.7 (single precision)
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 32
QMlevel: RHF/3-21G

number of CPUs for gaussian = 1
memory for gaussian = 5000
accuracy in l510 = 8
NOT using cp-mcscf in l1003
Level of SA at start = 0
[c63:25888] *** Process received signal ***
[c63:25888] Signal: Segmentation fault (11)
[c63:25888] Signal code: Address not mapped (1)
[c63:25888] Failing at address: (nil)
[c63:25888] [ 0] /lib64/libpthread.so.0 [0x2b2d89ac1a90]
[c63:25888] [ 1] /lib64/libc.so.6(strlen+0x40) [0x2b2d89d4b590]
[c63:25888] [ 2] /lib64/libc.so.6(fputs+0x1e) [0x2b2d89d33dde]
[c63:25888] [ 3] mdrun(init_gaussian+0x4c3) [0x51e993]
[c63:25888] [ 4] mdrun(init_QMMMrec+0xef8) [0x517578]
[c63:25888] [ 5] mdrun(mdrunner+0x1019) [0x42e109]
[c63:25888] [ 6] mdrun(main+0x3c5) [0x434b95]
[c63:25888] [ 7] /lib64/libc.so.6(__libc_start_main+0xe6) [0x2b2d89ced586]
[c63:25888] [ 8] mdrun [0x415cb9]
[c63:25888] *** End of error message ***
Segmentation fault

Could you tell what is the problem.

Nilesh


-- 
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] g_current

[Nilesh Dhumal]

Hello,
I am calculating the correlation of rotational and translation dipole
moment of ionic liquids. I run the 1 ns simulation and saved the
trajectory at 1 fs.

g_current -f md.trr -s md.tpr -n index.ndx -mc

I selected system group.

Here I pasted the initial j(t) vales and the final value is infinity.

# This file was created Sun Jul  7 20:51:59 2013
# by the following command:
# g_current -f md.trr -s md.tpr -e 10.0 -mc
#
# g_current is part of G R O M A C S:
#
# Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
#
@title M\sD\N - current  autocorrelation function
@xaxis  label Time (ps)
@yaxis  label  M\sD\N (0)\c7\CJ(t)   (e nm/ps)\S2
@TYPE xy
# time   M_D(0) J(t) acf Integral acf
0.000   -5.20584e-15 0
0.001   -6.97466e-15-1.42702e-17
0.002   -6.97511e-15-5.25081e-17
0.003   -6.97474e-15-9.07484e-17
0.004   -6.97391e-15-1.28987e-16



Why final value is infinity? If I do autocorrelation function of these
values, I get all values 0.

Why J(t)values are in range of e-15?

Nilesh



-- 
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

RE: [gmx-users] g_current

[Nilesh Dhumal]

Thanks for reply.

Still I have a question why it is -inf  (infinity)  at the end.

Nilesh

 Hi,

  I would say the problem is too less statistics. In the paper where the
 tool
 was introduced, a simulation of 100ns has been performed in order to
 achieved sufficient sampling.

 The order of magnitude is given due to the units.

 Simulate for a longer time to get rid of the noise. Calculating these kind
 of correlations functions is really not a simple task.

 Schroeder et al. have published an article about fitting of dielectric
 spectra for ionic liquids, where this problem is discussed in detail.

 Cheers,
 Flo

 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
 boun...@gromacs.org] On Behalf Of Nilesh Dhumal
 Sent: Monday, July 08, 2013 10:32 PM
 To: gmx-users@gromacs.org
 Subject: [gmx-users] g_current

 Hello,
 I am calculating the correlation of rotational and translation dipole
 moment of ionic liquids. I run the 1 ns simulation and saved the
 trajectory at 1 fs.

 g_current -f md.trr -s md.tpr -n index.ndx -mc

 I selected system group.

 Here I pasted the initial j(t) vales and the final value is infinity.

 # This file was created Sun Jul  7 20:51:59 2013
 # by the following command:
 # g_current -f md.trr -s md.tpr -e 10.0 -mc
 #
 # g_current is part of G R O M A C S:
 #
 # Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
 #
 @title M\sD\N - current  autocorrelation function
 @xaxis  label Time (ps)
 @yaxis  label  M\sD\N (0)\c7\CJ(t)   (e nm/ps)\S2
 @TYPE xy
 # time   M_D(0) J(t) acf Integral acf
 0.000   -5.20584e-15 0
 0.001   -6.97466e-15-1.42702e-17
 0.002   -6.97511e-15-5.25081e-17
 0.003   -6.97474e-15-9.07484e-17
 0.004   -6.97391e-15-1.28987e-16



 Why final value is infinity? If I do autocorrelation function of these
 values, I get all values 0.

 Why J(t)values are in range of e-15?

 Nilesh



 --
 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!
 * 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!
* 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] No default Ryckaert-Bell. types

[Nilesh Dhumal]

Hello,

I am getting No default Ryckaert-Bell. types error for grompp.

I have define all this parameter in  .itp file

Here is .itp file

; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080
; Derived from parsing of runfiles/alat.top.orig
;[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_124   S   1632.06000 0.312   A3.56000e-01 
1.65268e+00 opls_125   O   8 15.99940-0.556   A   
2.93000e-01  1.17152e+00 opls_126   CT  6 15.03500-0.148   A 
  3.81000e-01  6.69440e-01 opls_140   HC  1  1.00800 0.090  
A2.5e-01  1.25520e-01


[ bondtypes ]
; ij  func   b0  kb
S O   10.1530   225936.0
S CT  10.1800   100416.0
CTHC  10.1110   134724.8


[ angletypes ]
;  ijk  func   th0   cth
  CT S  CT  195.0  142.256
  CT S  O   1   106.75 330.536
  S  CT HC  1   111.3  192.8824
  HC CT HC  1   108.4  148.532


[ dihedraltypes ]
;  ijkl   func coefficients
; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form
; according to the formula in the Gromacs manual.
CT S  CT HC  3  1.35352   4.06057   0.0  -5.41410
 0.0   0.0 ; sulfide all-atom
 O S CT  HC  3  0.0   0.0   0.0   0.0 
0.0   0.0 ; small ring



Why I am getting this error.

I am using Gromacs VERSION 4.0.7.

Thanks

Nilesh





-- 
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

Re: [gmx-users] No default Ryckaert-Bell. types

[Nilesh Dhumal]

I checked the line number in .top file. Its not reading any dihedral
parameter defined in .itp file.

NIlesh

 On 6/6/13 9:22 AM, Nilesh Dhumal wrote:
 Hello,

 I am getting No default Ryckaert-Bell. types error for grompp.

 I have define all this parameter in  .itp file

 Here is .itp file

 ; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080
 ; Derived from parsing of runfiles/alat.top.orig
 ;[ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 ;1   3   yes 0.5 0.5
 ; comb-rule 3 is square-root sigma, the OPLSAA version

 [ atomtypes ]
 ; full atom descriptions are available in ffoplsaa.atp
 ; name  bond_typemasscharge   ptype  sigma  epsilon
   opls_124   S   1632.06000 0.312   A3.56000e-01
 1.65268e+00 opls_125   O   8 15.99940-0.556   A
 2.93000e-01  1.17152e+00 opls_126   CT  6 15.03500-0.148   A
3.81000e-01  6.69440e-01 opls_140   HC  1  1.00800 0.090
 A2.5e-01  1.25520e-01


 [ bondtypes ]
 ; ij  func   b0  kb
 S O   10.1530   225936.0
 S CT  10.1800   100416.0
 CTHC  10.1110   134724.8


 [ angletypes ]
 ;  ijk  func   th0   cth
CT S  CT  195.0  142.256
CT S  O   1   106.75 330.536
S  CT HC  1   111.3  192.8824
HC CT HC  1   108.4  148.532


 [ dihedraltypes ]
 ;  ijkl   func coefficients
 ; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans
 form
 ; according to the formula in the Gromacs manual.
 CT S  CT HC  3  1.35352   4.06057   0.0
 -5.41410
   0.0   0.0 ; sulfide all-atom
   O S CT  HC  3  0.0   0.0   0.0
 0.0
 0.0   0.0 ; small ring



 Why I am getting this error.


 Apparently grompp is failing to find some needed parameter.  You should
 get a
 line number in the topology where this is occurring, which will allow you
 to map
 back the atoms involved.

 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 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


-- 
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] Unknown bond_atomtype C2

[Nilesh Dhumal]

Hello,

I am getting Unknown bond_atomtype C2 error for grompp.

I don't have C2 atom in my .itp file. Here I used the .itp file

; For parameters see J. Phys. Chem. A. 2002, 106, 1074-1080
; Derived from parsing of runfiles/alat.top.orig
;[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_124   S   1632.06000 0.312   A3.56000e-01  1.65268e+00
 opls_125   O   8 15.99940-0.556   A2.93000e-01  1.17152e+00
 opls_126   CT  6 15.03500-0.148   A3.81000e-01  6.69440e-01
 opls_140   HC  1  1.00800 0.090   A2.5e-01  1.25520e-01


[ bondtypes ]
; ij  func   b0  kb
S O   10.1530   225936.0
S CT  10.1800   100416.0
CTHC  10.1110   134724.8


[ angletypes ]
;  ijk  func   th0   cth
  CT S  CT  195.0  142.256
  CT S  O   1   106.75 330.536
  S  CT HC  1   111.3  192.8824
  HC CT HC  1   108.4  148.532


[ dihedraltypes ]
;  ijkl   func coefficients
; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form
; according to the formula in the Gromacs manual.
CT S  CT HC  3  1.35352   4.06057   0.0  -5.41410 
 0.0   0.0 ; sulfide all-atom
 O S CT  HC  3  0.0   0.0   0.0   0.0 
 0.0   0.0 ; small ring

I am not using atom C2 in my bonded parameters.

Why I am getting this error.

I am using Gromacs VERSION 4.0.7.

Thanks

Nilesh



-- 
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] g_hbond : autocorrelation funciton

[Nilesh Dhumal]

Hello,

I am calculating  the hyrogen bond life time my system using g_hbond in
Gromacs. Program calculate the hydrogen bond life time from the
autocorrelation function. Program calculate the hydrogen bond
autocorrelation function with the hydrogen bond criteria.
What quantity program use such as distance between donor-acceptor, to
calculate the autocorrelation function?

Thanks

Nilesh



-- 
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

Re: [gmx-users] g_hbond : autocorrelation funciton

[Nilesh Dhumal]

-ac: average over all autocorrelations of the existence functions (either
0 or 1) of all hydrogen bonds.

Program collect the data 0 or 1 along time?

nilesh

 On 4/14/13 7:21 PM, Nilesh Dhumal wrote:
 Hello,

 I am calculating  the hyrogen bond life time my system using g_hbond in
 Gromacs. Program calculate the hydrogen bond life time from the
 autocorrelation function. Program calculate the hydrogen bond
 autocorrelation function with the hydrogen bond criteria.
 What quantity program use such as distance between donor-acceptor, to
 calculate the autocorrelation function?


 This is an adjustable option.  Please read g_hbond -h.

 -Justin

 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 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


-- 
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] autocorrelation function of hydrogen bond : g_hbond

[Nilesh Dhumal]

Hello,

I am calculating the hydrogen bond autocorrelation function using g_hbond
for O-H---O hydrogen bond in system.

I made two groups 1. O-H atoms numbers 2. two oxygen atoms are interacting
with OH bond.

I am using default hydrogen bond criteria (donor-acceptor distance 3.5 and
angle 30) for calculating the autocorrelation function.

I am not getting a smooth exponential plot. I get a small bump in the plot.

Attached the autocorrelation plot.

Why there is not smooth exponential plot.

Nilesh




-- 
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

Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond

[Nilesh Dhumal]

 On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal
 ndhu...@andrew.cmu.eduwrote:

 Hello,

 I am calculating the hydrogen bond autocorrelation function using
 g_hbond
 for O-H---O hydrogen bond in system.

 I made two groups 1. O-H atoms numbers 2. two oxygen atoms are
 interacting
 with OH bond.

 I am using default hydrogen bond criteria (donor-acceptor distance 3.5
 and
 angle 30) for calculating the autocorrelation function.

 I am not getting a smooth exponential plot. I get a small bump in the
 plot.

 Attached the autocorrelation plot.


 Attachments are not allowed on this list. Please provide a link to the
 image.


 Why there is not smooth exponential plot.


 There is no way to tell, and even with the image there is still no way to
 tell. How much sampling do you have? Have you looked at overall
 convergence, etc?


I saved the trajectory at 3fs.

It converged.

Nilesh





 -Justin

 --

 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540)
 231-9080http://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



-- 
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

Re: [gmx-users] autocorrelation function of hydrogen bond : g_hbond

[Nilesh Dhumal]

Is oscillation is because of change in hydrogen bonded distance?

Do program consider the change in hydrogen bonded distance during ACF
calculation?

Nilesh

 There's a known oscillation in the ACF that occurs at ~100 fs or so. Is
 that what you see?

 Erik

 On 9 Apr 2013, at 18:02, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:



 On Tue, Apr 9, 2013 at 11:47 AM, Nilesh Dhumal
 ndhu...@andrew.cmu.eduwrote:

 Hello,

 I am calculating the hydrogen bond autocorrelation function using
 g_hbond
 for O-H---O hydrogen bond in system.

 I made two groups 1. O-H atoms numbers 2. two oxygen atoms are
 interacting
 with OH bond.

 I am using default hydrogen bond criteria (donor-acceptor distance 3.5
 and
 angle 30) for calculating the autocorrelation function.

 I am not getting a smooth exponential plot. I get a small bump in the
 plot.

 Attached the autocorrelation plot.


 Attachments are not allowed on this list. Please provide a link to the
 image.


 Why there is not smooth exponential plot.


 There is no way to tell, and even with the image there is still no way
 to
 tell. How much sampling do you have? Have you looked at overall
 convergence, etc?


 I saved the trajectory at 3fs.

 It converged.

 Nilesh





 -Justin

 --

 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 Department of Biochemistry
 Virginia Tech
 Blacksburg, VA
 jalemkul[at]vt.edu | (540)
 231-9080http://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



 --
 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!
 * 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!
* 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] g_hbond

[Nilesh Dhumal]

Hello,

I am calculating the hydrogen bond life time for my system, ionic liquids.

I am calculating the hydrogen bond life time using g_hbond in Groamcs.

Attached the plot p(t)vs time and the exponential decay is not sooth.

Can you tell why is there is lot of noise.

Nilesh



-- 
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] g_hbond

[Nilesh Dhumal]

Hello,

I am calculating the hydrogen bond life time for my system.

Do program consider the hydrogen bond criteria for calculation of
autocorrelation function?

Nilesh



-- 
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

Re: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current

[Nilesh Dhumal]

Hello,

I run a 500ps simulation and save the trajectory each 3fs.

g_current work till 498ps and later it shows -nan.

Can you tell where is the problem

Nilesh


 Hi,
  Now I've tested the version of g_current in 4.6 and for me it works fine.
 /Flo

 -Ursprüngliche Nachricht-
 Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
 boun...@gromacs.org] Im Auftrag von Florian Dommert
 Gesendet: Mittwoch, 27. Februar 2013 18:46
 An: 'Discussion list for GROMACS users'
 Betreff: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current

  -Ursprüngliche Nachricht-
  Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
  boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
  Gesendet: Mittwoch, 27. Februar 2013 17:38
  An: Discussion list for GROMACS users
  Betreff: Re: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
 
  Hello,
 
  I am using g_current for first time. Now I am running additional
 simulation and I
  will save trajectory at 2 fs.
 
  Is it possible to calculate contribution of rotational and
translation to
 dipole
  moment simultaneously with the simulation instead of saving the
trajectory
 at
  each 2fs?
 

 Hi,

  This is one of my majors on my to do list, but currently not possible.
 I
 think a
 saving frequency of 0.05 ps should be fine.

 /Flo


  Nilesh
 
   Hi,
  
Have you done a similar analysis with another IL system or is it
   the first time you use g_current? Currently I am not able to figure
out what the problem is. However 2ps saving interval is quite long
for such a kind of analysis. A zero value of the translational
dipole moment hints to neutral molecules which should not be the
case for your system. What is written in the output of mj.xvg. Is
filled with zeros?
  
   /Flo
  
  
   -Ursprüngliche Nachricht-
   Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
   boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
   Gesendet: Mittwoch, 27. Februar 2013 15:26
   An: Discussion list for GROMACS users
   Betreff: Re: AW: AW: AW: AW: AW: [gmx-users] g_current
  
   Hello,
  
   Yes. Segfault is solved. I saving velocites and coordinates at 2
 ps.
  
   Nilesh
  
Hi,
   
 At least the segfault is solved. However, the zero output of M_J
for your IL system is really strange. I'm thinking about a
reason, but I am currently not able to find one. How often do
you write out velocities and coordinates in your trr file?
   
/Flo
   
-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
Gesendet: Dienstag, 26. Februar 2013 17:50
An: Discussion list for GROMACS users
Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current
   
Hello,
   
I didn't get any segmental fault if I use Gromacs Version 4.5.5.
   
 g_current -f md.trr -s md.tpr -mc
   
Program didn't write the mc.xvg
   
Average translational dipole moment is zero.
   
Average translational dipole moment M_J [enm] after 15001
frames (|M|^2):
-0.00 -0.00 -0.00 (0.00)
   
Can you tell where is the problem?
   
Nilesh
   
 Hi,
 I am using the release branch of 4.5.

 /Flo

 ---
 Florian Dommert
 Dipl. Phys.

 Institut für Computerphysik
 Universität Stuttgart
 Allmandring 3
 D-70569 Stuttgart

 Tel.: 0711-68563613
 Fax: 0711-68563658


 -Ursprüngliche Nachricht-
 Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
 Gesendet: Montag, 25. Februar 2013 15:35
 An: Discussion list for GROMACS users
 Betreff: Re: AW: AW: AW: [gmx-users] g_current

 Hello,

 Thanks.

 I will update Gromacs version. Can you tell which version
you are using ?

 Nilesh

  Hi,
 
   Can you update your Gromacs version to an actual release
  and check if the problem still occurs. It is very strange
that the Einstein-Helfand fit gives
  0 for sigma and M_J^2.
 
  Cheers,
  Flo
 
  ---
  Florian Dommert
  Dipl. Phys.
 
  Institut für Computerphysik Universität Stuttgart
  Allmandring 3
  D-70569 Stuttgart
 
  Tel.: 0711-68563613
  Fax: 0711-68563658
 
  -Ursprüngliche Nachricht-
  Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
Gesendet: Montag, 25. Februar 2013 14:00
  An: Discussion list for GROMACS users
  Betreff: Re: AW: AW: [gmx-users] g_current
 
  Hello,
 
   I am using Gromacs VERSION 4.0.7.
 
  Nilesh
 
 
   Hi,
  
Which version of gromacs are you using. I am applying
   this tool also to ILs and it works fine for me in the
release-4-5
   branch.
   It is especially strange that you have a rotational
dipole moment of
 zero.
   However, currently I have no idea

Re: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current

[Nilesh Dhumal]

Hello,

I run a 500ps simulation and save the trajectory each 3fs.

g_current work till 498ps and later it shows -nan.

Can you tell where is the problem

Nilesh


 Hi,
  Now I've tested the version of g_current in 4.6 and for me it works fine.
 /Flo

 -Ursprüngliche Nachricht-
 Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
 boun...@gromacs.org] Im Auftrag von Florian Dommert
 Gesendet: Mittwoch, 27. Februar 2013 18:46
 An: 'Discussion list for GROMACS users'
 Betreff: AW: AW: AW: AW: AW: AW: AW: [gmx-users] g_current

  -Ursprüngliche Nachricht-
  Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
  boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
  Gesendet: Mittwoch, 27. Februar 2013 17:38
  An: Discussion list for GROMACS users
  Betreff: Re: AW: AW: AW: AW: AW: AW: [gmx-users] g_current
 
  Hello,
 
  I am using g_current for first time. Now I am running additional
 simulation and I
  will save trajectory at 2 fs.
 
  Is it possible to calculate contribution of rotational and translation
  to
 dipole
  moment simultaneously with the simulation instead of saving the
  trajectory
 at
  each 2fs?
 

 Hi,

  This is one of my majors on my to do list, but currently not possible.
 I
 think a
 saving frequency of 0.05 ps should be fine.

 /Flo


  Nilesh
 
   Hi,
  
Have you done a similar analysis with another IL system or is it
   the first time you use g_current? Currently I am not able to figure
   out what the problem is. However 2ps saving interval is quite long
   for such a kind of analysis. A zero value of the translational
   dipole moment hints to neutral molecules which should not be the
   case for your system. What is written in the output of mj.xvg. Is
   filled with zeros?
  
   /Flo
  
  
   -Ursprüngliche Nachricht-
   Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
   boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
   Gesendet: Mittwoch, 27. Februar 2013 15:26
   An: Discussion list for GROMACS users
   Betreff: Re: AW: AW: AW: AW: AW: [gmx-users] g_current
  
   Hello,
  
   Yes. Segfault is solved. I saving velocites and coordinates at 2
 ps.
  
   Nilesh
  
Hi,
   
 At least the segfault is solved. However, the zero output of M_J
for your IL system is really strange. I'm thinking about a
reason, but I am currently not able to find one. How often do you
write out velocities and coordinates in your trr file?
   
/Flo
   
-Ursprüngliche Nachricht-
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
Gesendet: Dienstag, 26. Februar 2013 17:50
An: Discussion list for GROMACS users
Betreff: Re: AW: AW: AW: AW: [gmx-users] g_current
   
Hello,
   
I didn't get any segmental fault if I use Gromacs Version 4.5.5.
   
 g_current -f md.trr -s md.tpr -mc
   
Program didn't write the mc.xvg
   
Average translational dipole moment is zero.
   
Average translational dipole moment M_J [enm] after 15001 frames
(|M|^2):
-0.00 -0.00 -0.00 (0.00)
   
Can you tell where is the problem?
   
Nilesh
   
 Hi,
 I am using the release branch of 4.5.

 /Flo

 ---
 Florian Dommert
 Dipl. Phys.

 Institut für Computerphysik
 Universität Stuttgart
 Allmandring 3
 D-70569 Stuttgart

 Tel.: 0711-68563613
 Fax: 0711-68563658


 -Ursprüngliche Nachricht-
 Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
 boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
 Gesendet: Montag, 25. Februar 2013 15:35
 An: Discussion list for GROMACS users
 Betreff: Re: AW: AW: AW: [gmx-users] g_current

 Hello,

 Thanks.

 I will update Gromacs version. Can you tell which version you
 are using ?

 Nilesh

  Hi,
 
   Can you update your Gromacs version to an actual release
  and check if the problem still occurs. It is very strange
  that the Einstein-Helfand fit gives
  0 for sigma and M_J^2.
 
  Cheers,
  Flo
 
  ---
  Florian Dommert
  Dipl. Phys.
 
  Institut für Computerphysik Universität Stuttgart
  Allmandring 3
  D-70569 Stuttgart
 
  Tel.: 0711-68563613
  Fax: 0711-68563658
 
  -Ursprüngliche Nachricht-
  Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
  boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
  Gesendet: Montag, 25. Februar 2013 14:00
  An: Discussion list for GROMACS users
  Betreff: Re: AW: AW: [gmx-users] g_current
 
  Hello,
 
   I am using Gromacs VERSION 4.0.7.
 
  Nilesh
 
 
   Hi,
  
Which version of gromacs are you using. I am applying
   this tool also to ILs and it works fine for me in the
   release-4-5
   branch.
   It is especially strange that you have a rotational

Re: AW: [gmx-users] g_current

[Nilesh Dhumal]

Hello,

My system is ionic liquids composed of 128 cation (EMIM) and 128 anion 
(ethyl sulfate). I choose system (0) as index group.

Nilesh

 Hi,

  Can you be a little bit more specific about your system, and what you
 have
 chosen as index groups ?

 /Flo

 ---
 Florian Dommert
 Dipl. Phys.

 Institut für Computerphysik
 Universität Stuttgart
 Allmandring 3
 D-70569 Stuttgart

 Tel.: 0711-68563613
 Fax: 0711-68563658

 -Ursprüngliche Nachricht-
 Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-
 boun...@gromacs.org] Im Auftrag von Nilesh Dhumal
 Gesendet: Samstag, 23. Februar 2013 16:17
 An: gmx-users@gromacs.org
 Betreff: [gmx-users] g_current

 Hello,

 I am calculating the correlation of the rotational and translational
 dipole
 moment of the system using g_current.

 I used following command

 g_current -f md.trr -s md.tpr –mc

 It crashed with segmental fault.
 Last frame  15000 time 3.002
 Prefactor fit E-H: 1 / 6.0*V*k_B*T: 2.45747e-11


 Average translational dipole moment M_J [enm] after 15001 frames
 (|M|^2):
 -0.00 -0.00 -0.00 (0.00)


 Average molecular dipole moment M_D [enm] after 15001 frames (|M|^2):
 -7.281919 17.954138 5.845435 (490.493744)

 

 Absolute values:
  epsilon=2723.718750
  M_D^2 , M_J^2, (M_J*M_D)^2:  (490.493744, 0.00, -0.03)

 


 Fluctuations:
  epsilon=450.336090


  deltaM_D , deltaM_J, deltaM_JD:  (80.947235, 0.00, 0.00)

 

 Static dielectric constant using integral and fluctuations: 450.336090

   M_JM_D  via integral:  -0.000

 ***

 Average volume V=42.031509 nm^3 at T=300.00 K and corresponding
 refactor 1.0 / 3.0*V*k_B*T*EPSILON_0: 5.550975

 Start fit at 98.08 ps (100.00).
 End fit at 398.31 ps (400.00).

 Einstein-Helfand fit to the MSD of the translational dipole moment
 yields:

 sigma=0.
 translational fraction of M^2: 0.
 Dielectric constant using EH: 2723.7188
 Segmentation fault


 Can you whats the problem?

 Nilesh

 --
 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!
 * 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!
* 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] Dipole moment

[Nilesh Dhumal]

Hello,

I am calculating the dipole moment auto-correlation function for my system
which have 128 cation and 128 anion.

I am saving the trajectory at each 2 ps and using this trajectory for
further analysis.

Can I save the dipole moment and three vectors at each 3 fs?



Thanks

Nilesh




-- 
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

Re: [gmx-users] Dipole moment

[Nilesh Dhumal]

In short, I can save dipole moment  with the same frequency, the
trajectory save.

Nilesh




 On 10/18/12 1:45 PM, Javier Cerezo wrote:
 Hi

 The dipole is stored in the edr file, which output frequency is
 controlled by
 nstenergy option in the mdp parameter file. Set it appropriately
 during your
 run (nstenergy=0.003) but keep in mind that it should be a multiple of
 the time
 step.


 nstenergy cannot be set this way; it is an integer indicating the interval
 (in
 number of steps) for writing energy values.  If the values have been saved
 every
 2 ps, there is no way to retrieve them every 3 fs; if more frequent
 information
 is needed, it needs to be saved more frequently.

 -Justin


 El 18/10/12 18:09, Nilesh Dhumal escribió:
 Hello,

 I am calculating the dipole moment auto-correlation function for my
 system
 which have 128 cation and 128 anion.

 I am saving the trajectory at each 2 ps and using this trajectory for
 further analysis.

 Can I save the dipole moment and three vectors at each 3 fs?



 Thanks

 Nilesh






 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 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




-- 
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

Re: [gmx-users] Dipole moment

[Nilesh Dhumal]

In short, I can not save dipole moment directly. I can calculate dipole
moment only using .trr file.

Nilesh

 On 10/18/12 1:45 PM, Javier Cerezo wrote:
 Hi

 The dipole is stored in the edr file, which output frequency is
 controlled by
 nstenergy option in the mdp parameter file. Set it appropriately
 during your
 run (nstenergy=0.003) but keep in mind that it should be a multiple of
 the time
 step.


 nstenergy cannot be set this way; it is an integer indicating the interval
 (in
 number of steps) for writing energy values.  If the values have been saved
 every
 2 ps, there is no way to retrieve them every 3 fs; if more frequent
 information
 is needed, it needs to be saved more frequently.

 -Justin


 El 18/10/12 18:09, Nilesh Dhumal escribió:
 Hello,

 I am calculating the dipole moment auto-correlation function for my
 system
 which have 128 cation and 128 anion.

 I am saving the trajectory at each 2 ps and using this trajectory for
 further analysis.

 Can I save the dipole moment and three vectors at each 3 fs?



 Thanks

 Nilesh






 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 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




-- 
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

Re: [gmx-users] Dipole moment

[Nilesh Dhumal]

How can I save the total dipole moment extacted by .edr file?

I could not find the option in g_energy.

Nilesh


 Justin is right. I've slipped a bit, that was not the way to set
 nstenergy. But still, you can save the dipole directly in the edr file.
 Not from your existing trajectory, but in a new run. Say your dt=1fs,
 then you should set nstenergy=3 to get your dipole moment every 3fs
 which you can retrieve with g_energy.

 Javier


 El 18/10/12 20:43, Nilesh Dhumal escribió:
 In short, I can not save dipole moment directly. I can calculate dipole
 moment only using .trr file.

 Nilesh
 On 10/18/12 1:45 PM, Javier Cerezo wrote:
 Hi

 The dipole is stored in the edr file, which output frequency is
 controlled by
 nstenergy option in the mdp parameter file. Set it appropriately
 during your
 run (nstenergy=0.003) but keep in mind that it should be a multiple of
 the time
 step.

 nstenergy cannot be set this way; it is an integer indicating the
 interval
 (in
 number of steps) for writing energy values.  If the values have been
 saved
 every
 2 ps, there is no way to retrieve them every 3 fs; if more frequent
 information
 is needed, it needs to be saved more frequently.

 -Justin

 El 18/10/12 18:09, Nilesh Dhumal escribió:
 Hello,

 I am calculating the dipole moment auto-correlation function for my
 system
 which have 128 cation and 128 anion.

 I am saving the trajectory at each 2 ps and using this trajectory for
 further analysis.

 Can I save the dipole moment and three vectors at each 3 fs?



 Thanks

 Nilesh




 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 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




 --
 Javier CEREZO BASTIDA
 Ph.D. Student
 Physical Chemistry
 Universidad de Murcia
 30100, Murcia (SPAIN)
 T: (0034)868887434

 --
 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!
* 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

Re: [gmx-users] Dipole moment

[Nilesh Dhumal]

Is it possible to calcualte the dipole moment at 3fs by modifing the
source code?

Nilesh


 How can I save the total dipole moment extacted by .edr file?

 I could not find the option in g_energy.

 Nilesh


 Justin is right. I've slipped a bit, that was not the way to set
 nstenergy. But still, you can save the dipole directly in the edr file.
 Not from your existing trajectory, but in a new run. Say your dt=1fs,
 then you should set nstenergy=3 to get your dipole moment every 3fs
 which you can retrieve with g_energy.

 Javier


 El 18/10/12 20:43, Nilesh Dhumal escribió:
 In short, I can not save dipole moment directly. I can calculate dipole
 moment only using .trr file.

 Nilesh
 On 10/18/12 1:45 PM, Javier Cerezo wrote:
 Hi

 The dipole is stored in the edr file, which output frequency is
 controlled by
 nstenergy option in the mdp parameter file. Set it appropriately
 during your
 run (nstenergy=0.003) but keep in mind that it should be a multiple
 of
 the time
 step.

 nstenergy cannot be set this way; it is an integer indicating the
 interval
 (in
 number of steps) for writing energy values.  If the values have been
 saved
 every
 2 ps, there is no way to retrieve them every 3 fs; if more frequent
 information
 is needed, it needs to be saved more frequently.

 -Justin

 El 18/10/12 18:09, Nilesh Dhumal escribió:
 Hello,

 I am calculating the dipole moment auto-correlation function for my
 system
 which have 128 cation and 128 anion.

 I am saving the trajectory at each 2 ps and using this trajectory
 for
 further analysis.

 Can I save the dipole moment and three vectors at each 3 fs?



 Thanks

 Nilesh




 --
 

 Justin A. Lemkul, Ph.D.
 Research Scientist
 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




 --
 Javier CEREZO BASTIDA
 Ph.D. Student
 Physical Chemistry
 Universidad de Murcia
 30100, Murcia (SPAIN)
 T: (0034)868887434

 --
 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!
 * 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!
* 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] g_dipole

[Nilesh Dhumal]

Hello,

I am calculating the dipole moment auto-correlation function for my system
which have 128 cation and 128 anion.

Due to the PBC, the function of the total dipole moment in time is not
continuous.

Can I removed PBC for g_dipole?



Thanks

Nilesh


-- 
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] g_velacc

[Nilesh Dhumal]

Hello,

I am calculating the velocity auto-correlation function for my system
which have 128 cation and 128 anion.

How the program calculate the total velocity auto-correlation function?

Does it average the velocity over all atoms at each time step?

Thanks

Nilesh

-- 
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] PBC

[Nilesh Dhumal]

Hello,

I have question about periodic boundary condition. Suppose if one atom is
going out of the box (x axis distance is more than L/2) and it will come
inside the box from other side (distance-L).
Distance before the pbc  should be same or it will be different from center.

Thanks

Nilesh


-- 
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] grompp error

[Nilesh Dhumal]

Hello,



I am doing solvation dynamics for my system.


 When I am running grompp command I get  the error.

grompp -f md.mdp  -c  solvent-bmi-pf6-128.pdb   -p 
solvent-bmi-pf6-128.top  -o md-rerun.tpr


Fatal error:
No such combination rule 0

I using Gromacs VERSION 4.0.5.


What this error means?

Thanks

NIlesh




-- 
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] (no subject)

[Nilesh Dhumal]

Hello,

 I am doing solvation dynamics for my system.
 I have system with diatomic (PA---NE)solute surrounded by water molecules.

 I am running simulation for two differcent cases.
 1. PA charge=0 and NE charge=0 : No charge on solute

 2. PA charge=+1 and NE charge=-1 : Charge on solute

For second case I am using rerun option to calculate the energy with
charge for same configuration.


grompp -f md.mdp  -c  solvent-bmi-pf6-128.pdb   -p 
solvent-bmi-pf6-128.top  -o md-rerun.tpr
/opt/mpich_intel/ch-p4/bin/mpirun -machinefile cp -np 2 
/usr/local/gromacs/bin/mdrun_mpi  -s md-rerun.tpr  -o md-rerun.trr -c
solvent-bmi-pf6-128.pdb -e md-rerun.edr -rerun md.trr  -g md-rerun.log


The total energy difference between change and neutal is large around ~350
kj/mole. It should be around 30 kJ /mole.


Can you tell why I getting large high energy differmece.


I using Gromacs VERSION 4.0.5.

NIlesh


-- 
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] g_hbond

[Nilesh Dhumal]

Hello,

How can I add chlorin atom as a acceptor in g_hbond.

I am using  Gromacs VERSION 4.0.7

NIlesh




-- 
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] Graphene - force field

[Nilesh Dhumal]

Hello,

I am trying to run simulation of graphene oxide.  I have 16 carbon atoms
of same type. I am using opls force field.  could make the .itp file and
pasted here

[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
opls_071  CG  6  12.01100  0.00   A  3.5e-01 2.92880e-01
opls_072  CO  6  12.01100  0.265  A  3.5e-01 3.59824e-01
opls_116  OH  8  15.99940 -0.683  A  3.12000e-01 7.11280e-01
opls_117  HO  1  1.00800   0.418  A  0.0 0.0


[ bondtypes ]
; ij  func   b0  kb
  COOH  10.14100   133888.0
  OHHO  10.09600   231375.0
  CGCG  10.14000   392459.2   ; TRP,TYR,PHE
  CGCO  10.14000   392459.2   ; TRP,TYR,PHE


[ angletypes ]
;  ijk  func   th0   cth
  CG CO OH  190.000292.880
  CO OH HO  1   108.500230.120
  CG CG CG  1   120.000527.184  ; TYR(OL)


[ dihedraltypes ]
;  ijkl   func coefficients
; OPLS Fourier function (func=5)
CJ CJ CJ CJ  3 30.33400   0.0 -30.33400   0.0 
 0.0   0.0 ;
  CG CO OH HO  3  0.0   0.0   6.27600   0.0
  CG CG CO OH  3  7.15882  -2.09200   2.77399   0.0

My question how can I step for the parameters ffoplsaa.rtp file. I made
the parameters as follow

 [ SMA  ]
 [ atoms ]
CG  opls_071 0.00   1
CG  opls_071 0.00   1
CG  opls_071 0.00   1
CG  opls_071 0.00   1
CO  opls_072 0.265  2
CG  opls_071 0.00   1
CG  opls_071 0.00   1
CO  opls_072 0.265  2
CG  opls_071 0.00   1
CG  opls_071 0.00   1
CG  opls_071 0.00   1
CG  opls_071 0.00   1
CG  opls_071 0.00   1
CG  opls_071 0.00   1
CG  opls_071 0.00   1
CG  opls_071 0.00   1
OH  opls_116-0.683  3
HO  opls_117 0.000  4
OH  opls_116-0.683  3
HO  opls_117 0.000  4

 [ bonds ]
CG CG
CG CO
CO OH
OH HO


I am geting trouble to create .top file using pdb2gmx.

Can you tell how to set up force field parameter for graphene.

I am usinng Gromacs  VERSION 4.0.7.

Thanks

Nilesh


-- 
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] dihedral angle

[Nilesh Dhumal]

Hello,

I am trying to calculate the dihedral angle between four points.

I considered two planes (ABC  BCD) and calculate the dot products of two
normals (n1 and n2)to these plane.

theta=cos-1(n1.n2)

I compared theeta values of dihedral angle with ampac and some values are
negative. I am geting all positive value.

Any one knows how to calculate sign of dihedral angle.

Thanks

Nilesh











-- 
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

Re: [gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

Justin,

I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
atoms).


1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx  -o
4-600.xtc
here I choose group 0:system (3328 atoms)

2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o 4-600-1.xtc

 For Centering I choose group: solute (26 atoms)
 For output I choose group : Solvent (3302 atoms)


3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb

Here I choose the group: 0 (system).

I am geting for error for last command.

Fatal error:
Index[3302] 3303 is larger than the number of atoms in the trajectory file
(3302).

It look that there are no solute atoms in trajectory file.

Nilesh


On Mon, October 17, 2011 7:25 am, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Hello,


 I have system with solute is surrounded by 256 solvent molecules. I run
  the simulation for 20 ns. I save the snap shot at 500 ps using
 following command.

 trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc
 nojump -center   -o 500-11.pdb

 I tried to keep the solute at the center box. In visualization, the
 solute is not at center , its close to box edges.

 How can I keep the solute at the center.




 You're doing too many things at once.  Split the trjconv operation:


 1. Run trjconv -pbc mol on the whole trajectory
 2. Run trjconv -center on the output of (1)
 3. Run trjconv -dump 500 on the output of (2)


 -Justin


 I am using Gromacs 4.0.7 version.


 Thanks


 Nilesh












 --
 


 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





-- 
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

Re: [gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

In 2nd step I choose system instaed of solvent.

 I could not make the solute at the center.

Thanks
NIlesh

On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Justin,


 I have 26 solute atoms and 3302 solvent atoms in my sytems (total 3328
 atoms).


 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n 500-1.ndx
 -o
 4-600.xtc
 here I choose group 0:system (3328 atoms)

 2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o 4-600-1.xtc


 For Centering I choose group: solute (26 atoms)
 For output I choose group : Solvent (3302 atoms)



 3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb


 Here I choose the group: 0 (system).


 I am geting for error for last command.


 Fatal error:
 Index[3302] 3303 is larger than the number of atoms in the trajectory
 file (3302).


 It look that there are no solute atoms in trajectory file.



 In step 2, you chose to save only the solvent.


 -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





-- 
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

Re: [gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

Thanks Justin,

Still solute is not at center.

Nilesh


On Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 In 2nd step I choose system instaed of solvent.


 I could not make the solute at the center.



 Don't use -b and -e when running trjconv.  I have found that PBC routines
 are not always correctly applied when parsing out sections of the
 trajectory.  This can affect your ability to center the molecule.

 -Justin


 Thanks
 NIlesh


 On Mon, October 17, 2011 11:05 am, Justin A. Lemkul wrote:


 Nilesh Dhumal wrote:


 Justin,



 I have 26 solute atoms and 3302 solvent atoms in my sytems (total
 3328
 atoms).


 1. trjconv -f 3.trr -s 3.tpr -pbc mol -b 400 -e 600 -dt 1 -n
 500-1.ndx
 -o
 4-600.xtc
 here I choose group 0:system (3328 atoms)

 2. trjconv -f 4-600.xtc -s 3.tpr  -n 500-1.ndx -center  -o
 4-600-1.xtc



 For Centering I choose group: solute (26 atoms)
 For output I choose group : Solvent (3302 atoms)




 3. trjconv -f 4-600-1.xtc -s 3.tpr  -dump 500  -o 500-11.pdb



 Here I choose the group: 0 (system).



 I am geting for error for last command.



 Fatal error:
 Index[3302] 3303 is larger than the number of atoms in the
 trajectory file (3302).


 It look that there are no solute atoms in trajectory file.



 In step 2, you chose to save only the solvent.



 -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








 --
 


 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





-- 
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

Re: [gmx-users] trjconv:solute at the center

[Nilesh Dhumal]

Ya, I want to center solute w.r.t to the solvent.

I have more question, if I want to save the coordinates of a snapshot with
no pbc effect, can I use -pbc nojump in trjconv.

nilesh

On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote:
 Hey :)


 The reference plays no role in centering. But I guess that Nilesh expects
  centering of the solute w.r.t. to the solvent, or is looking at the
 wrong center (tric/rect).

 Cheers,


 Tsjerk


 On Oct 17, 2011 7:06 PM, Justin A. Lemkul jalem...@vt.edu wrote:


 Nilesh Dhumal wrote:   Thanks Justin,   Still solute is not at
 center. 

 Is your reference frame (i.e. the .tpr file) centered?  If not, centering
  likely won't work as desired.  I assumed that it was centered, per
 normal system building procedures.

 -Justin


 NileshOn Mon, October 17, 2011 11:27 am, Justin A. Lemkul wrote:
 

 Nilesh Dhumal wrote...

 --
 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!
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] box dimension

[Nilesh Dhumal]

Hello,

I have saved the coordinates of snapshot from trajectory in pdb file.

The dimesnion of box in pdb file are
32.805   32.805   32.805  90.00  90.00  90.00 P 1

I am trying to find  atoms close to center of box.

there are  atoms whose distance from center is more that ~17 A. My center
coordinates are 0.0 0.0 0.0.

How is it possible?

I am using Gromacs 4.0.7 version.

Thanks

Nilesh











-- 
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

Re: [gmx-users] box dimension

[Nilesh Dhumal]

I used -pbc nojump to remove pbc effect.

 trjconv 3.trr  -s 3.tpr -pbc nojump -o 500-11.pdb

Basically I want to find the conformer close to center of box.

Nilesh

On Mon, October 17, 2011 6:36 pm, Mark Abraham wrote:
 On 18/10/2011 7:05 AM, Nilesh Dhumal wrote:

 Hello,


 I have saved the coordinates of snapshot from trajectory in pdb file.


 The dimesnion of box in pdb file are
 32.805   32.805   32.805  90.00  90.00  90.00 P 1


 I am trying to find  atoms close to center of box.


 there are  atoms whose distance from center is more that ~17 A. My
 center coordinates are 0.0 0.0 0.0.

 How is it possible?


 Molecules diffuse across periodic boundaries during the simulation.
 While computing interactions, mdrun corrects for periodicity on the fly,
 but does not trouble itself to guess what manner of post-processing you
 would like to do. There is a suggested trjconv workflow on the the GROMACS
 website. I suggest you try it.

 Mark
 --
 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!
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] trjconv:solute at the center

[Nilesh Dhumal]

Hello,

I have system with solute is surrounded by 256 solvent molecules. I run
the simulation for 20 ns. I save the snap shot at 500 ps using following
command.

trjconv -f 3.trr -s 3.tpr -n 500-1.ndx -b 500.0 -e 501.0 -dt 1.0 -pbc
nojump -center   -o 500-11.pdb

I tried to keep the solute at the center box. In visualization, the solute
is not at center , its close to box edges.

How can I keep the solute at the center.


I am using Gromacs 4.0.7 version.

Thanks

Nilesh










-- 
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

Re: [gmx-users] snap shot

[Nilesh Dhumal]

Hello,

How can I save the coordinates  (in pdb or xyz format) for a particular
snap shot.

Nilesh

On Sat, October 8, 2011 10:06 am, lina wrote:
 On Sat, Oct 8, 2011 at 2:21 AM, Nilesh Dhumal
 ndhu...@andrew.cmu.eduwrote:


 Hello,


 I have a system with 128 emi (cations) and 128 Cl (anions). I run the
 simulation for 20 ns.

 I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.


 trjconv  use -dt 5000


 I don't want to save snap shot for 128 ion-pairs. How can I take
 average over 128 ion pairs and save snap shot for a single ion pair.

 I don't understand the average mean here?
 if you wanna get the average.pdb in some time interval try g_rmsf -ox  -b
 -e


 you may wait for some other better answers.


 Basically I want to use classical md geometry for quatum chemical
 calculation.

 I am using Gromacs 4.0.7 version.


 Thanks


 Nilesh










 --
 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!
 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!
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] snap shot

[Nilesh Dhumal]

Hello,

I have a system with 128 emi (cations) and 128 Cl (anions). I run the
simulation for 20 ns.

I want to save snap-shot at 5ns, 10ns, 15ns and 20ns.

I don't want to save snap shot for 128 ion-pairs. How can I take average
over 128 ion pairs and save snap shot for a single ion pair.

Basically I want to use classical md geometry for quatum chemical
calculation.

I am using Gromacs 4.0.7 version.

Thanks

Nilesh









-- 
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] g_rdf

[Nilesh Dhumal]

Hello,

I run a 5ns simulation for a single glucose molecule in gas phase.

I tried to plot radial distribution function for O---H intramolecular
interactions using following command.

g_rdf -f 6.trr -s 6.tpr -n index -o

In rdf.xvg file there is no data.

Can you tell what could be the reason.


I am using Gromacs 4.0.7 version.


Thanks

Nilesh












-- 
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] constraints on angle

[Nilesh Dhumal]

Hello,

How can I put constraints on an angle.

I added following lines in .top file

[ constraints ]

2   8   18  3   109.5

But its giving error.


How can I put constraints on an angle.



I am using Gromacs 4.0.7 version.


Thanks

Nilesh











-- 
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] Velocity of atom

[Nilesh Dhumal]

Hello,

How can I print/calculate on velocity of a atom.


I am using Gromacs 4.0.7 version.


Thanks

Nilesh










-- 
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] (no subject)

[Nilesh Dhumal]

Hello,

Using g_velacc I can calculate the velocity autocorrelation function of a
group.

Can I calculate the speed of a group instead of velocity ?

I am using Gromacs 4.0.7 version.


Thanks

Nilesh









vac.pdf
Description: Adobe PDF document
-- 
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] Velocity autocorrelation function

[Nilesh Dhumal]

Hello,

Using g_velacc I can calculate the velocity autocorrelation function of a
group as a vector.

Can I calculate the velocity autocorrelation function as a scalar?

I am using Gromacs 4.0.7 version.


Thanks

Nilesh









-- 
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] (no subject)

[Nilesh Dhumal]

Hello,

I want to simulate system with 128 ionic liquids (128 cation+128 anion).

I have made a pdb file with a single ionic liquids ion pairs.

How can I genrate 128 ion pairs using single ion pair .pdb file.


I am using Gromacs 4.0.7 version.


Thanks

Nilesh









vac.pdf
Description: Adobe PDF document
-- 
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] g_velacc

[Nilesh Dhumal]

Hello,

I am calculating the velocity autocorrelation function for my
system. I have to calculate the g_velacc for 5 different groups within
system. I have  made the index file.

I have also written .sh script

 g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o
h20-vac.xvg
24
 g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o
h21-vac.xvg
25
 g_velacc -f 6.trr -s 6.tpr -n glu-emi-dmp-128-no.ndx -nonormalize -o
h24-vac.xvg
26

How can I select the group. In the above script  24, 25, 26 are the group
numbers in index file.



I am using Gromacs 4.0.7 version.


Thanks

Nilesh









vac.pdf
Description: Adobe PDF document
-- 
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] g_velacc

[Nilesh Dhumal]

Hello,

I am trying to calculate the velocity autocorrelation function for my
system. I have a system with glucose + ionic liquids (128 emi (cations)
and 128 Cl (anions)).

I am not getting proper velocity autocorrelation function.

 g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize  -e 10 -o


Attached the velocity autocorrelation function.


I am using Gromacs 4.0.7 version.


Thanks

Nilesh









vac.pdf
Description: Adobe PDF document
-- 
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] g_velacc

[Nilesh Dhumal]

Hello,

I am trying to calcualte the velocity autocorrelation function for my
system. I have a system with glucose + ionic liquids (128 emi (cations)
and 128 Cl (anions)).

I am not geting proper velocity autocorrelation function.

 g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize  -e 10 -o


Attached the velocity autocorrelation function.


I am using Gromacs 4.0.7 version.


Thanks

Nilesh









vac.pdf
Description: Adobe PDF document
-- 
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] g_velacc

[Nilesh Dhumal]

Hello,

I am trying to calcualte the velocity autocorrelation function for my
system. I have a system with glucose + ionic liquids (128 emi (cations)
and 128 Cl (anions)).

I am not geting proper velocity autocorrelation function.

 g_velacc -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -nonormalize  -e 10 -o


Attached the velocity autocorrelation function.


I am using Gromacs 4.0.7 version.


Thanks

Nilesh









vac.pdf
Description: Adobe PDF document
-- 
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] g_dist

[Nilesh Dhumal]

Hello,

I have a system with 128 emi (cations) and 128 Cl (anions).

I want to calculate how many CL atoms are in cutoff distance relative to
hydorgen aotm of cation.  I considered all CL atoms are distinguishable.

Basically I want to calcualte the distance between each CL atom and
correponing hydorgen and registered those CL atoms which are whthin
cutoff.

How can I do ?

I am using Gromacs 4.0.7 version.

Thanks

Nilesh








-- 
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] rdf

[Nilesh Dhumal]

Hello,

I have a system with 128 emi (cations) and 128 Cl (anions).

I want to study is there any bifurcated interaction between hydrogen of
cation and CL atoms or CL atom interacting with 2 different hydrogen of
cation.

For this I considered all CL atoms are distinguishable.

I am thinking to run rdf between each hydrogen and each cl atom (RDF 128
times).

In my index file I made 3 groups for 3 different hydrogen and 128 groups
for 128 cl atoms.

I have to run 128 * 3 = 384 times rdf

Is this the correct way? Is there any other easier way to do this?

I am using Gromacs 4.0.7 version.

Thanks

Nilesh







-- 
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

Re: [gmx-users] Lennard Jones interactions

[Nilesh Dhumal]

If eplilon of hydrogen atom is zero then the lennard jones interaction of
OH bond (at 0.22nm)is also zero.
Is it correct?

I used equation 4.5 to calculate LJ energy.

Nilesh

On Fri, June 10, 2011 2:47 pm, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Hello,


 How can I calculate Lennard Jones interaction for two selected atoms
 with a specific distance?


 Using energygrps might be an option if you need to monitor the
 interaction over time.  Otherwise, if the distance is fixed, just plug all
 the parameters into the LJ equation.  In theory, you could calculate the
 interactions this way over time, as well, even if the distance changes.

 -Justin


 I am using Gromacs 4.0.7 version.


 Thanks


 Nilesh








 --
 


 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





-- 
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

Re: [gmx-users] Lennard Jones interactions

[Nilesh Dhumal]

Basically I want to calculate LJ interaction for OH bond.

If I use eq. 4.5 in manual to calculate LJ interaction then zero.

How can I calculate LJ interaction of a bond?

Nilesh

On Fri, June 10, 2011 3:00 pm, Andrew Paluch wrote:
 The LJ interaction is 0. But you're asking about a bond. 1-2
 interactions are typically modeled with a harmonic potential. This is most
 definitely not zero.


 On Jun 10, 2011, at 2:54 PM, Nilesh Dhumal wrote:


 If eplilon of hydrogen atom is zero then the lennard jones
 interaction of OH bond (at 0.22nm)is also zero.
 Is it correct?


 I used equation 4.5 to calculate LJ energy.


 Nilesh


 On Fri, June 10, 2011 2:47 pm, Justin A. Lemkul wrote:




 Nilesh Dhumal wrote:


 Hello,



 How can I calculate Lennard Jones interaction for two selected
 atoms with a specific distance?


 Using energygrps might be an option if you need to monitor the
 interaction over time.  Otherwise, if the distance is fixed, just plug
 all the parameters into the LJ equation.  In theory, you could
 calculate the interactions this way over time, as well, even if the
 distance changes.

 -Justin



 I am using Gromacs 4.0.7 version.



 Thanks



 Nilesh









 --
 



 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






 --
 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!
 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!
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] (no subject)

[Nilesh Dhumal]

Hello,

I want to calculate velocity autocorrelation function using 50 ps
production trajectory.

I have trajectory of 20 ns.

I want to take 50 ps average over 20 ns trajectory to  improve my result.

How can do this average.

I am using Gromacs 4.0.7 version.

Thanks

Nilesh





-- 
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] g_dipoles + tpbconv

[Nilesh Dhumal]

Hello,

I have a system with a glucose molecule.

I want to calculate the dipole moment of a particular OH in glucose
molecule.I made an index file which have a group containing atoms.

[ O8 ]
  8   18

10 is oxygen no. and 20 is hydroen no.



But, if I try to use g_dipoles to get the dipole moment contribution from 
using following command:

g_dipoles -f 6.trr -s 6.tpr  -n index.ndx -corr mol -nonormalize  -c

I get the following error.

Fatal error:
index[1]=8 does not correspond to the first atom of a molecule

I read on gmx-users mailing list.

http://www.mail-archive.com/gmx-users@gromacs.org/msg40091.html

Calculating a dipole moment of a possibly-charged species requires that
there be a reference point, which is conventionally the center of mass of
the molecule. This means all the atoms of the molecule have to be known,
and g_dipoles assumes the index group consists of whole molecules.

So to do the partition you want, you will need to provide the same
molecules, but with zero charges. That will mean making a copy of your
.top and hacking those charges to zero to generate a new such .tpr.

Actually, tpbconv has the ability to set the charges of a group in a .tpr
to zero.

So I tried

tpbconv -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -e 6.edr  -o zero.tpr

I got the error

segmentataion fault

How can I solve this problem to calcualte the dipole moment of a bond?

I am using gromacs version 4.0.7.

Thanks

Nilesh






-- 
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

Re: [gmx-users] Re: g_velacc

[Nilesh Dhumal]

20 is hydrogen atom.
Sorry its typing mistake.

Nilesh

On Fri, May 27, 2011 3:52 am, Vitaly Chaban wrote:


 Hello,


 I have calculated the velocity autocorrelation function of OH bond
 in glucose molecule. For this calculation I modified the index file. The
  modified part is pasted below.

 [ O10 ]
  10   20


 10 is oxygen no. and 20 is oxygen.


 I used following command to calculate the velocity autocorrelation
 function.

  g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o



 My question is how does the prog. calculate the velocity autocorrlation
  function.

 Does is subtract the velocity of hydrogen from oxygen and then
 calculate the autocorrelation function?



 The program acts as if your hydrogen and oxygen are identical atoms.



 --
 Dr. Vitaly V. Chaban, Department of Chemistry
 University of Rochester, Rochester, New York 14627-0216
 --
 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!
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

Re: [gmx-users] g_velacc

[Nilesh Dhumal]

I am  calculating OH stretching frequency by fourier transform of velocity
autocorrelation function.

I could calculate the OH stretching frequnecy by calculating fourier
transform of OH bond.

I want to know how gromacs calculate the velocity autocorrelation function
of a bond (If I define a bond in index file).

Does is subtract the velocity of hydrogen from oxygen and then
calculate the autocorrelation function?

Nilesh




On Fri, May 27, 2011 2:37 am, David van der Spoel wrote:
 On 2011-05-26 22.48, Nilesh Dhumal wrote:

 Hello,


 I have calculated the velocity autocorrelation function of OH bond
 in glucose molecule. For this calculation I modified the index file. The
  modified part is pasted below.

 [ O10 ]
 10   20


 where is the hydrogen? g_velacc knows nothing about bonds just atoms.


 10 is oxygen no. and 20 is oxygen.


 I used following command to calculate the velocity autocorrelation
 function.

 g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o


 My question is how does the prog. calculate the velocity autocorrlation
  function.

 Does is subtract the velocity of hydrogen from oxygen and then
 calculate the autocorrelation function?

 I am using gromacs version 4.0.7.


 Thanks


 Nilesh








 --
 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!
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

Re: [gmx-users] Re: g_velacc

[Nilesh Dhumal]

How can I calculate the velocity autocorrelation function of a bond with
Gromacs?

Nilesh



On Fri, May 27, 2011 8:32 am, Vitaly Chaban wrote:
 As I said before, g_velacc treats all the atoms in your index file as
 if they were identical. It does NOT subtract anything.




 On Fri, May 27, 2011 at 8:19 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu
 wrote:

 I am  calculating OH stretching frequency by fourier transform of
 velocity autocorrelation function.

 I could calculate the OH stretching frequnecy by calculating fourier
 transform of OH bond.

 I want to know how gromacs calculate the velocity autocorrelation
 function of a bond (If I define a bond in index file).

 Does is subtract the velocity of hydrogen from oxygen and then
 calculate the autocorrelation function?

 Nilesh



 On Fri, May 27, 2011 8:11 am, Vitaly Chaban wrote:

 It does not change the situation, I believe.



 What is the sense of calculating such ACF? In order to understand the
  cross-correlation between the bonded atoms? It will be huge as I
 understand.


 --
 Dr. Vitaly V. Chaban, Department of Chemistry
 University of Rochester, Rochester, New York 14627-0216






 On Fri, May 27, 2011 at 8:07 AM, Nilesh Dhumal
 ndhu...@andrew.cmu.edu
 wrote:


 20 is hydrogen atom.
 Sorry its typing mistake.



 Nilesh



 On Fri, May 27, 2011 3:52 am, Vitaly Chaban wrote:




 Hello,




 I have calculated the velocity autocorrelation function of OH
 bond in glucose molecule. For this calculation I modified the
 index file. The
  modified part is pasted below.



 [ O10 ]
  10   20




 10 is oxygen no. and 20 is oxygen.




 I used following command to calculate the velocity
 autocorrelation function.

  g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize
  -o





 My question is how does the prog. calculate the velocity
 autocorrlation  function.


 Does is subtract the velocity of hydrogen from oxygen and then
 calculate the autocorrelation function?



 The program acts as if your hydrogen and oxygen are identical
 atoms.




 --
 Dr. Vitaly V. Chaban, Department of Chemistry
 University of Rochester, Rochester, New York 14627-0216
 --
 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_Lis










 --
 Dr. Vitaly V. Chaban, Department of Chemistry
 University of Rochester, Rochester, New York 14627-0216





-- 
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

Re: [gmx-users] g_velacc

[Nilesh Dhumal]

How can I calculate the velocity autocorrelation function of a bond with
Gromacs?

Nilesh



On Fri, May 27, 2011 8:31 am, David van der Spoel wrote:
 On 2011-05-27 14.26, Nilesh Dhumal wrote:

 I am  calculating OH stretching frequency by fourier transform of
 velocity autocorrelation function.

 I could calculate the OH stretching frequnecy by calculating fourier
 transform of OH bond.

 I want to know how gromacs calculate the velocity autocorrelation
 function of a bond (If I define a bond in index file).

 Does is subtract the velocity of hydrogen from oxygen and then
 calculate the autocorrelation function?

 No, see below! There is no tool that does exactly what you want, however
 doing the velacc of just the hydrogen will come close.
 Nilesh





 On Fri, May 27, 2011 2:37 am, David van der Spoel wrote:

 On 2011-05-26 22.48, Nilesh Dhumal wrote:


 Hello,



 I have calculated the velocity autocorrelation function of OH bond
 in glucose molecule. For this calculation I modified the index file.
 The
 modified part is pasted below.

 [ O10 ]
 10   20



 where is the hydrogen? g_velacc knows nothing about bonds just atoms.



 10 is oxygen no. and 20 is oxygen.



 I used following command to calculate the velocity autocorrelation
 function.

 g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o


 My question is how does the prog. calculate the velocity
 autocorrlation function.

 Does is subtract the velocity of hydrogen from oxygen and then
 calculate the autocorrelation function?

 I am using gromacs version 4.0.7.



 Thanks



 Nilesh









 --
 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








 --
 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!
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] g_velacc

[Nilesh Dhumal]

Hello,

I have calculated the velocity autocorrelation function of OH bond
in glucose molecule. For this calculation I modified the index file. The
modified part is pasted below.

[ O10 ]
  10   20

10 is oxygen no. and 20 is oxygen.

I used following command to calculate the velocity autocorrelation function.

 g_velacc -f 6.trr -s 6.tpr  -n index.ndx -e 100 -nonormalize  -o


My question is how does the prog. calculate the velocity autocorrlation
function.

Does is subtract the velocity of hydrogen from oxygen and then calculate
the autocorrelation function?

I am using gromacs version 4.0.7.

Thanks

Nilesh





-- 
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

Re: [gmx-users] dipole moment

[Nilesh Dhumal]

I want to see the change in dipole moment alond the simulation.


NIlesh

On Wed, May 25, 2011 11:32 am, David van der Spoel wrote:
 On 2011-05-25 17.14, Nilesh Dhumal wrote:

 Hello,


 Can I calculate a dipole moment of a particular bond?

 It is easier to do it manually. Otherwise g_dipoles with a suitable
 index file would do it. The sum of charges has to be zero of course.

 I am using gromacs version 4.0.7.


 Thanks


 Nilesh






 --
 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!
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

Re: [gmx-users] dipole moment

[Nilesh Dhumal]

Thanks for reply.

Here are more details about my simulation.

I have glucose molecule in my system. I am interested in change in dipole
moment of OH bond of glucose along the simulation.

I have made the index file.

How can I select two groups (oxygen and hydrogen) or should I put
particular oxygen and hydrogen in same group (manually).

Nilesh

On Wed, May 25, 2011 11:59 am, David van der Spoel wrote:
 On 2011-05-25 17.36, Nilesh Dhumal wrote:

 I want to see the change in dipole moment alond the simulation.

 g_dipoles -h



 NIlesh


 On Wed, May 25, 2011 11:32 am, David van der Spoel wrote:

 On 2011-05-25 17.14, Nilesh Dhumal wrote:


 Hello,



 Can I calculate a dipole moment of a particular bond?


 It is easier to do it manually. Otherwise g_dipoles with a suitable
 index file would do it. The sum of charges has to be zero of course.

 I am using gromacs version 4.0.7.



 Thanks



 Nilesh







 --
 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








 --
 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!
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

Re: [gmx-users] dipole moment

[Nilesh Dhumal]

Basically I want to calculate the stretching vibration of the bond by
fourier transfrom of dipole momenet autocorrelation fucntion or velocity
autocorrelation function.

Before going for vibration I wanted to check the fluctuation of dipole
moment along the simulation.


Can I calculate the velocity autocorrelation function for a bond.

Nilesh

On Wed, May 25, 2011 12:37 pm, David van der Spoel wrote:
 On 2011-05-25 18.03, Nilesh Dhumal wrote:

 Thanks for reply.


 Here are more details about my simulation.


 I have glucose molecule in my system. I am interested in change in
 dipole moment of OH bond of glucose along the simulation.

 The OH group is not neutral so your dipole is meaningless (position
 dependent).

 Otherwise the charges are constant and the fluctuation in bond length
 (if you have a flexible molecule) will be small, or zero with
 constraints. You should think what you want to get out. What experiment you
 want to compare to.

 I have made the index file.


 How can I select two groups (oxygen and hydrogen) or should I put
 particular oxygen and hydrogen in same group (manually).

 Nilesh


 On Wed, May 25, 2011 11:59 am, David van der Spoel wrote:

 On 2011-05-25 17.36, Nilesh Dhumal wrote:


 I want to see the change in dipole moment alond the simulation.


 g_dipoles -h



 NIlesh



 On Wed, May 25, 2011 11:32 am, David van der Spoel wrote:


 On 2011-05-25 17.14, Nilesh Dhumal wrote:



 Hello,




 Can I calculate a dipole moment of a particular bond?



 It is easier to do it manually. Otherwise g_dipoles with a
 suitable index file would do it. The sum of charges has to be zero
 of course.

 I am using gromacs version 4.0.7.




 Thanks




 Nilesh








 --
 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









 --
 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








 --
 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!
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] g_velacc

[Nilesh Dhumal]

Hello,

I am trying to calculate the velocity autocorrelation function of OH bond
in glucose molecule.

The calculate velocity autocorrelation function is not smooth. Its
fluctuating a lot so I am geting wide/think line.

Why I am not geting a smooth line?

I am using gromacs version 4.0.7.

Thanks

Nilesh




-- 
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] g_sdf

[Nilesh Dhumal]

Hello,

I have a system with glucose + ionic liquids (cation + anion).

I am trying calculate distribution of cation and anion around glucose
molecule using g_sdf. I want to plot distribution of cation and anion is
same figure. I run the following command

g_sdf -f 3.trr -s 3.tpr -n glu-emi-dmp-128-no.ndx -mode 2 -o -r

I selected two atoms from glucose and 3rd and 4th groups are cation and
anion respectively.

All the coordinates in  refmol.gro are zero.

I am using gromacs version 4.0.7.

Why all the coordinates in  refmol.gro are zero.

Thanks

Nilesh



-- 
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

Re: [gmx-users] Re: water dimer is gas phase

[Nilesh Dhumal]

I used the same topology file to run 256 water molecules simulation and I
got the proper result (compared with reported one).

 The problem is to visualize the trajectory in VMD since gromacs fails to
write valid pdb files when the coordinates are too large.

Nilesh


On Fri, May 20, 2011 5:22 am, Erik Marklund wrote:
 Justin A. Lemkul skrev 2011-05-19 22.42:



 Vitaly Chaban wrote:

 For vacuum systems, pbc = no in conjunction with zero cutoffs is
 correct to obtain a gas-phase system.


 For reasonably large box, this is the same heck.



 Setting a box size and using pbc = xyz precludes the use of infinite
 cutoffs, which should be the most rigorously correct way to treat this
 type of system. With PBC, there are long-range effects that should be
 avoided.

 Nilesh: visualize your system, using VMD or ngmx. The behavior of
 your molecular cluster during the first ps will provide an answer. Are
 you sure that your topology is healthy?


 I agree with this.  The system should be going absolutely haywire :)


 -Justin


 Yes, this is a good test, and the topology should be inspected. However,
 the observed result is expected for this system. A water dimer coupled to a
 thermostat will dissociate eventually (pretty rapidly) at 300 K. The water
 molecules themselves seem intact. The problem with visualization comes
 from the fact that gromacs fails to write valid pdb files when the
 coordinates are too large. I called this a bug on the developer list one
 or two years ago since this generates pdb files that gromacs itself can't
 read, but the other developers didn't catch on. You can postprocess the
 pdb and cap the coordinates so that they're confined to the range that the
 pdb format allows, but note that this will mess up the water moleucles as
 they get very far apart.

 Erik


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

Re: [gmx-users] Re: water dimer is gas phase

[Nilesh Dhumal]

I run the same mdp files for glucose in vaccum.

I ma geting the proper results, I can visualize the strucutre properly in
VMD.

If I use same for water why I am not geting proper structure ?

Nilesh

On Fri, May 20, 2011 9:48 am, Erik Marklund wrote:
 Exactly. So now is the time for skillful scripting.


 Erik


 Nilesh Dhumal skrev 2011-05-20 15.31:

 I used the same topology file to run 256 water molecules simulation and
 I
 got the proper result (compared with reported one).

 The problem is to visualize the trajectory in VMD since gromacs fails
 to write valid pdb files when the coordinates are too large.

 Nilesh



 On Fri, May 20, 2011 5:22 am, Erik Marklund wrote:

 Justin A. Lemkul skrev 2011-05-19 22.42:



 Vitaly Chaban wrote:


 For vacuum systems, pbc = no in conjunction with zero cutoffs
 is correct to obtain a gas-phase system.

 For reasonably large box, this is the same heck.



 Setting a box size and using pbc = xyz precludes the use of
 infinite cutoffs, which should be the most rigorously correct way to
 treat this type of system. With PBC, there are long-range effects
 that should be avoided.

 Nilesh: visualize your system, using VMD or ngmx. The behavior of
  your molecular cluster during the first ps will provide an
 answer. Are you sure that your topology is healthy?

 I agree with this.  The system should be going absolutely haywire
 :)



 -Justin



 Yes, this is a good test, and the topology should be inspected.
 However,
 the observed result is expected for this system. A water dimer coupled
 to a thermostat will dissociate eventually (pretty rapidly) at 300 K.
 The water
 molecules themselves seem intact. The problem with visualization comes
  from the fact that gromacs fails to write valid pdb files when the
 coordinates are too large. I called this a bug on the developer list
 one or two years ago since this generates pdb files that gromacs
 itself can't read, but the other developers didn't catch on. You can
 postprocess the pdb and cap the coordinates so that they're confined
 to the range that the pdb format allows, but note that this will mess
 up the water moleucles as they get very far apart.

 Erik



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







 --
 ---
 Erik Marklund, PhD student
 Dept. of Cell and Molecular Biology, Uppsala University.
 Husargatan 3, Box 596,75124 Uppsala, Sweden
 phone:+46 18 471 4537fax: +46 18 511 755
 er...@xray.bmc.uu.sehttp://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!
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] water dimer is gas phase

[Nilesh Dhumal]

Hello,

I am trying a simulation for water dimer in vaccum (gas phase).
Here I run the simulation with following steps

This is the .pdb file before energy minimization

TITLE S  C  A  M  O  R  G
REMARKTHIS IS A SIMULATION BOX
CRYST13.0003.0003.000  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  OW  WAT 1   0.317   1.494   1.565  1.00  0.00
ATOM  2  HW1 WAT 1  -0.091   2.293   1.258  1.00  0.00
ATOM  3  HW2 WAT 1  -0.144   0.788   1.129  1.00  0.00
ATOM  4  OW  WAT 2   3.172   1.515   1.356  1.00  0.00
ATOM  5  HW1 WAT 2   2.224   1.482   1.459  1.00  0.00
ATOM  6  HW2 WAT 2   3.522   1.427   2.231  1.00  0.00
TER
ENDMDL

I run the energy minimization

grompp -f minim-gas.mdp  -c dimer.pdb -p dimer.top -o dimer.tpr

mdrun -pd   -s dimer.tpr -o dimer.trr -c dimer.pdb -e dimer.edr -g dimer.log

I got the following file which I could visualize


TITLE Protein
MODEL1
ATOM  1  OW  WAT 1   0.351   1.490   1.592  1.00  0.00
ATOM  2  HW1 WAT 1  -0.106   2.335   1.248  1.00  0.00
ATOM  3  HW2 WAT 1  -0.162   0.750   1.112  1.00  0.00
ATOM  4  OW  WAT 2   3.198   1.519   1.321  1.00  0.00
ATOM  5  HW1 WAT 2   2.174   1.481   1.457  1.00  0.00
ATOM  6  HW2 WAT 2   3.544   1.423   2.268  1.00  0.00
TER
ENDMDL

minim-gas.mdp file

title   =  cpeptide
cpp = /usr/bin/cpp
constraints = none
integrator  = steep
dt  =  0.002; ps !
nsteps  =  5
nstlist =  1
coulombtype = cut-off
vdwtype = cut-off
ns_type =  simple
rlist   =  0.0
rcoulomb=  0.0
rvdw=  0.0
fourierspacing  = 0.12
fourier_nx   = 0
fourier_ny   = 0
fourier_nz   = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
pbc = no
;   Energy minimizing stuff
;
emtol   =  1000.0
emstep  =  0.01

the I run equlibration

grompp -f minim-pr.mdp  -c dimer.pdb -p dimer.top -o dimer.tpr

mdrun -pd   -s dimer.tpr -o dimer.trr -c dimer.pdb -e dimer.edr -g dimer.log

I got the following file which I could not visualize


TITLE Protein
MODEL1
ATOM  1  OW  WAT 1-2737.208 974.242-2091.510  1.00  0.00
ATOM  2  HW1 WAT 1-2737.949 973.910-2090.885  1.00  0.00
ATOM  3  HW2 WAT 1-2736.363 974.004-2091.048  1.00  0.00
ATOM  4  OW  WAT 22740.655-971.0932094.500  1.00  0.00
ATOM  5  HW1 WAT 22740.852-971.7332093.873  1.00  0.00
ATOM  6  HW2 WAT 22740.420-971.4722095.431  1.00  0.00
TER
ENDMDL

the equlibration file I used

title   =  cpeptid position restraining
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.001; ps !
nsteps  =  100  ; total 1.0 ps.
nstcomm =  1
nstxout =  1
nstvout =  1
nstfout =  0
nstlog  =  10
nstenergy   =  10
nstlist =  10
ns_type =  simple
comm_mode   = none
coulombtype = cut-off
vdwtype = cut-off
rlist   =  0.0
rcoulomb=  0.0
rvdw=  0.0
pbc =  no
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
Tcoupl = nose-hoover
tau_t = 0.1
tc-grps  =system
ref_t =   298
; Pressure coupling is  on
Pcoupl  = NO ;Parrinello-Rahman
pcoupltype  = isotropic
tau_p   =  2.0
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  298.0
gen_seed=  173529

Is ther any thing wrong with my mdp files.
WHy they is so much change is cooridnates in the .pdb file.

I am using gromacs version 4.0.7.

Thanks

Nilesh


-- 
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

Re: [gmx-users] Re: water dimer is gas phase

[Nilesh Dhumal]

if I set pbc=xyz in energy minimization mdp file  then I get following error

ERROR: can only have neighborlist cut-off zero (=infinite)
with coulombtype = Cut-off or coulombtype = User and simple neighborsearch
without periodic boundary conditions (pbc = no) and
rcoulomb and rvdw set to zero

ERROR: One of the box lengths is smaller than twice the cut-off length.
Increase the box size or decrease rlist.


Nilesh

On Thu, May 19, 2011 3:57 pm, Vitaly Chaban wrote:
 the equlibration file I used

 title               =  cpeptid position restraining cpp                
 =  /usr/bin/cpp
 constraints         =  none integrator          =  md dt                
  =  0.001    ; ps !
 nsteps              =  100      ; total 1.0 ps. nstcomm             =
  1
 nstxout             =  1 nstvout             =  1 nstfout        
     =  0
 nstlog              =  10 nstenergy           =  10 nstlist             =
  10
 ns_type             =  simple comm_mode           = none coulombtype      
   = cut-off
 vdwtype             = cut-off rlist               =  0.0 rcoulomb        
    =  0.0
 rvdw                =  0.0 pbc                 =  no 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
 Tcoupl = nose-hoover
 tau_t = 0.1 tc-grps  =system ref_t =   298 ; Pressure coupling is  on
 Pcoupl              = NO ;Parrinello-Rahman
 pcoupltype          = isotropic tau_p               =  2.0 compressibility
     =  4.5e-5
 ref_p               =  1.0 ; Generate velocites is on at 300 K.
 gen_vel             =  yes gen_temp            =  298.0 gen_seed          
  =  173529


 Is ther any thing wrong with my mdp files.
 WHy they is so much change is cooridnates in the .pdb file.





 Nilesh:


 Set periodic conditions. This will restrict the coordinates to small
 numbers.


 --
 Dr. Vitaly V. Chaban, Department of Chemistry
 University of Rochester, Rochester, New York 14627-0216
 --
 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!
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] pressure in NPT and NVT

[Nilesh Dhumal]

Hello,

I am using NPT simulation for water - spce model (opls-aa force field).
I have the reference pressure set at ref_p = 1.0 bar.
I checked the average pressure using g_energy and it is 2.81972 bar.

Why there increase in pressure?



For NVT simulatin I get the value around average pressure 710.685 bar.

I am running the simulation at 295 k and  average temp. is 294.98 K which
look ok.


Can you tell why there is increase in pressure for NPT and  why there is
so high value of pressure in NVT.

I am using gromacs version 4.0.7.

Thanks

Nilesh

-- 
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

Re: [gmx-users] Re: [gmx-developers] flexible water model

[Nilesh Dhumal]

Hello Justin,

I used 0.1fs timestep and I could get dielectric constant around 56 which
looks ok. To get the dielectric constant around ~75, should I reduce the
timestep around 0.05fs.

I used temperature 298k for my simulation and average tmep. I got is
297.83 K. I am doing NPT and used 1.0 bar as reference pressure in my
.mdp. I am getting average pressure around 2.58 bar.

I run the equilibration for 1ns.

Energy  Average   RMSD Fluct.  Drift 
Tot-Drift
---
Temperature  297.8310.968710.9643 -0.00165807  
-1.07774
Pressure (bar)  2.575514246.514246.51 -0.0360116  
-23.4075

Why there is change in pressure? Is there any wrong with simulation?


Nilesh

On Wed, May 11, 2011 4:18 pm, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 I have general question. If this parameters are not giving the proper
 results then How come I get the proper results with same parameter if I
 use 1/2 value of Kbond with the same parameters.


 Random chance, I imagine.  Your .mdp settings are not correct and the
 cutoffs are unreasonably short for any modern force field.  If you're
 seeking to reproduce others' work, then you have to use the same protocol.
 You're not
 doing that.

 I checked the temp when I use half value of Kbond and it goes max.
 ~320.



 This would also indicate instability.  You managed to get a correct
 result for one observable from an incorrect simulation wherein the
 thermodynamic observables do not correspond to what you have set.

 The way I found all of this out was first and foremost by watching the
 trajectory.  After about 30 ps, the water molecules freeze in place and
 vibrate as if they are about to shear apart.  At this exact time, the
 value of epsilon (from epsilon.xvg, output by g_dipoles) plummets down,
 after having steadily increased for the first 30 ps, as expected.  The
 temperature spikes and the pressure begins to oscillate by +/- 10^5, far
 higher than what it should for a system of a few hundred water molecules.

 Watch your trajectories, make sure you're getting the right average
 temperature and pressure, and that all your other energetic terms
 stabilize, then analyze the result of the simulation.  Otherwise, any
 inferred output is meaningless.

 -Justin


 Nilesh


 On Wed, May 11, 2011 4:03 pm, Justin A. Lemkul wrote:


 Nilesh Dhumal wrote:


 Hello Justin,



 I used 0.5 fs time step and still I got  dielectric constant ~2.



 This is the md.mdp file  I used. I checked the temperature it
 didn't go more than ~ 320 K.

 Still, that's unacceptable if your ref_t is 295.  The fact that the
 temperature is still rocketing up suggests the same instability I
 found.

 title   =  cpeptide MD cpp =
 /usr/bin/cpp
 integrator  =  md dt  =  0.001; ps !
 nsteps =  650 ; total 5 ps.
 nstcomm =  1000 nstxout =  1000 nstvout =
 1000
 nstfout =  1 nstlist =  1 ns_type
 =
 grid rlist   =  0.6 rcoulomb=  0.6 rvdw =
 0.7


 These cutoffs make no sense.  The paper you've cited used 0.9 nm.  If
  you're trying to reproduce previous work, use the same settings.

 coulombtype = PME vdwtype = cut-off
 Similarly here, you haven't applied dispersion correction, which you
 should, per the methods used in the JCP article.

 -Justin



 pbc = xyz 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
 Tcoupl = v-rescale
 tau_t = 0.1 tc-grps  =system ref_t =   295 ; Pressure coupling is
 on Pcoupl  = parrinello-rahman
 pcoupltype  = isotropic tau_p   =  0.5
 compressibility =  4.5e-5
 ref_p   =  1.0 ; Generate velocites is on at 300 K.
 gen_vel =  yes gen_temp=  295.0 gen_seed =
 173529




 Nilesh




 On Tue, May 10, 2011 6:14 pm, Justin A. Lemkul wrote:



 The gmx-developers list is not the forum for these types of
 questions.  I am replying via gmx-users, which is where the
 discussion should stay.

 I took a few minutes to dig into this.  My conclusion is that
 your system is not stable.  I would encourage you to analyze the
 temperature and pressure of your systems that are giving odd
 results. When I used the
 topology you provided, the temperature spiked to over 600 K and
 the box began to oscillate extensively as if the system were about
 to explode. The resulting epsilon value was about 1.6.



 If I reduce the timestep to 0.5 fs, the results are much more
 reasonable, and using the Ka and Kb values in the paper (not
 halved!) I get a much
 more sensible result, even after just 100 ps.  It looks to me as
 if the combination of these parameters and a 1-fs timestep

Re: [gmx-users] Re: [gmx-developers] flexible water model

[Nilesh Dhumal]

Hello Justin,

I used 0.5 fs time step and still I got  dielectric constant ~2.

This is the md.mdp file  I used. I checked the temperature it didn't go
more than ~ 320 K.

title   =  cpeptide MD
cpp =  /usr/bin/cpp
integrator  =  md
dt  =  0.001; ps !
nsteps  =  650 ; total 5 ps.
nstcomm =  1000
nstxout =  1000
nstvout =  1000
nstfout =  1
nstlist =  1
ns_type =  grid
rlist   =  0.6
rcoulomb=  0.6
rvdw=  0.7
coulombtype = PME
vdwtype = cut-off
pbc = xyz
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
Tcoupl = v-rescale
tau_t = 0.1
tc-grps  =system
ref_t =   295
; Pressure coupling is  on
Pcoupl  = parrinello-rahman
pcoupltype  = isotropic
tau_p   =  0.5
compressibility =  4.5e-5
ref_p   =  1.0
; Generate velocites is on at 300 K.
gen_vel =  yes
gen_temp=  295.0
gen_seed=  173529


Nilesh


On Tue, May 10, 2011 6:14 pm, Justin A. Lemkul wrote:


 The gmx-developers list is not the forum for these types of questions.  I
 am replying via gmx-users, which is where the discussion should stay.

 I took a few minutes to dig into this.  My conclusion is that your system
 is not stable.  I would encourage you to analyze the temperature and
 pressure of your systems that are giving odd results.  When I used the
 topology you provided, the temperature spiked to over 600 K and the box
 began to oscillate extensively as if the system were about to explode.
 The resulting epsilon value was about 1.6.


 If I reduce the timestep to 0.5 fs, the results are much more reasonable,
 and using the Ka and Kb values in the paper (not halved!) I get a much
 more sensible result, even after just 100 ps.  It looks to me as if the
 combination of these parameters and a 1-fs timestep is not entirely
 stable.  I know the original authors used dt = 1 fs, but the point
 remains.

 -Justin


 Nilesh Dhumal wrote:

 Hello,


 I am using flexible water model for my system. I am referring a paper
 J.
 Chem. Phys. 124, 024503 (2006). Author have used Amber type force field.


 i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2.

 Kbond = 443153.3808 kJ/mol nm**2


 Kangle= 317.5656 kJ/mol rad**2.


 I am using olss-aa force field parameters in Gromacs  VERSION 4.0.7.


 I checked some papers in which author have used oplsaa force field in
 Gromacs. 1/2 factor is not in opls force field if I compare opls and
 amber.


 I didn’t get the proper dielectric constant for water when I used the
 parameters reported in paper

 (Kbond = 443153.3808 kJ/mol nm**2,Kangle= 317.5656 kJ/mol rad**2)


 I half the value of Kb and get the proper dielectric constant (~80) for
  water reported in paper. If I half Kangle  then I don’t get proper
 value. Below are the results for the dielectric constant of water.
 Bond length is nm.


 Here I have done some analysis.  The original value reported in J.
 Chem.
 Phys. 124, 024503 2006, paper are


 Kbond = 443153.3808 kJ/mol nm**2
 Kangle = 317.5656 kJ/mol rad**2.



 bond lengthKbond   angleKangledielectric constant
 0.1012
 443153.3808113.24  317.5656   ~1.9 : orginal value



 0.1012   221576.6904113.24  317.5656   ~80   : 1/2 (Kbond)



 0.1012   443153.3808113.24  158.7828   ~1.58 : 1/2 (kangle)



 0.1012  221576.6904113.24  317.5656   ~1.9   : 1/2
 (Kbond)(Kangle)



 Here I pasted spc_fw.itp file used for the simulation.


 ; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 ;1   3   yes 0.5 0.5
 ; comb-rule 3 is square-root sigma, the OPLSAA version


 [ atomtypes ]
 ; full atom descriptions are available in ffoplsaa.atp
 ; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_1001  OW  8 15.99940-0.820   A3.1655e-01
 6.503e-01
 opls_1002  HW  1  1.00800 0.410   A0.00e+00 0.00e+00


 [ bondtypes ]
 ; ij  func   b0  kb
 OWHW  10.1012   443153.3808   ; J. Chem. Phys.
 (2006),124,024503
 [ angletypes ]
 ;  ijk  func   th0   cth
 HW OW HW  1   113.24  317.5656 ; J. Chem. Phys.
 (2006),124,024503


 [ moleculetype ]
 ; Namenrexcl
 WAT 3


 [ atoms ]
 ; nr   type  resnr residue  atom   cgnr charge   mass  typeB
  chargeB  massB 1   opls_1001 1WAT OW  1  -0.82
 15.99940 ;
 2   opls_1002 1WATHW1  1   0.41  1.008   ;
 3   opls_1002 1WATHW2  1   0.41  1.008   ;


 [ bonds ]
 ; i

Re: [gmx-users] Re: [gmx-developers] flexible water model

[Nilesh Dhumal]

I have general question. If this parameters are not giving the proper
results then How come I get the proper results with same parameter if I
use 1/2 value of Kbond with the same parameters.

I checked the temp when I use half value of Kbond and it goes max. ~320.

Nilesh

On Wed, May 11, 2011 4:03 pm, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Hello Justin,


 I used 0.5 fs time step and still I got  dielectric constant ~2.


 This is the md.mdp file  I used. I checked the temperature it didn't go
  more than ~ 320 K.


 Still, that's unacceptable if your ref_t is 295.  The fact that the
 temperature is still rocketing up suggests the same instability I found.

 title   =  cpeptide MD cpp =  /usr/bin/cpp
 integrator  =  md dt  =  0.001; ps ! nsteps
 =  650 ; total 5 ps.
 nstcomm =  1000 nstxout =  1000 nstvout
 =  1000
 nstfout =  1 nstlist =  1 ns_type =
 grid rlist   =  0.6 rcoulomb=  0.6 rvdw
 =  0.7


 These cutoffs make no sense.  The paper you've cited used 0.9 nm.  If
 you're trying to reproduce previous work, use the same settings.

 coulombtype = PME vdwtype = cut-off

 Similarly here, you haven't applied dispersion correction, which you
 should, per the methods used in the JCP article.

 -Justin


 pbc = xyz 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
 Tcoupl = v-rescale
 tau_t = 0.1 tc-grps  =system ref_t =   295 ; Pressure coupling is  on
 Pcoupl  = parrinello-rahman
 pcoupltype  = isotropic tau_p   =  0.5 compressibility
 =  4.5e-5
 ref_p   =  1.0 ; Generate velocites is on at 300 K.
 gen_vel =  yes gen_temp=  295.0 gen_seed
 =  173529



 Nilesh



 On Tue, May 10, 2011 6:14 pm, Justin A. Lemkul wrote:


 The gmx-developers list is not the forum for these types of
 questions.  I am replying via gmx-users, which is where the discussion
 should stay.

 I took a few minutes to dig into this.  My conclusion is that your
 system is not stable.  I would encourage you to analyze the
 temperature and pressure of your systems that are giving odd results.
 When I used the
 topology you provided, the temperature spiked to over 600 K and the
 box began to oscillate extensively as if the system were about to
 explode. The resulting epsilon value was about 1.6.



 If I reduce the timestep to 0.5 fs, the results are much more
 reasonable, and using the Ka and Kb values in the paper (not halved!)
 I get a much
 more sensible result, even after just 100 ps.  It looks to me as if
 the combination of these parameters and a 1-fs timestep is not
 entirely stable.  I know the original authors used dt = 1 fs, but the
 point remains.

 -Justin



 Nilesh Dhumal wrote:


 Hello,



 I am using flexible water model for my system. I am referring a
 paper J.
 Chem. Phys. 124, 024503 (2006). Author have used Amber type force
 field.


 i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2.

 Kbond = 443153.3808 kJ/mol nm**2



 Kangle= 317.5656 kJ/mol rad**2.



 I am using olss-aa force field parameters in Gromacs  VERSION
 4.0.7.



 I checked some papers in which author have used oplsaa force field
 in Gromacs. 1/2 factor is not in opls force field if I compare opls
 and amber.


 I didn’t get the proper dielectric constant for water when I used
 the parameters reported in paper

 (Kbond = 443153.3808 kJ/mol nm**2,Kangle= 317.5656 kJ/mol rad**2)



 I half the value of Kb and get the proper dielectric constant (~80)
 for water reported in paper. If I half Kangle  then I don’t get
 proper value. Below are the results for the dielectric constant of
 water. Bond length is nm.



 Here I have done some analysis.  The original value reported in J.
 Chem.
 Phys. 124, 024503 2006, paper are



 Kbond = 443153.3808 kJ/mol nm**2
 Kangle = 317.5656 kJ/mol rad**2.




 bond lengthKbond   angleKangledielectric constant
 0.1012
 443153.3808113.24  317.5656   ~1.9 : orginal value




 0.1012   221576.6904113.24  317.5656   ~80   : 1/2
 (Kbond)




 0.1012   443153.3808113.24  158.7828   ~1.58 : 1/2
 (kangle)




 0.1012  221576.6904113.24  317.5656   ~1.9   : 1/2
 (Kbond)(Kangle)




 Here I pasted spc_fw.itp file used for the simulation.



 ; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 ;1   3   yes 0.5 0.5
 ; comb-rule 3 is square-root sigma, the OPLSAA version



 [ atomtypes ]
 ; full atom descriptions are available in ffoplsaa.atp
 ; name  bond_typemasscharge   ptype  sigma
 epsilon opls_1001  OW  8 15.99940-0.820

Re: [gmx-users] ambar to opls force field

[Nilesh Dhumal]

Thanks Justin.

I am using flexibale water model for my system. I am refering a paper J.
Chem. Phys. 124, 024503 (2006). Author have used Amber type force field.

i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2.

Kbond = 443153.3808 kJ/mol nm**2

Kangle= 317.5656 kJ/mol rad**2.

I am using olss-aa force field parameters in Gromacs  VERSION 4.0.7.

I checked some papers in which author have used opls aa force field. 1/2
factor is not in opls force field IF I compare opls and amber.

My question is in .itp file should I use Kbond and Kangle as it is or
should I consider the 1/2 factor then I use them.

Thanks

Nilesh

On Fri, May 6, 2011 6:36 pm, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Hello,


 How can I convert ambar force field to opls force field.


 Should I half the force constant of bond (Ka)  and angle (Kb)?



 Why would you do that?  Most of the bonded parameters in OPLS were taken
 from AMBER directly, IIRC.  If you need to parameterize some new bonded
 parameters, you'd be better served deriving them in a way that is
 compatible with the modern OPLS-AA force field (probably QM/geometry
 optimization), rather than trying to hack something together.

 -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





-- 
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

Re: [gmx-users] ambar to opls force field

[Nilesh Dhumal]

Hello Justin,

Here I have done some analysis.  The original value reported in J.Chem.
Phys. 124, 024503 2006, paper are
Kbond = 443153.3808 kJ/mol nm**2
Kangle = 317.5656 kJ/mol rad**2.


Below are the results for the dielectric constant of water.I made the .itp
file  pasted below the table. Bond length is nm.

bond length  Kbond angleKangledielectric constant
0.1012   443153.3808113.24  317.5656   ~1.9 : orginal value

0.1012   221576.6904113.24  317.5656   ~80   : 1/2 (Kbond)

0.1012   443153.3808113.24  158.7828   ~1.58 : 1/2 (kangle)

0.1012  221576.6904113.24  317.5656   ~1.9   : 1/2
(Kbond)(Kangle)


When I use half Kbond value I get proper dielectic constant for water
(~80). I checked the Kbond for OH in opls force field is around ~ 44.

I don't now where I am going wrong.
Here I pasted spc_fw.itp file

; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

 [ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_1001  OW  8 15.99940-0.820   A3.1655e-01   6.503e-01
 opls_1002  HW  1  1.00800 0.410   A0.00e+00 0.00e+00

[ bondtypes ]
; ij  func   b0  kb
  OWHW  10.1012   443153.3808   ; J. Chem. Phys.
(2006),124,024503
[ angletypes ]
;  ijk  func   th0   cth
  HW OW HW  1   113.24  158.7828 ; J. Chem. Phys.
(2006),124,024503

[ moleculetype ]
; Namenrexcl
 WAT 3

[ atoms ]
; nr   type  resnr residue  atom   cgnr charge   mass  typeB  
 chargeB  massB
 1   opls_1001 1WAT OW  1  -0.82 15.99940 ;
 2   opls_1002 1WATHW1  1   0.41  1.008   ;
 3   opls_1002 1WATHW2  1   0.41  1.008   ;

[ bonds ]
; i j   funct
1 2 1
1 3 1

[ angles ]
; i j   k   funct
   2 1 3 1

In water.top file, I included spc_fw.itp file.

; Include water topology
#include spc_fw.itp

Is there any thing worng in .itp file or where I am making mistake.

Thanks

Nilesh


On Sun, May 8, 2011 10:55 am, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Thanks Justin.


 I am using flexibale water model for my system. I am refering a paper
 J.
 Chem. Phys. 124, 024503 (2006). Author have used Amber type force field.


 i.e. 1/2 Kbond (r-req)**2 + 1/2 Kangle(theta-thetaeq)**2.

 Kbond = 443153.3808 kJ/mol nm**2


 Kangle= 317.5656 kJ/mol rad**2.


 I am using olss-aa force field parameters in Gromacs  VERSION 4.0.7.


 I checked some papers in which author have used opls aa force field.
 1/2
 factor is not in opls force field IF I compare opls and amber.

 My question is in .itp file should I use Kbond and Kangle as it is or
 should I consider the 1/2 factor then I use them.


 Both of those terms are simple harmonic expressions, which do not require
 any modification.  Per the manual, Gromacs uses these expressions as is,
 so Kb and Ka should be appropriate as listed.  They are of comparable
 magnitude to existing bonded parameters for such terms.

 You can, of course, test this by using the same parameters under the
 original AMBER force field used in the paper you cite, and then again
 after incorporation into the OPLS-AA force field.  If the resulting
 averages are the same, then the new parameters have been incorporated
 correctly.

 -Justin


 Thanks


 Nilesh


 On Fri, May 6, 2011 6:36 pm, Justin A. Lemkul wrote:


 Nilesh Dhumal wrote:


 Hello,



 How can I convert ambar force field to opls force field.



 Should I half the force constant of bond (Ka)  and angle (Kb)?



 Why would you do that?  Most of the bonded parameters in OPLS were
 taken from AMBER directly, IIRC.  If you need to parameterize some new
 bonded parameters, you'd be better served deriving them in a way that
 is compatible with the modern OPLS-AA force field (probably
 QM/geometry
 optimization), rather than trying to hack something together.

 -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

[gmx-users] ambar to opls force field

[Nilesh Dhumal]

Hello,

How can I convert ambar force field to opls force field.

Should I half the force constant of bond (Ka)  and angle (Kb)?


NIlesh




-- 
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] constraints

[Nilesh Dhumal]

Hello,

In my input file if I don't specify constraints then

What is default

constraints=none

constraints=all bonds


NIlesh



-- 
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] flexiable water - model

[Nilesh Dhumal]

Hello,

I am trying to run a simulation for flexiable water. I use the parameters
from J. Chem. Phys. (2006),124,024503 paper and made floowing changes.

I addes WAT as a new residue name in aminoacids.dat

I addred two atom times in ffoplsaa.atp

 opls_1001   15.99940  ; O SPC_fw Water
 opls_10021.00800  ; H SPC_fw Water


I added following parameters in ffoplsaa.rtp

[ WAT]
 [ atoms ]
 OWA   opls_1001  -0.82 1
 HWA1  opls_1002   0.41 2
 HWA2  opls_1002   0.41 2

  [ bonds ]
 OWA   HWA1
 OWA   HWA2

I made a spc_fw.itp file.

; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

 [ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_1001   OWA  815.99940 -0.820   A3.1655e-01  6.503e-01
 opls_1002   HWA  1 1.00800  0.410   A0.00e+00  0.00e+00

[ bondtypes ]
; ij  func   b0  kb
 OWAHWA  10.1012   443153.3808 ; J. Chem. Phys. (2006),124,024503


[ angletypes ]
;  ijk  func   th0   cth
  HWA OWA HWA  1   113.24   317.5656  ; J. Chem. Phys.
(2006),124,024503

[ moleculetype ]
; Namenrexcl
 WAT 3

[ atoms ]

; nr   type  resnr residue  atom   cgnr charge   mass  typeB  
 chargeB  massB
1  opls_1001   1WAT OWA  1  -0.82
2  opls_1002   1WATHWA1  1   0.41
3  opls_1002   1WATHWA2  1   0.41

[ bonds ]
; i j   funct
1   2   1
1   3   1


[ angles ]
; i j   k   funct
2   1   3   1


Finally I made changes in ffoplsaa.itp file

;#include ffoplsaanb.itp
;#include ffoplsaabon.itp
#include spc_fw.itp
#include spc_fw_mol.itp

For pdb2gmx

 pdb2gmx -f water.pdb -o water.pdb -p water.top -ter

I get following error

Fatal error:
Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms
 while sorting atoms


WHy is reading HOH residue. In my pdb file I mentioned WAT as residure.

How can I fix this error?

Nilesh





-- 
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

Re: [gmx-users] flexiable water - model

[Nilesh Dhumal]

I have total 256 water molecules. I am trying to genrate the .top file
from  .pdb so I used pdb2gmx.

How can I genrate the .top file with pdb2gmx for 256 water molecules.

Nilesh

On Tue, April 26, 2011 1:01 pm, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Hello,


 I am trying to run a simulation for flexiable water. I use the
 parameters from J. Chem. Phys. (2006),124,024503 paper and made floowing
 changes.

 I addes WAT as a new residue name in aminoacids.dat


 I addred two atom times in ffoplsaa.atp


 opls_1001   15.99940  ; O SPC_fw Water opls_10021.00800  ; H SPC_fw
 Water



 I added following parameters in ffoplsaa.rtp


 [ WAT]
 [ atoms ]
 OWA   opls_1001  -0.82 1
 HWA1  opls_1002   0.41 2
 HWA2  opls_1002   0.41 2


 [ bonds ]
 OWA   HWA1
 OWA   HWA2


 I made a spc_fw.itp file.


 ; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 ;1   3   yes 0.5 0.5
 ; comb-rule 3 is square-root sigma, the OPLSAA version


 [ atomtypes ]
 ; full atom descriptions are available in ffoplsaa.atp
 ; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_1001   OWA  815.99940 -0.820   A3.1655e-01
 6.503e-01
 opls_1002   HWA  1 1.00800  0.410   A0.00e+00  0.00e+00

 [ bondtypes ]
 ; ij  func   b0  kb
 OWAHWA  10.1012   443153.3808 ; J. Chem. Phys.
 (2006),124,024503



 [ angletypes ]
 ;  ijk  func   th0   cth
 HWA OWA HWA  1   113.24   317.5656  ; J. Chem. Phys.
 (2006),124,024503


 [ moleculetype ]
 ; Namenrexcl
 WAT 3


 [ atoms ]


 ; nr   type  resnr residue  atom   cgnr charge   mass
 typeB chargeB  massB 1  opls_1001   1WAT OWA  1
 -0.82
 2  opls_1002   1WATHWA1  1   0.41
 3  opls_1002   1WATHWA2  1   0.41


 [ bonds ]
 ; i j   funct
 1   2   1
 1   3   1



 [ angles ]
 ; i j   k   funct
 2   1   3   1



 Finally I made changes in ffoplsaa.itp file


 ;#include ffoplsaanb.itp
 ;#include ffoplsaabon.itp
 #include spc_fw.itp
 #include spc_fw_mol.itp


 For pdb2gmx


 pdb2gmx -f water.pdb -o water.pdb -p water.top -ter

 I get following error


 Fatal error:
 Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms
 while sorting atoms


 WHy is reading HOH residue. In my pdb file I mentioned WAT as residure.


 How can I fix this error?



 If I recall, pdb2gmx does some internal translations to standardize water
  nomenclature.  In reality, you don't need pdb2gmx at all - you've
 already shown that you're created a topology for the water model.

 -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





-- 
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] grompp error

[Nilesh Dhumal]

Hello,

I am trying to run a simulation for flexiable water. I use the parameters
from J. Chem. Phys. (2006),124,024503 paper and made a spc_fw.itp file.

; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

 [ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_116   OW  8  9.95140-0.820   A3.165492e-01 
6.50299455e-01
 opls_117   HW  1  4.03200 0.410   A0.0e+00  0.0e+00

[ bondtypes ]
; ij  func   b0  kb
 OWHW  11.012   443153.3808  ; J. Chem. Phys. (2006),124,024503


[ angletypes ]
;  ijk  func   th0   cth
  HW OW HW  1   113.24317.5656  ; J. Chem. Phys.
(2006),124,024503


I am geting the error for

 grompp -f minim.mdp  -c water.pdb -p water.top  -o 1.tpr


 error I am getting

rogram grompp, VERSION 4.0.7
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File water.top, line 26
Last line read:
'[ system ]'
Invalid order for directive system

 How can I fix this error?

Nilesh




-- 
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

Re: [gmx-users] grompp error

[Nilesh Dhumal]

Thanks Justin,

Here I pasted water.top

;
;   File 'water.top' was generated
;   By user: ndhumal (36026)
;   On host: c63
;   At date: Thu Apr 21 14:52:38 2011
;
;   This is your topology file
;   Protein
;
; Include forcefield parameters
#include ffoplsaa.itp

; Include water topology
;#include spc.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
;#include ions.itp

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
SOL   256

Nilesh

On Thu, April 21, 2011 8:03 pm, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Hello,


 I am trying to run a simulation for flexiable water. I use the
 parameters from J. Chem. Phys. (2006),124,024503 paper and made a
 spc_fw.itp file.

 ; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
 ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
 ;1   3   yes 0.5 0.5
 ; comb-rule 3 is square-root sigma, the OPLSAA version


 [ atomtypes ]
 ; full atom descriptions are available in ffoplsaa.atp
 ; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_116   OW  8  9.95140-0.820   A3.165492e-01
 6.50299455e-01
 opls_117   HW  1  4.03200 0.410   A0.0e+00
 0.0e+00


 [ bondtypes ]
 ; ij  func   b0  kb
 OWHW  11.012   443153.3808  ; J. Chem. Phys.
 (2006),124,024503



 [ angletypes ]
 ;  ijk  func   th0   cth
 HW OW HW  1   113.24317.5656  ; J. Chem. Phys.
 (2006),124,024503



 I am geting the error for


 grompp -f minim.mdp  -c water.pdb -p water.top  -o 1.tpr


 error I am getting

 rogram grompp, VERSION 4.0.7 Source code file: topio.c, line: 415


 Fatal error:
 Syntax error - File water.top, line 26
 Last line read:
 '[ system ]'
 Invalid order for directive system


 How can I fix this error?



 Assemble the components of your .top in the correct order, as described
 in chapter 5 of the manual.  Without seeing the contents of water.top
 that's the best anyone can offer.

 -Justin


 Nilesh






 --
 


 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





-- 
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

Re: [gmx-users] saving coordinates

[Nilesh Dhumal]

Hello Justin,

THanks for your reply.

Suppose any atom that leaves a simulation box by, say, the right-hand
face, then enters the simulation box by the left-hand face.

For these atom how gromacs save the coordinate.
Does it save the coordinate when it enter from left-hand face?

Nilesh

On Wed, April 13, 2011 9:26 pm, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Hello,



 If some part of molecule is outside the box. How Gromacs save the
 coordinates in trajectory.


 There is no such thing as outside in a periodic system.


 http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Condit
 ions

 -Justin



 Nilesh





 --
 


 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





-- 
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] make a patch

[Nilesh Dhumal]

Hello,

I want to file a patch for g_hbond.

How can I do that.

Nilesh




-- 
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] saving coordinates

[Nilesh Dhumal]

Hello,


If some part of molecule is outside the box. How Gromacs save the
coordinates in trajectory.


Nilesh



-- 
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] g_hbond

[Nilesh Dhumal]

Hello,

I am trying to calculate number of hydrogen bond (O-H---CL)in my system.

I use the following command


 g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


Output file hbnum.xvg shows zero number of hydorgen bond.

Can you tell me why its showing zero no.

A strong peak is found in rdf between H and CL at 2.0 A.

I am using Gromacs 4.0.7 version.



Nilesh




-- 
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

Re: [gmx-users] g_hbond

[Nilesh Dhumal]

Is there any way to specify clorin and florin atoms as a receptor.

Nilesh

On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:



 Nilesh Dhumal wrote:

 Hello,


 I am trying to calculate number of hydrogen bond (O-H---CL)in my
 system.

 I use the following command



 g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


 Output file hbnum.xvg shows zero number of hydorgen bond.


 Can you tell me why its showing zero no.


 A strong peak is found in rdf between H and CL at 2.0 A.



 Chlorine is not considered a receptor in g_hbond.


 -Justin


 I am using Gromacs 4.0.7 version.




 Nilesh






 --
 


 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





-- 
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

Re: [gmx-users] g_hbond

[Nilesh Dhumal]

Is it possible to find number of hydrogen bonds using g_hbond by
considering the distance between Acceptor-hydrogen instead of the distance
between Acceptor-Donor atoms.

Nilesh

On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote:
 Try the -contact option.


 Erik



 Nilesh Dhumal skrev 2011-04-11 17.12:

 Is there any way to specify clorin and florin atoms as a receptor.


 Nilesh


 On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:

 Nilesh Dhumal wrote:


 Hello,



 I am trying to calculate number of hydrogen bond (O-H---CL)in my
 system.

 I use the following command




 g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


 Output file hbnum.xvg shows zero number of hydorgen bond.



 Can you tell me why its showing zero no.



 A strong peak is found in rdf between H and CL at 2.0 A.



 Chlorine is not considered a receptor in g_hbond.



 -Justin



 I am using Gromacs 4.0.7 version.





 Nilesh






 --
 



 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







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

Re: [gmx-users] g_hbond

[Nilesh Dhumal]

I tried to use contact and -da together with following  command

g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc   -noda   -r 0.5
-contact   -num

I am getting following error.

Fatal error:Can not analyze contact between H and A: turn off -noda

Nilesh



On Mon, April 11, 2011 5:05 pm, Nilesh Dhumal wrote:
 Is it possible to find number of hydrogen bonds using g_hbond by
 considering the distance between Acceptor-hydrogen instead of the distance
  between Acceptor-Donor atoms.

 Nilesh


 On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote:

 Try the -contact option.



 Erik




 Nilesh Dhumal skrev 2011-04-11 17.12:


 Is there any way to specify clorin and florin atoms as a receptor.



 Nilesh



 On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:


 Nilesh Dhumal wrote:



 Hello,




 I am trying to calculate number of hydrogen bond (O-H---CL)in my
 system.

 I use the following command





 g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num


 Output file hbnum.xvg shows zero number of hydorgen bond.




 Can you tell me why its showing zero no.




 A strong peak is found in rdf between H and CL at 2.0 A.




 Chlorine is not considered a receptor in g_hbond.




 -Justin




 I am using Gromacs 4.0.7 version.






 Nilesh







 --
 




 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








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

[Nilesh Dhumal]

Hello,

I want to calculat the coordination number of solute in first solvation
shell.

integration of (4*pi*r^2*g(r)) from 0 to 2.6 A(first solvation shell)

If I calcualte the g_rdf for first solvation shell (till 2.6 A) and then I
integrate this using g_analysis.

Can I go this way.

Nilesh



-- 
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

Re: [gmx-users] g_dipole: dipole moment autocorrelation function

[Nilesh Dhumal]

Thanks Flo for detail reply.

Is it possible to put PBC off during calculation of dipole moment
autocorrelation function.

I will run the simulation for 50ns ans try to save trajectroy of 0.02ps.

Thanks

NIlesh

Nilesh

On Thu, March 31, 2011 5:38 am, Dommert Florian wrote:
 On Thu, 2011-03-31 at 10:39 +0200, David van der Spoel wrote:

 On 2011-03-31 09.25, Dommert Florian wrote:

 On Wed, 2011-03-30 at 20:23 +0200, David van der Spoel wrote:

 On 2011-03-30 20.16, Nilesh Dhumal wrote:

 Thanks.
 How can I take average.

 summing up and dividing by the number of sims.

 How much long I should run the simulation.

 until the average converges.

 Nilesh


 On Wed, March 30, 2011 12:59 pm, David van der Spoel wrote:

 On 2011-03-30 18.54, Nilesh Dhumal wrote:


 Hello,



 I am trying to calculate the dipole moment autocorrelation
 function for my system (ionic liquid). I am using gromacs
 4.0.7 version.


 Hello,


 I think you will get into some trouble when you try to calculate an
 autocorrelation function of property that is not continuous in time.
 In
 an ionic liquid you have contributions of the molecular dipole and
 contribution of the charged molecules to the dipole. The latter part
 is unfortunately not continuous due to jumping of the molecules over
 the PBCs. It depends what kind of property you want to calculate, but
 we experienced that simulations in the range of 50-100ns are required
 to reliably determine properties like the dielectric constant. The
 next point is that you have to save your coordinates and velocities
 quite often ( every 0.02ps we used)

 Check corresponding literature for further advice.


 Thanks Florian, for pointing that out. I forgot about it in my previous
  mail. In order to compute the dielectric constant one could in
 principle apply constant electric fields at different strengths and then
  extrapolate to zero. Don't know whether that has been done.


 In the ionic liquids commmunity dielectric spectra of ILs are usually
 calulated from equilibrium MD without application of an E-field. The
 generalized dielectric constant is calculated and a Fourier Laplace
 transformation finally allows to determine the full dielectric spectrum.
 Schröder et. al from the University of Vienna have published some
 articles about this topic.

 Cheers,
 Flo


 Cheers,


 Flo



 I run the simulation for 4 ns.  I run the following command
 to calculate the dipole moment autocorrelation function

 g_dipoles -f water.trr -s water.tpr -corr total -c

 The function is not geting converge to zero.



 I want to use this data for calculation of power spectra by
 fourier transfom of dipole moment autocorrelation function.

 Can you tell why its not geting converge to zero?



 You have to simulate at least a few 10s of ns for such slow
 liquids to converge. Alternatively you can average over many
 independent simulations (10s).



 Thanks



 Nilesh







 --
 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








 --
 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




 --
 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


 --
 Florian Dommert
 Dipl. - Phys.


 Institute for Computational Physics
 University Stuttgart


 Pfaffenwaldring 27
 70569 Stuttgart


 EMail: domm...@icp.uni-stuttgart.de
 Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert


 Tel.: +49 - (0)711 - 68563613
 Fax.: +49 - (0)711 - 68563658
 --
 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!
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