date:20130513

Re: [gmx-users] Initial velocity

2013-05-13 Thread Brighter Agyemang

Thanks so much for your support,
The point is that, I have this mathematical theory on coarse grain
simulation for which is supposed to resolve the potential existing between
atoms suspended by an angle theta(like the triangle share for two atoms).
To solve for the potential, the theta between these two atoms has to be
resolved first and then with the use of some functions in the
math.h(acos,math.pow,log) I get the final potential. The mathematical model
has been resolved and I have coded everything in C. When I made inquiries
on how to implement it in GROMACS, I learnt that I have to modify the
bondfree.c file in ./src/gmxlib directory.
Theta is found based on the euclidian distance property and some
differentiation afterwards and this theta is then supplied together with
initial coordinates of the two atoms, boltzmann constant, and the mixing
paramter (fine grain + coarse grain) and then the potential is supposed to
be found.
My supervisor seems not to be remembering what he did some years ago with
GROMACS and it is really making life a though thing for me now
I hope this information will be useful, let me know if I still need to
clarify myself more pls.
The whole idea is the determine the potential existing between fine-grain
and coarse-grain multiscalled simulation

Thanks so much


On 13 May 2013 05:48, Acoot Brett acootbr...@yahoo.com wrote:

 Dear All,

 Will you please explain how the initial velocity may affect the MD
 results? What the initial velocity really means? How the velocity of the
 atoms in the protein changes in the MD process? What is the reasonable
 scope of the initial velocity? Any suggestions on how to manually input a
 defined initial velocity?

 Cheers,

 Acoot

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Re: [gmx-users] question about energygrps

2013-05-13 Thread Jesper Sørensen

Huyjin,

If you look in your log file from the rerun you will see that when running 
using the GPU, energy groups are ignored or unused for energy reporting. Thus 
for this to work you need to run it on the CPUs.

This is what I get in my output md.log when trying the same thing...
 NOTE: With GPUs, reporting energy group contributions is not supported

Best regards,
Jesper



On May 12, 2013, at 11:06 AM, Hyunjin Kim hyunj...@andrew.cmu.edu wrote:

 
 
 On 5/12/13 1:53 PM, Hyunjin Kim wrote:
 
 
 On 5/12/13 1:31 PM, Hyunjin Kim wrote:
 
 
 On 5/12/13 1:14 PM, Hyunjin Kim wrote:
 
 
 On 5/12/13 12:54 PM, Hyunjin Kim wrote:
 
 
 On 5/12/13 2:25 AM, Hyunjin Kim wrote:
 Dear,
 
 I want to calculate LJ and Electrostatic energies between two
 groups
 defined in index.ndx during rerun with original trajectory.
 
 The following is what I tried:
 
 1. insert energygrps r_1 r_25 in the test.mdp file.
 
 2. grompp -f test.mdp -c x.gro -o x.tpr -p x.top -n index.ndx
 
 3. mdrun -nt 2 -rerun o.trr -s x.tpr -o x.trr -c x.gro -g x.log
 -e
 x.ene
 
 The simulation runs properly, but if I collect energy using
 g_energy,
 then
 values of all energy terms are same, although I choose different
 groups.
 
 Which specific groups did you choose?
 
 Thanks a lot. I chose residues 1 and 25.
 
 
 I understood that from the original post.  What I was asking about
 was
 the
 exact
 groups you chose from the g_energy selection menu.
 
 
 When I use g_energy, I chose 4 5 6 7 8 9 10 from the below list.
 Thanks.
 
 1  Bond 2  Angle3  Ryckaert-Bell.   4
 LJ-14
 5  Coulomb-14   6  LJ-(SR)  7  Disper.-corr.8
 Coulomb-(SR)
 9  Coul.-recip.10  Potential   11  Kinetic-En. 12
 Total-Energy
 
 Dispersion correct, PME mesh (Coul-recip), and total potential are
 not
 decomposable.  The other terms you selected should be.  The fact the
 these
 options do not appear in the .edr file indicate either (1) you did
 not
 rerun
 with the right .tpr file or (2) you analyzed the wrong .edr file.
 The
 approach
 you have suggested is correct and should result in the desired energy
 groups
 being present.  What version of Gromacs are you using?
 
 I use 4.6.1 with gpu.
 
 
 Are you doing the rerun on GPU, as well, or on CPU?  What happens if
 you
 run in
 serial (-nt 1)?  I don't believe reruns work properly in parallel, but
 maybe
 that's outdated information.  Does a rerun on the .xtc file produce the
 desired
 output?
 
 
 I am about test on rerun with -nt 1 or CPU. But, previously, I only
 tested
 rerun with -nt 2 and GPU and looked to produce proper output. However,
 what you mean desired output seems nonbonded interactions between two
 
 The proper output is an .edr file with the decomposed energy terms you
 want, so
 I don't understand what looked to produce proper output means.  Any
 other
 output (trajectory, coordinate, log, etc) should be identical to the
 previous
 run, since you're doing a rerun, not a new simulation.
 
 -Justin
 
 I see. Then no I have not obtained the proper result yet. I will test what
 you suggested.
 Thanks. Hyunjin.
 
 
 groups I set, which I have not. I will test rerun in CPU and even -nt 1
 and see whether I got results properly.
 Thanks a lot for your support.
 
 Hyunjin.
 
 
 -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
 
 
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 --
 
 
 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
 
 
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[gmx-users] Issue running gromacs in Cluster

2013-05-13 Thread Sainitin Donakonda

Hello,

I am trying to run 20 ns protein ligand simulation on cluster using
following MD.MDP file

; 7.3.3 Run Control
integrator  = md; leap-frog integrator
dt  = 0.002 ; 2 fs
nsteps  = 500; maximum number of steps
to integrate



; 7.3.8 Output Control
nstxout = 200 ; suppress .trr output
nstvout = 200; suppress .trr output
nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 1000  ; write .xtc trajectory every 2 ps
energygrps  = Protein LIG

; 7.3.9 Neighbor Searching
nstlist = 5 ; [steps] freq to update neighbor
list
ns_type = grid  ; method of updating neighbor list
pbc = xyz   ; periodic boundary conditions in
all directions
rlist   = 1.2   ; [nm] cut-off distance for the
short-range neighbor list

; 7.3.10 Electrostatics
coulombtype = PME   ; Particle-Mesh Ewald electrostatics
rcoulomb= 1.2   ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype = switch   ; twin-range cut-off with rlist
where rvdw = rlist
rvdw= 1.2   ; [nm] distance for LJ cut-off
rvdw_switch = 0.8   ; Start switching th LJ potential
DispCorr= EnerPres ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
when using PME
pme_order   = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol  = 1e-5  ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl  = V-rescale ; temperature
coupling with Berendsen-thermostat
tc_grps = Protein_LIG Water_and_ions; groups to couple
seperately to temperature bath
tau_t   = 0.10.1; [ps] time
constant for coupling
ref_t   = 300300; [K] reference
temperature for coupling

; Pressure coupling
pcoupl  = Parrinello-Rahman ; pressure coupling is on for
NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility of
water, bar^-1
refcoord_scaling= com

; 7.3.17 Velocity Generation
gen_vel = no; velocity generation turned off

; 7.3.18 Bonds
constraints = all-bonds ; convert all bonds to constraints
constraint_algorithm= LINCS ; LINear Constraint Solver
continuation= yes   ; apply constraints to the start
configuration
lincs_order = 4 ; highest order in the expansion of
the contraint coupling matrix
lincs_iter  = 1 ; number of iterations to correct
for rotational lengthening
lincs_warnangle = 30; [degrees] maximum angle that a
bond can rotate before LINCS will complain


*and im using following commands dividing 20 ns to 10 ns each via extending
simulation*


*#This is the first simulation MD.mdp file contains 20 ns setup*
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_first10.tpr

mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16

*#This extends 10 ns simulation*
tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr

mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi
MD_first10.cpt -append -np 16


But it is crashed giving following error

*XTC error - maybe you are out of quota?*
*
*
*dont know why it happened it is because as im saving .trr file every
200ps? is it creating large files? or should i give different name in
extending simulation?*
*
*
*Please help*
*
*
*Thanks,*
*Nitin*
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Re: [gmx-users] Issue running gromacs in Cluster

2013-05-13 Thread XAvier Periole


You may have created large files and thus got out of quota on the disc. 

Check your quota and consider reducing the frequency of saving coordinates. 

On May 13, 2013, at 9:46, Sainitin Donakonda saigr...@gmail.com wrote:

 Hello,
 
 I am trying to run 20 ns protein ligand simulation on cluster using
 following MD.MDP file
 
 ; 7.3.3 Run Control
 integrator  = md; leap-frog integrator
 dt  = 0.002 ; 2 fs
 nsteps  = 500; maximum number of steps
 to integrate
 
 
 
 ; 7.3.8 Output Control
 nstxout = 200 ; suppress .trr output
 nstvout = 200; suppress .trr output
 nstenergy   = 1000  ; save energies every 2 ps
 nstlog  = 1000  ; update log file every 2 ps
 nstxtcout   = 1000  ; write .xtc trajectory every 2 ps
 energygrps  = Protein LIG
 
 ; 7.3.9 Neighbor Searching
 nstlist = 5 ; [steps] freq to update neighbor
 list
 ns_type = grid  ; method of updating neighbor list
 pbc = xyz   ; periodic boundary conditions in
 all directions
 rlist   = 1.2   ; [nm] cut-off distance for the
 short-range neighbor list
 
 ; 7.3.10 Electrostatics
 coulombtype = PME   ; Particle-Mesh Ewald electrostatics
 rcoulomb= 1.2   ; [nm] distance for Coulomb cut-off
 
 ; 7.3.11 VdW
 vdwtype = switch   ; twin-range cut-off with rlist
 where rvdw = rlist
 rvdw= 1.2   ; [nm] distance for LJ cut-off
 rvdw_switch = 0.8   ; Start switching th LJ potential
 DispCorr= EnerPres ; apply long range dispersion
 corrections for energy
 
 ; 7.3.13 Ewald
 fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
 when using PME
 pme_order   = 4 ; interpolation order for PME, 4 =
 cubic
 ewald_rtol  = 1e-5  ; relative strength of
 Ewald-shifted potential at rcoulomb
 
 ; 7.3.14 Temperature Coupling
 tcoupl  = V-rescale ; temperature
 coupling with Berendsen-thermostat
 tc_grps = Protein_LIG Water_and_ions; groups to couple
 seperately to temperature bath
 tau_t   = 0.10.1; [ps] time
 constant for coupling
 ref_t   = 300300; [K] reference
 temperature for coupling
 
 ; Pressure coupling
 pcoupl  = Parrinello-Rahman ; pressure coupling is on for
 NPT
 pcoupltype  = isotropic ; uniform scaling of box vectors
 tau_p   = 2.0   ; time constant, in ps
 ref_p   = 1.0   ; reference pressure, in bar
 compressibility = 4.5e-5; isothermal compressibility of
 water, bar^-1
 refcoord_scaling= com
 
 ; 7.3.17 Velocity Generation
 gen_vel = no; velocity generation turned off
 
 ; 7.3.18 Bonds
 constraints = all-bonds ; convert all bonds to constraints
 constraint_algorithm= LINCS ; LINear Constraint Solver
 continuation= yes   ; apply constraints to the start
 configuration
 lincs_order = 4 ; highest order in the expansion of
 the contraint coupling matrix
 lincs_iter  = 1 ; number of iterations to correct
 for rotational lengthening
 lincs_warnangle = 30; [degrees] maximum angle that a
 bond can rotate before LINCS will complain
 
 
 *and im using following commands dividing 20 ns to 10 ns each via extending
 simulation*
 
 
 *#This is the first simulation MD.mdp file contains 20 ns setup*
 grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
 MD_first10.tpr
 
 mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16
 
 *#This extends 10 ns simulation*
 tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr
 
 mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi
 MD_first10.cpt -append -np 16
 
 
 But it is crashed giving following error
 
 *XTC error - maybe you are out of quota?*
 *
 *
 *dont know why it happened it is because as im saving .trr file every
 200ps? is it creating large files? or should i give different name in
 extending simulation?*
 *
 *
 *Please help*
 *
 *
 *Thanks,*
 *Nitin*
 -- 
 gmx-users mailing listgmx-users@gromacs.org
 http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] Issue running gromacs in Cluster

2013-05-13 Thread Broadbent, Richard



On 13/05/2013 08:46, Sainitin Donakonda saigr...@gmail.com wrote:

Hello,

I am trying to run 20 ns protein ligand simulation on cluster using
following MD.MDP file

; 7.3.3 Run Control
integrator  = md; leap-frog integrator
dt  = 0.002 ; 2 fs
nsteps  = 500; maximum number of steps
to integrate



; 7.3.8 Output Control
nstxout = 200 ; suppress .trr output
nstvout = 200; suppress .trr output

This writes out every 0.4 ps I doubt that¹s what you want

nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 1000  ; write .xtc trajectory every 2 ps
energygrps  = Protein LIG

; 7.3.9 Neighbor Searching
nstlist = 5 ; [steps] freq to update neighbor
list
ns_type = grid  ; method of updating neighbor list
pbc = xyz   ; periodic boundary conditions in
all directions
rlist   = 1.2   ; [nm] cut-off distance for the
short-range neighbor list

; 7.3.10 Electrostatics
coulombtype = PME   ; Particle-Mesh Ewald
electrostatics
rcoulomb= 1.2   ; [nm] distance for Coulomb
cut-off

; 7.3.11 VdW
vdwtype = switch   ; twin-range cut-off with rlist
where rvdw = rlist
rvdw= 1.2   ; [nm] distance for LJ cut-off
rvdw_switch = 0.8   ; Start switching th LJ potential
DispCorr= EnerPres ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
when using PME
pme_order   = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol  = 1e-5  ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl  = V-rescale ; temperature
coupling with Berendsen-thermostat
tc_grps = Protein_LIG Water_and_ions; groups to couple
seperately to temperature bath
tau_t   = 0.10.1; [ps] time
constant for coupling
ref_t   = 300300; [K] reference
temperature for coupling

; Pressure coupling
pcoupl  = Parrinello-Rahman ; pressure coupling is on for
NPT
pcoupltype  = isotropic ; uniform scaling of box
vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility
of
water, bar^-1
refcoord_scaling= com

; 7.3.17 Velocity Generation
gen_vel = no; velocity generation turned off

; 7.3.18 Bonds
constraints = all-bonds ; convert all bonds to constraints
constraint_algorithm= LINCS ; LINear Constraint Solver
continuation= yes   ; apply constraints to the start
configuration
lincs_order = 4 ; highest order in the expansion
of
the contraint coupling matrix
lincs_iter  = 1 ; number of iterations to correct
for rotational lengthening
lincs_warnangle = 30; [degrees] maximum angle that a
bond can rotate before LINCS will complain


*and im using following commands dividing 20 ns to 10 ns each via
extending
simulation*


*#This is the first simulation MD.mdp file contains 20 ns setup*
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_first10.tpr

mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16

*#This extends 10 ns simulation*
tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr

mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi
MD_first10.cpt -append -np 16


But it is crashed giving following error

*XTC error - maybe you are out of quota?*
*
*
*dont know why it happened it is because as im saving .trr file every
200ps? is it creating large files? or should i give different name in
extending simulation?*

No you are writing every 200 steps not ps this is explained in the
turtorials and the manual
You can check the file size by looking at ls -lh my guess is both the trr
and xtc will be gigantic

*
*
*Please help*
*
*
*Thanks,*
*Nitin*
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[gmx-users] umbrella sampling

2013-05-13 Thread Nawel Mele

HI,

I would like to compute an umbrella sampling simulation for o protein
divided in two domain, with Center of mass pulling using as constraint
between the two domains. And the  constraint is applied instead of a
harmonic potential
I create a pull.mdp file with this option for the pull:

title   = Umbrella pulling simulation
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 25; 500 ps
nstcomm = 10
; Output parameters
nstxout = 5000  ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout   = 500   ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
*; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = domain_1 domain_2
tau_t   = 0.50.5
ref_t   = 310310*
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
*; Pull code
pull= constraint
pull_geometry   = distance  ; simple distance increase
pull_dim= Y Y Y
pull_start  = yes   ; define initial COM distance  0
pull_ngroups= 2
pull_group0 = domain_1
pull_group1 = domain_2
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1 nm^-2*


I don't know if I use the good option for compute this king of umbrella
sampling.
When I run the grompp command: *grompp -f md_pull.mdp -c min1.gro -p
topol.top -n index.ndx -o pull.tpr* I optain this error:
*
Fatal error:
108147 atoms are not part of any of the T-Coupling groups*


I am little confuse with the mdp file option. I don't know which name I
should clarify for  T-Coupling groups ( in green) ??

If some one can help me .
THanks a lot.

Nawel


-- 
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg
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Re: [gmx-users] Difference between g_rms and g_rmsdist

2013-05-13 Thread Nawel Mele

Thanks a lot for your answer.

2013/5/10 Justin Lemkul jalem...@vt.edu

On 5/10/13 4:24 AM, Nawel Mele wrote:

Hi,

I am trying to understand what is the difference between g_rms and
g_rmsdist commands.
I have looked at the manual and all I can find is that:

*g_rms*: The root mean square deviation (RM SD) of certain atoms in a

molecule with respect to a reference
structure can be calculated with the program g_rms by least-square fitting
the structure to the reference
structure (t2 = 0) and subsequently calculating the RMSD
*
g_rmsdist*: Alternatively the RMSD can be computed using a fit-free method

with the program g_rmsdist

What fit is this referring to ?

RMSD is normally calculated after a least-squares fit to eliminate the
influence of global rotations and translations that would otherwise result
in spuriously high RMSD values. In the case of g_rmsdist, no fitting is
done, and has different applications (explained in the help description).

-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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==
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--
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg
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Re: [gmx-users] Issue running gromacs in Cluster

2013-05-13 Thread Sainitin Donakonda

Thank you very much for inputs but i forgot to mention in previous query i
got one error ..with other protein ligand simulation i used same MD file
saving 200 steps..

*Cannot write trajectory frame; maybe you are out of quota?*
*
*
Whats the solution for this error ? is this same problem with saving 200
steps? or some thing else

Thanks,
Sainitin


On Mon, May 13, 2013 at 10:25 AM, Broadbent, Richard 
richard.broadben...@imperial.ac.uk wrote:



 On 13/05/2013 08:46, Sainitin Donakonda saigr...@gmail.com wrote:

 Hello,
 
 I am trying to run 20 ns protein ligand simulation on cluster using
 following MD.MDP file
 
 ; 7.3.3 Run Control
 integrator  = md; leap-frog integrator
 dt  = 0.002 ; 2 fs
 nsteps  = 500; maximum number of steps
 to integrate
 
 
 
 ; 7.3.8 Output Control
 nstxout = 200 ; suppress .trr output
 nstvout = 200; suppress .trr output

 This writes out every 0.4 ps I doubt that¹s what you want

 nstenergy   = 1000  ; save energies every 2 ps
 nstlog  = 1000  ; update log file every 2 ps
 nstxtcout   = 1000  ; write .xtc trajectory every 2 ps
 energygrps  = Protein LIG
 
 ; 7.3.9 Neighbor Searching
 nstlist = 5 ; [steps] freq to update neighbor
 list
 ns_type = grid  ; method of updating neighbor list
 pbc = xyz   ; periodic boundary conditions in
 all directions
 rlist   = 1.2   ; [nm] cut-off distance for the
 short-range neighbor list
 
 ; 7.3.10 Electrostatics
 coulombtype = PME   ; Particle-Mesh Ewald
 electrostatics
 rcoulomb= 1.2   ; [nm] distance for Coulomb
 cut-off
 
 ; 7.3.11 VdW
 vdwtype = switch   ; twin-range cut-off with rlist
 where rvdw = rlist
 rvdw= 1.2   ; [nm] distance for LJ cut-off
 rvdw_switch = 0.8   ; Start switching th LJ potential
 DispCorr= EnerPres ; apply long range dispersion
 corrections for energy
 
 ; 7.3.13 Ewald
 fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
 when using PME
 pme_order   = 4 ; interpolation order for PME, 4 =
 cubic
 ewald_rtol  = 1e-5  ; relative strength of
 Ewald-shifted potential at rcoulomb
 
 ; 7.3.14 Temperature Coupling
 tcoupl  = V-rescale ; temperature
 coupling with Berendsen-thermostat
 tc_grps = Protein_LIG Water_and_ions; groups to couple
 seperately to temperature bath
 tau_t   = 0.10.1; [ps] time
 constant for coupling
 ref_t   = 300300; [K] reference
 temperature for coupling
 
 ; Pressure coupling
 pcoupl  = Parrinello-Rahman ; pressure coupling is on for
 NPT
 pcoupltype  = isotropic ; uniform scaling of box
 vectors
 tau_p   = 2.0   ; time constant, in ps
 ref_p   = 1.0   ; reference pressure, in bar
 compressibility = 4.5e-5; isothermal compressibility
 of
 water, bar^-1
 refcoord_scaling= com
 
 ; 7.3.17 Velocity Generation
 gen_vel = no; velocity generation turned off
 
 ; 7.3.18 Bonds
 constraints = all-bonds ; convert all bonds to constraints
 constraint_algorithm= LINCS ; LINear Constraint Solver
 continuation= yes   ; apply constraints to the start
 configuration
 lincs_order = 4 ; highest order in the expansion
 of
 the contraint coupling matrix
 lincs_iter  = 1 ; number of iterations to correct
 for rotational lengthening
 lincs_warnangle = 30; [degrees] maximum angle that a
 bond can rotate before LINCS will complain
 
 
 *and im using following commands dividing 20 ns to 10 ns each via
 extending
 simulation*
 
 
 *#This is the first simulation MD.mdp file contains 20 ns setup*
 grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
 MD_first10.tpr
 
 mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16
 
 *#This extends 10 ns simulation*
 tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr
 
 mpirun -n 16 mdrun -s md_extended.tpr -deffnm MD_first10 -cpi
 MD_first10.cpt -append -np 16
 
 
 But it is crashed giving following error
 
 *XTC error - maybe you are out of quota?*
 *
 *
 *dont know why it happened it is because as im saving .trr file every
 200ps? is it creating large files? or should i give different name in
 extending simulation?*

 No you are writing every 200 steps not ps this is explained in the
 turtorials and the manual
 You can check the file size by looking at ls -lh my guess is both the trr
 and xtc will be gigantic

 *
 *

[gmx-users] Center of Mass (COM) spacing between protein and ligand

2013-05-13 Thread Arunima Shilpi

Respected Sir
many many thanks for your reply to my last mail. I was able able to debug
the error

Here I have new set of queries..

How much COM spacing should i consider for my protein-ligand interactiom
How much total distance I should move along z-axis/...
and which all conf file should i take into consideration for
npt_umbrella.mdp...

I have   my summary_distance.dat as an attachment

Here in your example I could not understand as to why have you taken conf0
extending to con450 for ur npt_umbrella.mdp..

I request you to kindly guide me to the next step...





-- 

Thanking You with Regards.

Arunima Shilpi

Ph. D Research Scholar(Cancer  Epigenetics)
Department of Life Science
National Institute of Technology
Rourkela
Odisha
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[gmx-users] air-water-interface

2013-05-13 Thread Nawel Mele

Hi all,

I am performing a simulation of protein at air/water interface.

For create an air-water interface I just expand the box in the z direction.
So,aAfter minimization we can noticed that water molecules moved out of
bulk water in the z direction.

Why you just need to expand the z-axis for obtain this interface?? I don't
understand the mechanism.

Thanks a lot for your answer


-- 
*Mlle* Mele Nawel
Master 2 In Silico Drug Design
University of Paris Diderot/Strasbourg
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[gmx-users] Residue renaming during mdrun

2013-05-13 Thread Laura Leay

All, I have a system of nitric acid modelled as NO3- and HO3+ plus SPC water. 
After setting the system up using genbox I then energy minimise. Althouth the 
input conf.gro file looks fine (NO3- labelled 'NO3', HO3+ labelled 'HO3' and 
water labelled 'SOL') the confout file has all of the H3O renamed to 'SOL'. 
This makes it difficult to analyse my system if I can't distinguish between 
water and hydronium.

To construct the system I started with a single NO3- and a single HO3+ in 
separate gro files. I used the following commands in this order:

genbox -cs NO3.gro -nmol 124 -box 4 4 4 -o NO3conf.gro
genbox -cp NO3conf.gro -ci hydronium.gro -nmol 124 -o NO3+H3Oconf.gro
genbox -cp NO3+HO3conf.gro -cs -o conf.gro

This results in the following order in the gro file: NO3, HO3, SOL (I manually 
edit the topology file so that the number of water molecules matches those 
added by genbox).
This is the same as the order in the topology file. Residues in the topology 
file have the same name as in the original gro files.

I should point out that I'm using my own force field file, based on information 
on the literature, with the parameters for SPC water taken from the gromacs 
AMBER force field (all the literature data is based on AMBER). I don't see that 
this would affect residue naming though.

I'm using gromacs v 4.5.4

If anyone can shed some light on this, or suggest a work around, I'd appreciate 
it.

Laura
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[gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be

2013-05-13 Thread aixintiankong

 Dear,
  i want to study how ligands change the conformations using the gromacs 
software and i want to run 100ns, but i don't konw how to reasonably set the  
nstxout nstvout nstenergy nstlog and nstxtcout.
 Thank you very much!
  
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[gmx-users] mdrun and simulation time

2013-05-13 Thread Francesco

Good morning all,
This morning I checked the output of a 8ns (4 x 2ns) of simulation and I
noticed a strange behaviour:
The fist two simulations (each 2ns) ended up correctly and they both
took 2h 06min to finish.
The second two were still running when the cluster time was over  (I
asked for 2.30)  and
were truncated.
My system contains around 160k atoms and all the previous 2ns simulation
took between 2h and 2h:10min (77 cores, no gpu).

I had a look at the log and it seems that in the last two simulations
mdrun
did only 120.000 steps instead of 1.000.000.

Is it strange or it is possible/normal that with the increase of the ns
(always splitted in 2ns and extended) the running time is bigger?

thank you

Fra

-- 
Francesco Carbone
PhD student
Institute of Structural and Molecular Biology
UCL, London
fra.carbone...@ucl.ac.uk
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[gmx-users] Re: umbrella sampling

2013-05-13 Thread Thomas Schlesier


Hi,
it seems that you've only coupled your protein to the thermostat, but 
not the solvent, hence the error message.
Generally one would couple both domains of the protein to one thermostat 
and the solvent (inluding ions) to another thermostat.


Side note: If you want to use the WHAM method for constructing the PMF 
from the simulations, you need to use an harmonic potential instead of 
constraints. This method is named 'umbrella sampling'.
Using constraints and integrating the constraint force to obtain the PMF 
is called 'thermodynamic integration'.


Greetings
Thomas


Am 13.05.2013 10:33, schrieb gmx-users-requ...@gromacs.org:

HI,

I would like to compute an umbrella sampling simulation for o protein
divided in two domain, with Center of mass pulling using as constraint
between the two domains. And the  constraint is applied instead of a
harmonic potential
I create a pull.mdp file with this option for the pull:

title   = Umbrella pulling simulation
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 25; 500 ps
nstcomm = 10
; Output parameters
nstxout = 5000  ; every 10 ps
nstvout = 5000
nstfout = 500
nstxtcout   = 500   ; every 1 ps
nstenergy   = 500
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes   ; continuing from NPT
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
*; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = domain_1 domain_2
tau_t   = 0.50.5
ref_t   = 310310*
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
refcoord_scaling = com
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
*; Pull code
pull= constraint
pull_geometry   = distance  ; simple distance increase
pull_dim= Y Y Y
pull_start  = yes   ; define initial COM distance  0
pull_ngroups= 2
pull_group0 = domain_1
pull_group1 = domain_2
pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns
pull_k1 = 1000  ; kJ mol^-1  nm^-2*


I don't know if I use the good option for compute this king of umbrella
sampling.
When I run the grompp command: *grompp -f md_pull.mdp -c min1.gro -p
topol.top -n index.ndx -o pull.tpr* I optain this error:
*
Fatal error:
108147 atoms are not part of any of the T-Coupling groups*


I am little confuse with the mdp file option. I don't know which name I
should clarify for  T-Coupling groups ( in green) ??

If some one can help me .
THanks a lot.

Nawel


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Re: [gmx-users] Initial velocity

2013-05-13 Thread Justin Lemkul




On 5/13/13 1:48 AM, Acoot Brett wrote:

Dear All,

Will you please explain how the initial velocity may affect the MD results?


We use different initial velocities to improve sampling, i.e. to allow the 
trajectory to evolve in different ways.  In the end, in the limit of infinite 
sampling, the trajectory ensemble averages should be the same.



What the initial velocity really means?


Just what it claims to be - the initial (first) velocities of each atom.


How the velocity of the atoms in the protein changes in the MD process?


Please read about MD integration algorithms.


What is the reasonable scope of the initial velocity?


I don't know what this means.


Any suggestions on how to manually input a defined initial velocity?


Provide grompp with an input file that has velocities - .trr, .edr, .gro, .cpt.

-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


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Re: [gmx-users] Issue running gromacs in Cluster

2013-05-13 Thread Justin Lemkul




On 5/13/13 4:44 AM, Sainitin Donakonda wrote:

Thank you very much for inputs but i forgot to mention in previous query i
got one error ..with other protein ligand simulation i used same MD file
saving 200 steps..

*Cannot write trajectory frame; maybe you are out of quota?*
*
*
Whats the solution for this error ? is this same problem with saving 200
steps? or some thing else



You already got an answer to this - you're saving full-precision output far too 
often.  The sysadmins of clusters typically put in place quotas (limits) on how 
much disk space any one user can occupy, to prevent one person from sucking up 
all the available resources.  Or, if you're running on a local workstation or 
small cluster, you're just filling up your hard disk.  Just because it worked 
before doesn't mean it will again - you have run out of available room to write 
data.  Consider whether you need full-precision output every 0.4 ps - the answer 
is almost certainly no.


-Justin


On Mon, May 13, 2013 at 10:25 AM, Broadbent, Richard 
richard.broadben...@imperial.ac.uk wrote:




On 13/05/2013 08:46, Sainitin Donakonda saigr...@gmail.com wrote:


Hello,

I am trying to run 20 ns protein ligand simulation on cluster using
following MD.MDP file

; 7.3.3 Run Control
integrator  = md; leap-frog integrator
dt  = 0.002 ; 2 fs
nsteps  = 500; maximum number of steps
to integrate



; 7.3.8 Output Control
nstxout = 200 ; suppress .trr output
nstvout = 200; suppress .trr output


This writes out every 0.4 ps I doubt that¹s what you want


nstenergy   = 1000  ; save energies every 2 ps
nstlog  = 1000  ; update log file every 2 ps
nstxtcout   = 1000  ; write .xtc trajectory every 2 ps
energygrps  = Protein LIG

; 7.3.9 Neighbor Searching
nstlist = 5 ; [steps] freq to update neighbor
list
ns_type = grid  ; method of updating neighbor list
pbc = xyz   ; periodic boundary conditions in
all directions
rlist   = 1.2   ; [nm] cut-off distance for the
short-range neighbor list

; 7.3.10 Electrostatics
coulombtype = PME   ; Particle-Mesh Ewald
electrostatics
rcoulomb= 1.2   ; [nm] distance for Coulomb
cut-off

; 7.3.11 VdW
vdwtype = switch   ; twin-range cut-off with rlist
where rvdw = rlist
rvdw= 1.2   ; [nm] distance for LJ cut-off
rvdw_switch = 0.8   ; Start switching th LJ potential
DispCorr= EnerPres ; apply long range dispersion
corrections for energy

; 7.3.13 Ewald
fourierspacing  = 0.12  ; [nm] grid spacing for FFT grid
when using PME
pme_order   = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol  = 1e-5  ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl  = V-rescale ; temperature
coupling with Berendsen-thermostat
tc_grps = Protein_LIG Water_and_ions; groups to couple
seperately to temperature bath
tau_t   = 0.10.1; [ps] time
constant for coupling
ref_t   = 300300; [K] reference
temperature for coupling

; Pressure coupling
pcoupl  = Parrinello-Rahman ; pressure coupling is on for
NPT
pcoupltype  = isotropic ; uniform scaling of box
vectors
tau_p   = 2.0   ; time constant, in ps
ref_p   = 1.0   ; reference pressure, in bar
compressibility = 4.5e-5; isothermal compressibility
of
water, bar^-1
refcoord_scaling= com

; 7.3.17 Velocity Generation
gen_vel = no; velocity generation turned off

; 7.3.18 Bonds
constraints = all-bonds ; convert all bonds to constraints
constraint_algorithm= LINCS ; LINear Constraint Solver
continuation= yes   ; apply constraints to the start
configuration
lincs_order = 4 ; highest order in the expansion
of
the contraint coupling matrix
lincs_iter  = 1 ; number of iterations to correct
for rotational lengthening
lincs_warnangle = 30; [degrees] maximum angle that a
bond can rotate before LINCS will complain


*and im using following commands dividing 20 ns to 10 ns each via
extending
simulation*


*#This is the first simulation MD.mdp file contains 20 ns setup*
grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
MD_first10.tpr

mpirun -n 16 mdrun -s MD_first10.tpr -deffnm MD_first10 -np 16

*#This extends 10 ns simulation*
tpbconv -s MD_first10.tpr -extend 1 -o md_extended.tpr

mpirun -n 16 mdrun -s

Re: [gmx-users] Center of Mass (COM) spacing between protein and ligand

2013-05-13 Thread Justin Lemkul




On 5/13/13 5:33 AM, Arunima Shilpi wrote:

Respected Sir
many many thanks for your reply to my last mail. I was able able to debug
the error

Here I have new set of queries..

How much COM spacing should i consider for my protein-ligand interactiom
How much total distance I should move along z-axis/...
and which all conf file should i take into consideration for
npt_umbrella.mdp...

I have   my summary_distance.dat as an attachment



Attachments are not allowed by the list, nor is this one particularly useful in 
any sense to anyone who's not familiar with your exact system.



Here in your example I could not understand as to why have you taken conf0
extending to con450 for ur npt_umbrella.mdp..

I request you to kindly guide me to the next step...



I think you should spend some time familiarizing yourself with published 
literature on this topic.  There is a ton of information out there, and it 
really isn't possible to give someone step-by-step instructions via mailing 
list.  The mailing list archive does have some pieces of information that may be 
useful, but the literature should cover everything you need to know.


-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


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Re: [gmx-users] air-water-interface

2013-05-13 Thread Justin Lemkul




On 5/13/13 6:10 AM, Nawel Mele wrote:

Hi all,

I am performing a simulation of protein at air/water interface.

For create an air-water interface I just expand the box in the z direction.
So,aAfter minimization we can noticed that water molecules moved out of
bulk water in the z direction.

Why you just need to expand the z-axis for obtain this interface?? I don't
understand the mechanism.



You're not creating an air-water interface by doing this, you're creating an 
vacuum-water interface and your water molecules are evaporating into the empty 
space.


-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


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Re: [gmx-users] Residue renaming during mdrun

2013-05-13 Thread Justin Lemkul




On 5/13/13 6:30 AM, Laura Leay wrote:

All, I have a system of nitric acid modelled as NO3- and HO3+ plus SPC water. 
After setting the system up using genbox I then energy minimise. Althouth the 
input conf.gro file looks fine (NO3- labelled 'NO3', HO3+ labelled 'HO3' and 
water labelled 'SOL') the confout file has all of the H3O renamed to 'SOL'. 
This makes it difficult to analyse my system if I can't distinguish between 
water and hydronium.

To construct the system I started with a single NO3- and a single HO3+ in 
separate gro files. I used the following commands in this order:

genbox -cs NO3.gro -nmol 124 -box 4 4 4 -o NO3conf.gro
genbox -cp NO3conf.gro -ci hydronium.gro -nmol 124 -o NO3+H3Oconf.gro
genbox -cp NO3+HO3conf.gro -cs -o conf.gro

This results in the following order in the gro file: NO3, HO3, SOL (I manually 
edit the topology file so that the number of water molecules matches those 
added by genbox).
This is the same as the order in the topology file. Residues in the topology 
file have the same name as in the original gro files.

I should point out that I'm using my own force field file, based on information 
on the literature, with the parameters for SPC water taken from the gromacs 
AMBER force field (all the literature data is based on AMBER). I don't see that 
this would affect residue naming though.

I'm using gromacs v 4.5.4

If anyone can shed some light on this, or suggest a work around, I'd appreciate 
it.



Residue naming in output files is dependent upon residue naming found in the 
topology.  If the coordinate file is out of order with respect to the topology, 
grompp warns about this very clearly.  Naming mismatches are the only way I can 
see that this would happen.


-Justin

--


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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


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Re: [gmx-users] mdrun and simulation time

2013-05-13 Thread Justin Lemkul




On 5/13/13 6:41 AM, Francesco wrote:

Good morning all,
This morning I checked the output of a 8ns (4 x 2ns) of simulation and I
noticed a strange behaviour:
The fist two simulations (each 2ns) ended up correctly and they both
took 2h 06min to finish.
The second two were still running when the cluster time was over  (I
asked for 2.30)  and
were truncated.
My system contains around 160k atoms and all the previous 2ns simulation
took between 2h and 2h:10min (77 cores, no gpu).

I had a look at the log and it seems that in the last two simulations
mdrun
did only 120.000 steps instead of 1.000.000.

Is it strange or it is possible/normal that with the increase of the ns
(always splitted in 2ns and extended) the running time is bigger?



Random performance loss often happens when one or more nodes being used for the 
job get stuck or have errors.  If you're submitting to a queuing system, there 
should be diagnostic information that your admins can access that would suggest 
why this is happening.


-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


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[gmx-users] Fw: probability from COM of micelle

2013-05-13 Thread mohammad agha

- Forwarded Message -
From: Justin Lemkul jalem...@vt.edu
To: mohammad agha mra...@yahoo.com
Cc: 
Sent: Monday, May 13, 2013 4:11 PM
Subject: Re: probability from COM of micelle

It is much better to post this information to the list so that others can 
benefit from it.

-Justin

On 5/13/13 5:25 AM, mohammad agha wrote:
 Dear Justin,

 I found one way to obtain probability(nm^-1) plot with respect to COM. I 
 thought it is better that I say you.

 1- g_rdf -f md.xtc -s md.tpr -n index.ndx -o prob.xvg -com -nonorm
 2- Then values of probability are divided by r(box length).

 Best Regards
 Sara

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] air-water-interface

2013-05-13 Thread Nawel Mele

So we just compute an interface vacuum-water like the picture in attach in
increase the coordinate value of the z-axis of the box?
BUt I don't understand how just like that we creat an empty place and water
move to this place??

2013/5/13 Justin Lemkul jalem...@vt.edu

On 5/13/13 6:10 AM, Nawel Mele wrote:

Hi all,

I am performing a simulation of protein at air/water interface.

For create an air-water interface I just expand the box in the z
direction.
So,aAfter minimization we can noticed that water molecules moved out of
bulk water in the z direction.

Why you just need to expand the z-axis for obtain this interface?? I don't
understand the mechanism.

You're not creating an air-water interface by doing this, you're creating
an vacuum-water interface and your water molecules are evaporating into the
empty space.

-Justin

--
==**==

[gmx-users] Fwd: electrostatic potential map

2013-05-13 Thread tarak karmakar

Dear All,

 I am running a simulation of ligand binding in a protein. Ligand is
mostly negatively charged, so as expected it should bind to the positive
region of the protein. To check the possible binding zone, I try to
calculate or rather visualize the electrostatic potential map of a protein
in PYMOL. In this context I am utilizing pdb2pqr and then APBS in PYMOL.
Surprisingly, I see two different types of pictures, in presence and in
absence of water molecules present in the protein pdb file. In presence of
water molecules, some regions in the protein are showing positive while in
absence of water molecules these (same) regions are showing negative
potential. I don't know, exactly, what is the effect of water molecules in
this calculations.
Any short of suggestions would be greatly appreciated. ( I apologize
for posting bit different topic in this mailing list)
Thanks and regards,
Tarak
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Re: [gmx-users] air-water-interface

2013-05-13 Thread Justin Lemkul




On 5/13/13 8:01 AM, Nawel Mele wrote:

So we just compute an interface vacuum-water like the picture in attach in
increase the coordinate value of the z-axis of the box?


The list does not accept attachments.  If you want to post an image or file, 
provide a public link to access it.



BUt I don't understand how just like that we creat an empty place and water
move to this place??



Seems like intuitive behavior to me.  Think about basic physics and 
thermodynamics.

-Justin




2013/5/13 Justin Lemkul jalem...@vt.edu




On 5/13/13 6:10 AM, Nawel Mele wrote:


Hi all,

I am performing a simulation of protein at air/water interface.

For create an air-water interface I just expand the box in the z
direction.
So,aAfter minimization we can noticed that water molecules moved out of
bulk water in the z direction.

Why you just need to expand the z-axis for obtain this interface?? I don't
understand the mechanism.



You're not creating an air-water interface by doing this, you're creating
an vacuum-water interface and your water molecules are evaporating into the
empty space.

-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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

==**==
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jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] mdrun and simulation time

2013-05-13 Thread Francesco

thank you for the reply, I'm in contact with my admin and I hope that he
will tell me something soon.
One thing that I really don't understand is why only the last
nanoseconds are affected.
I run the same simulation (with the same paramenters) and I've never had
problems in the first 4 ns , only in the last 4.

Fra

On Mon, 13 May 2013, at 11:53 AM, Justin Lemkul wrote:
 
 
 On 5/13/13 6:41 AM, Francesco wrote:
  Good morning all,
  This morning I checked the output of a 8ns (4 x 2ns) of simulation and I
  noticed a strange behaviour:
  The fist two simulations (each 2ns) ended up correctly and they both
  took 2h 06min to finish.
  The second two were still running when the cluster time was over  (I
  asked for 2.30)  and
  were truncated.
  My system contains around 160k atoms and all the previous 2ns simulation
  took between 2h and 2h:10min (77 cores, no gpu).
 
  I had a look at the log and it seems that in the last two simulations
  mdrun
  did only 120.000 steps instead of 1.000.000.
 
  Is it strange or it is possible/normal that with the increase of the ns
  (always splitted in 2ns and extended) the running time is bigger?
 
 
 Random performance loss often happens when one or more nodes being used
 for the 
 job get stuck or have errors.  If you're submitting to a queuing system,
 there 
 should be diagnostic information that your admins can access that would
 suggest 
 why this is happening.
 
 -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
 
 
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-- 
Francesco Carbone
PhD student
Institute of Structural and Molecular Biology
UCL, London
fra.carbone...@ucl.ac.uk
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Re: [gmx-users] air-water-interface

2013-05-13 Thread Nawel Mele

Thanks a lot for your answer.
So by increasing the z coordinate after solvated the system we induce
creation of a empty space above the solvated box.
After minimisation a few water molecules move above its new empty space
because their link are not strong enough.

2013/5/13 Justin Lemkul jalem...@vt.edu

On 5/13/13 8:01 AM, Nawel Mele wrote:

So we just compute an interface vacuum-water like the picture in attach in
increase the coordinate value of the z-axis of the box?

The list does not accept attachments. If you want to post an image or
file, provide a public link to access it.

BUt I don't understand how just like that we creat an empty place and
water
move to this place??

Seems like intuitive behavior to me. Think about basic physics and
thermodynamics.

-Justin

2013/5/13 Justin Lemkul jalem...@vt.edu

On 5/13/13 6:10 AM, Nawel Mele wrote:

Hi all,

I am performing a simulation of protein at air/water interface.

For create an air-water interface I just expand the box in the z
direction.
So,aAfter minimization we can noticed that water molecules moved out of
bulk water in the z direction.

Why you just need to expand the z-axis for obtain this interface?? I
don't
understand the mechanism.

You're not creating an air-water interface by doing this, you're
creating
an vacuum-water interface and your water molecules are evaporating into
the
empty space.

-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/justinhttp://vt.edu/Pages/Personal/justin
h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

====

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Re: [gmx-users] issue in replica exchange

2013-05-13 Thread XAvier Periole


Ok, the redmine is filled up and anybody who has time to help finding the issue 
is welcome :) I can't do much more!

As an alternative a colleague suggested that I could potentially get around the 
problem by using a compilation combining Open-MP or thread-MPI for each replica 
running on one node (shared memory=no need of decomposition) and MPI across 
nodes. 
Would it work? 

But I might have a problem, the CG uses shifted potentials and they seem not to 
be implemented with OpenMP and thread-MPI is not compatible with MPI … 

Any other solution one could imagine?

XAvier.

On May 9, 2013, at 1:01 PM, XAvier Periole x.peri...@rug.nl wrote:

 
 I finally could reproduce the problem in gmx461 and have fled up a red mine 
 report. 
 
 I hope we can fix this easily but I am not sure how things go go from now! 
 Someone will get the bug assigned and fix it when ever possible or something 
 else?
 
 Thank you all for the help,
 XAvier.
 
 On May 2, 2013, at 10:15 PM, XAvier Periole x.peri...@rug.nl wrote:
 
 
 I'll look at the 4.6.1 version next week, I could install it but I got a 
 conflict between the environmental variable defining openMP variable but I 
 turned it off during compilation … 
 
 You could try to run on particle decomposition to see if you get a problem … 
 it should one quite quick.
 
 On May 2, 2013, at 2:36 PM, Michael Shirts mrshi...@gmail.com wrote:
 
 Both.  So if 4.6.1 doesn't work, I want to know so we can patch it
 before 4.6.2 comes out.  If it does work, then there is probably stuff
 that can be backported.
 
 On Thu, May 2, 2013 at 8:32 AM, XAvier Periole x.peri...@rug.nl wrote:
 
 You mean working with or working on the code?
 
 I'll try gmx-4.6.1
 
 On May 2, 2013, at 2:26 PM, Michael Shirts mrshi...@gmail.com wrote:
 
 Quick check here -- is 4.6 behaving correctly?  I actually spent some
 time working on REMD in 4.6, and it seems to be behaving  correctly in
 my hands with temperature and pressure control.
 
 Thanks for any additional info on this!
 
 On Thu, May 2, 2013 at 8:18 AM, Mark Abraham mark.j.abra...@gmail.com 
 wrote:
 On Thu, May 2, 2013 at 12:58 PM, XAvier Periole x.peri...@rug.nl wrote:
 
 
 I saw that redmine report, which could be related but it seems to happen
 only for runs done outside the domain and particle decompositions.
 
 I'll fill up a red mine.
 
 Anything I could do to help speeding the fix?
 
 
 What'd be really nice is some thought on how one can demonstrate that the
 implementation of the exchange matches what would be expected from the
 theory. For T-exchange under NVT, it is sufficient to rescale velocities
 and quantities derived from them by the correct factor. That includes
 various things like T-coupling history and integrator half-step 
 quantities
 (and does REMD with leap-frog make sense anyway?). For NPT, there's
 probably also some P-coupling quantities to scale, and the box to 
 exchange.
 Anything I've missed? Hopefully virial contributions don't matter either
 way?
 
 Perhaps a decent first step is to hack the code to do a self exchange, 
 by
 clearing the entire state and rebuilding with what would/should be 
 received
 from an exchange with a hypothethetical replica in an identical
 pre-exchange state. Only if the code can do that (i.e. mdrun -reprod
 produces a trajectory indistinguishable from a run that does not attempt
 this self exchange) is it worth considering proper state exchanges, and 
 the
 process of making the code do the former should illustrate what is 
 required
 for the latter.
 
 Mark
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Re: [gmx-users] Initial velocity

2013-05-13 Thread Brighter Agyemang

Please thanks so much for your support but I still do not get what all you
are talking about is

On 13 May 2013 11:44, Justin Lemkul jalem...@vt.edu wrote:

On 5/13/13 1:48 AM, Acoot Brett wrote:

Dear All,

Will you please explain how the initial velocity may affect the MD
results?

We use different initial velocities to improve sampling, i.e. to allow the
trajectory to evolve in different ways. In the end, in the limit of
infinite sampling, the trajectory ensemble averages should be the same.

What the initial velocity really means?

Just what it claims to be - the initial (first) velocities of each atom.

How the velocity of the atoms in the protein changes in the MD process?

Please read about MD integration algorithms.

What is the reasonable scope of the initial velocity?

I don't know what this means.

Any suggestions on how to manually input a defined initial velocity?

Provide grompp with an input file that has velocities - .trr, .edr, .gro,
.cpt.

-Justin

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Re: [gmx-users] Initial velocity

2013-05-13 Thread Justin Lemkul

On 5/13/13 9:45 AM, Brighter Agyemang wrote:

Please thanks so much for your support but I still do not get what all you
are talking about is

These posts are not related to your question. Reading posts on other topics can
be very informative and should be augmented by literature and textbook reading.

-Justin

On 13 May 2013 11:44, Justin Lemkul jalem...@vt.edu wrote:

On 5/13/13 1:48 AM, Acoot Brett wrote:

Dear All,

Will you please explain how the initial velocity may affect the MD
results?

What the initial velocity really means?

Just what it claims to be - the initial (first) velocities of each atom.

How the velocity of the atoms in the protein changes in the MD process?

Please read about MD integration algorithms.

What is the reasonable scope of the initial velocity?

I don't know what this means.

Any suggestions on how to manually input a defined initial velocity?

Provide grompp with an input file that has velocities - .trr, .edr, .gro,
.cpt.

-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

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[gmx-users] QM/MM simulations

2013-05-13 Thread DavidPO

Dear GROMACS support!

For my experiment I should use QM/MM methods. For this reason I should link
mdrun program with ORCA.
I'm working with 4.6 gromacs version and doing following:
  download ORCA on my computer;
  set the flags:
  BASENAME=topol
  ORCA_PATH=/home/timofeev/ORCA/orca_2_9_1_linux_i686 (I think it
isn't matter)
  after this I run in terminal at right directory:
  cmake --with-qmmm-orca --without-qmmm-gaussian ../gromacs-4.6
  make
  make install
  And start mdrun:
mdrun -v -c qmmm1.gro -nt 1
  Finally It gives the following error:
 Ab-initio calculation only supported with Gamess, Gaussian or ORCA.

Thank you!
David 



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[gmx-users] RDF - water and protein

2013-05-13 Thread Steven Neumann

Dear Gmx Users,

I run long simulation of my protein with 50 small molecules in water.
I calculated the RDF (Protein - Water) using -surf mol and -rdf mol_com.
Please, take a look at my plot:

http://speedy.sh/tmJbD/rdf-P-W.png

Could you please, explain me why the second peak is so high? Shall I use
option -nopbc ?
How can I obtain the density [kg/m3] versus the distance? I wish to compare
it with RDF of Protein-Ligands so wish to use some normalization for them
to be comparable - peaks will be visible.

Steven
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Re: [gmx-users] QM/MM simulations

2013-05-13 Thread Justin Lemkul




On 5/13/13 9:51 AM, DavidPO wrote:

Dear GROMACS support!

For my experiment I should use QM/MM methods. For this reason I should link
mdrun program with ORCA.
I'm working with 4.6 gromacs version and doing following:
   download ORCA on my computer;
   set the flags:
   BASENAME=topol
   ORCA_PATH=/home/timofeev/ORCA/orca_2_9_1_linux_i686 (I think it
isn't matter)
   after this I run in terminal at right directory:
   cmake --with-qmmm-orca --without-qmmm-gaussian ../gromacs-4.6
   make
   make install
   And start mdrun:
 mdrun -v -c qmmm1.gro -nt 1
   Finally It gives the following error:
  Ab-initio calculation only supported with Gamess, Gaussian or ORCA.



Your cmake command is incorrect.  You're using some sort of hybrid 
cmake/autoconf syntax.  What you should be invoking is something like:


cmake -DGMX_QMMM_PROGRAM=ORCA ../gromacs-4.6

-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


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[gmx-users] REMD analysis

2013-05-13 Thread bharat gupta

Dear Sir,

I repeated the simulation again for 25 replicas with the following temp.
distribution .

280
289.1
298.5
308.2
318.2
328.6
339.3
350.3
361.7
373.5
385.6
398.1
411.1
424.4
438.3
452.5
467.2
482.4
498.1
514.3
531.0
548.3
566.1
584.5
603.5
623.2

The output of md.log file is :-

Replica exchange statistics
Repl  24999 attempts, 12500 odd, 12499 even
Repl  average probabilities:
Repl 0123456789   10   11   12
13   14   15   16   17   18   19   20   21   22   23   24   25
Repl  .63  .63  .62  .62  .61  .61  .60  .60  .59  .59  .58  .59  .59
.60  .60  .61  .62  .62  .63  .64  .64  .65  .65  .66  .66

Repl  number of exchanges:
Repl 0123456789   10   11   12
13   14   15   16   17   18   19   20   21   22   23   24   25
Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408
7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266

Repl  average number of exchanges:
Repl 0123456789   10   11   12
13   14   15   16   17   18   19   20   21   22   23   24   25
Repl  .63  .62  .63  .62  .61  .61  .60  .60  .59  .59  .58  .59  .59
.59  .60  .60  .61  .62  .63  .63  .63  .65  .65  .66  .66

The average acceptance ration is around 0.6 which is still high.

The link for replica_temp,replica_index :
https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png
https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png

The temp files look better but the index file looks weird ...

Do i need to experiment with the gap difference in order to get the
required ration of 0.2-0.3 ?? There is some problem with the .mdp file
settings??

-- 
Bharat
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Re: [Spam:*****] [gmx-users] REMD analysis

2013-05-13 Thread XAvier Periole


You need to increase the temperature gaps indeed if you want acceptance ratio 
~0.2/0.3. But again this won't work with the water … 

It is not clear what happens in your index file but probably a problem from 
grace to plot so many points … you can try to increase the Max drawing path 
length in the preference menu of grace.

On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com wrote:

 Dear Sir,
 
 I repeated the simulation again for 25 replicas with the following temp.
 distribution .
 
 280
 289.1
 298.5
 308.2
 318.2
 328.6
 339.3
 350.3
 361.7
 373.5
 385.6
 398.1
 411.1
 424.4
 438.3
 452.5
 467.2
 482.4
 498.1
 514.3
 531.0
 548.3
 566.1
 584.5
 603.5
 623.2
 
 The output of md.log file is :-
 
 Replica exchange statistics
 Repl  24999 attempts, 12500 odd, 12499 even
 Repl  average probabilities:
 Repl 0123456789   10   11   12
 13   14   15   16   17   18   19   20   21   22   23   24   25
 Repl  .63  .63  .62  .62  .61  .61  .60  .60  .59  .59  .58  .59  .59
 .60  .60  .61  .62  .62  .63  .64  .64  .65  .65  .66  .66
 
 Repl  number of exchanges:
 Repl 0123456789   10   11   12
 13   14   15   16   17   18   19   20   21   22   23   24   25
 Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408
 7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266
 
 Repl  average number of exchanges:
 Repl 0123456789   10   11   12
 13   14   15   16   17   18   19   20   21   22   23   24   25
 Repl  .63  .62  .63  .62  .61  .61  .60  .60  .59  .59  .58  .59  .59
 .59  .60  .60  .61  .62  .63  .63  .63  .65  .65  .66  .66
 
 The average acceptance ration is around 0.6 which is still high.
 
 The link for replica_temp,replica_index :
 https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png
 https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png
 
 The temp files look better but the index file looks weird ...
 
 Do i need to experiment with the gap difference in order to get the
 required ration of 0.2-0.3 ?? There is some problem with the .mdp file
 settings??
 
 -- 
 Bharat
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[gmx-users] Re: RDF - water and protein

2013-05-13 Thread Thomas Schlesier


Hi,
the manual mentions that with the option '-surf' no normalization is 
done. So it's normal the RDF will inrease with larger distances, since 
the further you'll go away from the protein, the bigger the spherical 
shell is (from which the RDF for distance r is calculated) and the more 
water molecules will be in this shell.


Because of this using the '-nopbc' option shouldn't change anything.
One thing which i find rather strange, is that for really high distances 
the RDF goes down. Would have thought that with pbc the RDF should 
increase all the time.


But i have no idea to perform a sensible normalization afterwards.

Greetings
Thomas


Am 13.05.2013 17:24, schrieb gmx-users-requ...@gromacs.org:

Dear Gmx Users,

I run long simulation of my protein with 50 small molecules in water.
I calculated the RDF (Protein - Water) using -surf mol and -rdf mol_com.
Please, take a look at my plot:

http://speedy.sh/tmJbD/rdf-P-W.png

Could you please, explain me why the second peak is so high? Shall I use
option -nopbc ?
How can I obtain the density [kg/m3] versus the distance? I wish to compare
it with RDF of Protein-Ligands so wish to use some normalization for them
to be comparable - peaks will be visible.

Steven


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Re: [gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be

2013-05-13 Thread Francesco

As usual there is no universal question, it depends on what do you want
to see from your MD.
The main factor to consider is the disk space that you can use if
you decide to save every 10 ps it means that for 100ns you'll have
10.000 frame, depending on your system this can be a huge amount of
data.
At the same time if you save every 100ps you may miss some interesting
conformations.

grompp tells you how much data you will generate with your .mdp.

Fra

On Mon, 13 May 2013, at 10:37 AM, aixintiankong wrote:
  Dear,
   i want to study how ligands change the conformations using the
   gromacs software and i want to run 100ns, but i don't konw how to
   reasonably set the  nstxout nstvout nstenergy nstlog and nstxtcout.
  Thank you very much!
   
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-- 
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PhD student
Institute of Structural and Molecular Biology
UCL, London
fra.carbone...@ucl.ac.uk
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Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

2013-05-13 Thread Reza

So I think I figured out what was causing the discrepancy of Charmm27 energies 
between gromacs and NAMD. It appears that it's related to the gromacs version: 
energies from 4.5.7 and NAMD match very well while 4.6.1 gives energies that 
are different from both 4.5.7 and NAMD.

Here are the results form my tests on POPC membrane:

===
  BONDANGLEDIH IMP   COULLJ  POT
gromacs-4.5.7/gromacs.log
  1539.1203111.9021250.540  16.284   -1705.306   -1219.345
2993.188

gromacs-4.6.1/gromacs.log
  1539.1203111.9021250.540  16.284   -5997.992 350.084 
269.945

namd-2.9/namd.out
  1539.1163111.9201250.542  16.284   -1705.307   -1219.343
2993.211
===


I think this could be due to either 1) the simulation setup should be different 
between 4.5.7 and 4.6.1 when running single point calculations, or 2) my 4.6.1 
compilation is not correct (although all regression tests passed), or 3) there 
is a bug somewhere.

I'll attach a script that automates the comparison between GROMACS and NAMD in 
a separate post (it will make this post  50kB). If you run it and got 
similar/different results as mine, I'll be happy to know. Also any comment on 
the simulations setup is highly appreciated.

Reza



On May 3, 2013, at 11:57 AM, Reza resa...@gmail.com wrote:

 
 Actually pdb which is similarly doesn't have velocity information.  In this 
 case however I'm mainly interested to see how the potential terms compare 
 between the two packages with Charmm27 ff.
 
 Reza
 
 
 
 
 On 5/3/13 11:33 AM, Reza wrote:
 Thanks Mark!
 
 No, they weren't. See
 http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
 You cannot hope to reproduce accurately the energy of a configuration if
 you let the coordinates be manipulated.
 
 
 
 The rerun option is interesting - in my case however the potential energy 
 terms stayed identical but the kinetic term became zero.
 
 
 If you are using an .xtc file for the rerun, this makes sense since the .xtc 
 does not store velocities and hence kinetic energy cannot be calculated.
 
 -Justin
 
 
 Something you think is equivalent is not :-) Move to testing a system with
 two lipids. Inspect all the logfile outputs very carefully for clues.
 
 
 I totally agree :) So far I found out that for no cut-off simulation in 
 Gromacs, rather that specifying a large cut-off, it needs 
 rlist=rvdw=rcoulomb=0 and pbc=no along with ns_type=simple and nstlist=0 
 (according to the manual). I am running various tests and will update if I 
 find out what is causing the discrepancy.
 
 Reza
 
 On May 1, 2013, at 5:46 PM, Mark Abraham mark.j.abra...@gmail.com wrote:
 
 On Wed, May 1, 2013 at 2:32 PM, Reza Salari resa...@gmail.com wrote:
 
 Hi Justin,
 
 I actually did :) but it ended up being bigger than 50 kb so it needed
 moderator approval to show up. I was hoping it would've been released by
 now. I'll attach a the details below.
 
 Any help/hint is highly appreciated.
 
 Reza
 
 Details:
 
 *1)* Both systems were prepared using VMD membrane package and then
 waters were removed. I used Gromacs 4.6.1 and NAMD 2.9.
 
 *2)* Simulations were run in vacuum as a single-point energy calculations
 (0 step).
 
 
 No, they weren't. See
 http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy
 You cannot hope to reproduce accurately the energy of a configuration if
 you let the coordinates be manipulated.
 
 PME was not used.
 
 *3) *For Gromacs runs, pdb2gmx was used to prepare the system and the
 output was saved as the pdb format. The mdp file:
 
 integrator= md
 nsteps= 0
 nstlog  = 1
 nstlist= 1
 ns_type= grid
 rlist= 100.0
 coulombtype= cut-off
 rcoulomb= 100.0
 rvdw= 100.0
 pbc = no
 
 *4) *NAMD input file:
 
 structure  ../0_prep/memb_nowat.psf
 paratypecharmm  on
 parameterspar_all27_prot_lipid.prm
 exclude scaled1-4
 1-4scaling 1.0
 switching off
 switchdist 8
 cutoff 1000
 pairlistdist 1000
 margin 0
 timestep 1.0
 outputenergies 1
 outputtiming 1
 binaryoutput no
 coordinates ../0_prep/memb_nowat.pdb
 outputname out
 dcdfreq 10
 temperature 300
 run 0
 
 *5)* Energies:
 
 For Single POPC  (kcal/mol)
 
 
 Gromacs NAMD Diff
 
 Bond 43.0022 43.0015 -0.0007
 Angle 80.6568 80.6571 0.0003
 Dih 29.8083 29.8083 0.
 Imp 0.8452 0.8452 0.
 
 Coul -17.2983 -17.2983 0.
 LJ -7.0798 -7.0798 0.
 
 Pot 129.9343 129.9340 -0.0003
 
 
 The intra-molecule terms look fine. Since this is a lipid, there are
 non-bonded interactions that are intra-molecule, so the non-bondeds also
 seem fine.
 
 For POPC Memb (kcal/mol)
 
 Gromacs NAMD Diff
 
 Bond 1539.1181 1539.1162 -0.0019
 Angle 3111.9264 3111.9197 -0.0067
 Dih 1250.5425 1250.5421 -0.0004
 Imp 16.2837 16.2837 0.
 
 Coul -1837.8585

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

2013-05-13 Thread Reza

Here is the script:
#!/bin/bash

# note: you must have par_all27_prot_lipid.prm in the starting directory


set -e

PROGRAMS=/g1/home/resal/Programs
GMX_BIN_457=$PROGRAMS/gromacs/4.5.7/thread/bin
GMX_BIN_461=$PROGRAMS/gromacs/4.6.1/thread/bin
NMD_BIN=$PROGRAMS/namd/NAMD_2.9_Linux-x86_64-multicore
VMD_BIN=$PROGRAMS/vmd/1.9.1/bin

if [ -d prep ]; then
rm -rf prep
fi
if [ -d gromacs-4.5.7 ]; then
rm -rf gromacs-4.5.7
fi
if [ -d gromacs-4.6.1 ]; then
rm -rf gromacs-4.6.1
fi

if [ -d namd-2.9 ]; then
rm -rf namd-2.9
fi

mkdir prep
cd prep
cat  psfgen  EOF

# create the membrane
package require membrane
membrane -l POPC -x 40 -y 40 -o membrane

mol delete all

# delete water molecules
mol load psf membrane.psf pdb membrane.pdb

package require psfgen
readpsf membrane.psf
coordpdb membrane.pdb

set wat_sel   [atomselect top water]
set wat_segs[lsort -unique [\$wat_sel get segid]]
foreach wseg \$wat_segs {
set sel [atomselect top segid \$wseg and water]
set wat_res [lsort -unique [\$sel get resid]]
foreach res \$wat_res {
delatom \$wseg \$res
}
}

writepsf memb_nowat.psf
writepdb memb_nowat.pdb
quit

EOF

$VMD_BIN/vmd -dispdev none -e psfgen

cd ..
mkdir gromacs-4.5.7
cd gromacs-4.5.7

cat  pdb2gmx.in  EOF
8
6

EOF

cat  mdpfile.mdp  EOF
integrator= md 
nsteps= 0  
nstlog= 1
nstlist   = 0
ns_type   = simple
rlist = 0
coulombtype   = cut-off 
rcoulomb  = 0
rvdw  = 0
pbc   = no

EOF

GMXBIN=$GMX_BIN_457
source $GMXBIN/GMXRC
$GMXBIN/pdb2gmx -f ../prep/memb_nowat.pdb #  pdb2gmx.in # choose CHARMM27 for 
ff, None for water
$GMXBIN/grompp  -f mdpfile.mdp -p topol.top -c ../prep/memb_nowat.pdb -o 
topol.tpr
$GMXBIN/mdrun   -nt 1 -s topol.tpr -g gromacs.log

cd ..
mkdir gromacs-4.6.1
cd gromacs-4.6.1
GMXBIN=$GMX_BIN_461
source $GMXBIN/GMXRC
$GMXBIN/pdb2gmx -f ../prep/memb_nowat.pdb  #  ../gromacs-4.5.7/pdb2gmx.in
$GMXBIN/grompp  -f ../gromacs-4.5.7/mdpfile.mdp -p topol.top -c 
../prep/memb_nowat.pdb -o topol.tpr
$GMXBIN/mdrun   -nt 1 -s topol.tpr -g gromacs.log


cd ..
mkdir namd-2.9
cd namd-2.9

cat  conf  EOF
structure../prep/memb_nowat.psf
coordinates  ../prep/memb_nowat.pdb

paratypecharmm  on
parameters  ../par_all27_prot_lipid.prm
exclude scaled1-4
1-4scaling  1.0

switching   off 
cutoff  1000
pairlistdist1000
timestep1.0
outputenergies  1
outputtiming1
binaryoutputno

outputname  namd
dcdfreq 1
temperature 300
run 0

EOF

$NMD_BIN/namd2 conf  namd.out


cd ..
cat  analyze_energies.py  EOF
import sys

lines = open(sys.argv[1]).readlines()

if sys.argv[1].endswith('log'):
match = lambda line, fields: all([f in line for f in fields])

for i, line in enumerate(lines):
if match(line, ('Bond', 'U-B', 'LJ-14')):
B, A, D, I, L1 = map(float, lines[i+1].split())
elif match(line, ('Coulomb-14','LJ (SR)')):
C1,L2, C2,P, K = map(float, lines[i+1].split())
elif match(line, ('Total Energy', 'Temperature', 'Pressure 
(bar)')):
break

print sys.argv[1]
print '%10.3f  %10.3f  %10.3f  %10.3f  %10.3f  %10.3f  %10.3f' % (
   B/4.184, A/4.184,D/4.184,I/4.184,
   (C1+C2)/4.184, (L1+L2)/4.184, P/4.184)

elif sys.argv[1].endswith('out'):

for line in lines:
if line.startswith('ENERGY:'):
f = line.split()
if f[1] == '0':
E = map(float, f[2:])
B, A, D, I, C, L = E[0:6]
P = E[11]
break
print sys.argv[1]
print '%10.3f  %10.3f  %10.3f  %10.3f  %10.3f  %10.3f  %10.3f' % (
   B, A,D,I,   C, L, P)
EOF

echo
echo ===
echo   BONDANGLEDIH IMP   COULLJ  
POT
python analyze_energies.py gromacs-4.5.7/gromacs.log
python analyze_energies.py gromacs-4.6.1/gromacs.log
python analyze_energies.py namd-2.9/namd.out
echo ===
echo

On May 13, 2013, at 3:57 PM, Reza resa...@gmail.com wrote:

 So I think I figured out what was causing the discrepancy of Charmm27 
 energies between gromacs and NAMD. It appears that it's related to the 
 gromacs version: energies from 4.5.7 and NAMD match very well while 4.6.1 
 gives energies that are different from both 4.5.7 and NAMD.
 
 Here are the results form my tests on POPC membrane:
 
 ===
  BONDANGLEDIH IMP   COULLJ  POT
 gromacs-4.5.7/gromacs.log
  1539.1203111.9021250.540  16.284   -1705.306   -1219.345

[gmx-users] Distance Restraints

2013-05-13 Thread Rama

Hi,

I'm new to Gromacs. How to convert NMR paramagnetic relaxation enhancement
distance restraints into gromacs format in topol.top file for structural MD
refinement.


--Rama



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Re: [gmx-users] setting up a simulation of an ionic liquid

2013-05-13 Thread Justin Lemkul




On 5/13/13 11:50 AM, Laura Leay wrote:

All,

I've seen a few threads about simulations in ionic liquds but have not come 
across anything that tells me what settings I should use in my mdp file. The 
system is nitric acid which has fully dissociated into NO3- and HO3+. The 
simulation will run fine with just the ions at low density under NVT. However, 
when I solvate the box with SPC water (using the Amber force field) the 
simulation energy minimises with a really maximum force, of the order of 10^5. 
If I try to run an NPT simulation it immediately crashes and the md.log fle 
reveals that the electrostatic potential was unreasonable high, resulting in 
NaN.



You should investigate which atom bears the maximum force; that will point to 
the source of your problem.



Below is the mdp file I've been using. I've been using PME electrostatics. If 
anyone can suggest some changes to make I would appreciate it.



The force field dictates most of the settings, most notably the cutoff.  The 
value of rvdw seems wrong, at least.


-Justin


Laura

PS, Justin, you were right earlier, there was a problem with my toplogy causing 
renaming of residues, I just hadn't spotted it. Thanks for your reply.

-


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

; RUN CONTROL PARAMETERS
integrator   = steep ;md for simulation, steep for Emin
; Start time and timestep in ps
tinit= 0
dt   = 0.0001
nsteps   = 5000 ;remove 3
; For exact run continuation or redoing part of a run
init_step= 0
; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1
; group(s) for center of mass motion removal
comm-grps=

; LANGEVIN DYNAMICS OPTIONS
; Temperature, friction coefficient (amu/ps) and random seed
;bd-temp  = 300
bd-fric  = 0
ld-seed  = 1993

; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol= 100
emstep   = 0.01
; Max number of iterations in relax_shells
niter= 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep   = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep   = 1000
nbfgscorr= 10

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout  = 0
nstvout  = 0
nstfout  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint= 1000
; Output frequency for energies to log file and energy file
nstlog   = 50
nstenergy= 50
; Output frequency and precision for xtc file
nstxtcout= 50
xtc-precision= 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps =
; Selection of energy groups
energygrps   =

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist  = 10
; ns algorithm (simple or grid)
ns_type  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
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 = Cut-off
; cut-off lengths
rvdw-switch  = 0
rvdw = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = EnerPres
; Extension of the potential lookup tables beyond the cut-off
table-extension  = 1
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; 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= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
epsilon_surface  = 0
optimize_fft = no

; GENERALIZED BORN ELECTROSTATICS
; Algorithm for calculating Born radii
gb_algorithm = Still
; Frequency of calculating the Born radii inside rlist
nstgbradii   = 1
; Cutoff for Born radii calculation; the contribution from atoms
; between rlist and rgbradii is updated every nstlist steps
rgbradii = 2
; Salt concentration in M for Generalized Born models
gb_saltconc

[gmx-users] Fwd: Rycaert-Bellemans function

2013-05-13 Thread Marcelo Vanean

Hello to all. I am simulating long-chain alcohols. For the dihedrals, I
used Rycaert-Bellemans function. In this case I should delete the pairs
from topology?
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Re: [gmx-users] Fwd: Rycaert-Bellemans function

2013-05-13 Thread Justin Lemkul




On 5/13/13 6:24 PM, Marcelo Vanean wrote:

Hello to all. I am simulating long-chain alcohols. For the dihedrals, I
used Rycaert-Bellemans function. In this case I should delete the pairs
from topology?



That depends on which force field you are using.  See manual section 4.2.12.

-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


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RE: [gmx-users] Fwd: Rycaert-Bellemans function

2013-05-13 Thread Dallas Warren

That really depends on where the function that you are using comes from and 
what forcefield you are using (because each forcefield can treat them 
differently).  If it is the one for alkane chains mentioned in the manual to be 
used with the GROMOS FFs, then as it states in the manual you have to remove 
pairs.  If it comes from the OPLS FFs, then you need to leave the pairs in.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 


 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
 boun...@gromacs.org] On Behalf Of Marcelo Vanean
 Sent: Tuesday, 14 May 2013 8:24 AM
 To: gmx-users@gromacs.org
 Subject: [gmx-users] Fwd: Rycaert-Bellemans function
 
 Hello to all. I am simulating long-chain alcohols. For the dihedrals, I
 used Rycaert-Bellemans function. In this case I should delete the pairs
 from topology?
 --
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Charge groups

2013-05-13 Thread Marcelo Vanean

Hi. I'm with doubts concerning the charge groups. I am simulating ethylene
glycol and the only way of charged groups are neutral is putting all atoms
in only one charge group. This is advisable? Is that a problem? What is the
greatest number of atoms in a charge group which is recommended?
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Re: [gmx-users] Charge groups

2013-05-13 Thread Justin Lemkul




On 5/13/13 8:23 PM, Marcelo Vanean wrote:

Hi. I'm with doubts concerning the charge groups. I am simulating ethylene
glycol and the only way of charged groups are neutral is putting all atoms
in only one charge group. This is advisable? Is that a problem? What is the
greatest number of atoms in a charge group which is recommended?



Most force fields do not use charge groups (i.e. one atom per charge group) 
and with PME, there is no requirement that a charge group have an integral charge.


-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


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Re: [Spam:*****] [gmx-users] REMD analysis

2013-05-13 Thread bharat gupta

Dear Sir,

Here's the result for the REMD trial with large temperature gaps.

Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4
447.1 471.0 496.1 522.6 550.5 579.9 610.8

Out of md16.log :

Replica exchange statistics
Repl  249 attempts, 125 odd, 124 even
Repl  average probabilities:
Repl 0123456789   10   11   12
13   14   15
Repl  .40  .34  .38  .43  .43  .36  .45  .40  .37  .48  .47  .45  .47
.44  .46

Repl  number of exchanges:
Repl 0123456789   10   11   12
13   14   15
Repl   50   42   46   52   57   40   58   49   42   53   61   63   56
57   58

Repl  average number of exchanges:
Repl 0123456789   10   11   12
13   14   15
Repl  .40  .34  .37  .42  .46  .32  .46  .40  .34  .43  .49  .51  .45
.46  .46
Average acceptance ratio : 0.46

But, the repli_index.xvg and replica_temp.xvg files still shows that the
replicas does not exchange equally well .

https://www.dropbox.com/s/zkbwpuj7l2o282b/replica_index.png
https://www.dropbox.com/s/0c8gp584v1hvlbx/replica_temp.png

what could be wrong in this case?? Is it the mdp file settings or implicit
solvent setting. Does the time to replica to exhange also affects their
swapping ??



On Tue, May 14, 2013 at 12:24 AM, XAvier Periole x.peri...@rug.nl wrote:


 You need to increase the temperature gaps indeed if you want acceptance
 ratio ~0.2/0.3. But again this won't work with the water …

 It is not clear what happens in your index file but probably a problem
 from grace to plot so many points … you can try to increase the Max
 drawing path length in the preference menu of grace.

 On May 13, 2013, at 4:22 PM, bharat gupta bharat.85.m...@gmail.com
 wrote:

  Dear Sir,
 
  I repeated the simulation again for 25 replicas with the following temp.
  distribution .
 
  280
  289.1
  298.5
  308.2
  318.2
  328.6
  339.3
  350.3
  361.7
  373.5
  385.6
  398.1
  411.1
  424.4
  438.3
  452.5
  467.2
  482.4
  498.1
  514.3
  531.0
  548.3
  566.1
  584.5
  603.5
  623.2
 
  The output of md.log file is :-
 
  Replica exchange statistics
  Repl  24999 attempts, 12500 odd, 12499 even
  Repl  average probabilities:
  Repl 0123456789   10   11   12
  13   14   15   16   17   18   19   20   21   22   23   24   25
  Repl  .63  .63  .62  .62  .61  .61  .60  .60  .59  .59  .58  .59  .59
  .60  .60  .61  .62  .62  .63  .64  .64  .65  .65  .66  .66
 
  Repl  number of exchanges:
  Repl 0123456789   10   11   12
  13   14   15   16   17   18   19   20   21   22   23   24   25
  Repl 7822 7752 7816 7760 7639 7628 7511 7442 7375 7332 7312 7424 7408
  7410 7522 7559 7684 7697 7878 7927 7917 8073 8151 8208 8266
 
  Repl  average number of exchanges:
  Repl 0123456789   10   11   12
  13   14   15   16   17   18   19   20   21   22   23   24   25
  Repl  .63  .62  .63  .62  .61  .61  .60  .60  .59  .59  .58  .59  .59
  .59  .60  .60  .61  .62  .63  .63  .63  .65  .65  .66  .66
 
  The average acceptance ration is around 0.6 which is still high.
 
  The link for replica_temp,replica_index :
  https://www.dropbox.com/s/c7soajnwc3uww8j/replica_temp.png
  https://www.dropbox.com/s/wvx82m4c6cnsfit/replica_index.png
 
  The temp files look better but the index file looks weird ...
 
  Do i need to experiment with the gap difference in order to get the
  required ration of 0.2-0.3 ?? There is some problem with the .mdp file
  settings??
 
  --
  Bharat
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[gmx-users] Large number of solvent molecules

2013-05-13 Thread Nikunj Maheshwari

Dear all,

I am trying to see the folding of a 89 aa peptide. So I am setting up the
system from linear conformation.
I gave the following commands to build the box and add the solvent
molecules.

editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro

genbox -cp outbox.gro -cs spc216.gro -p topol.top -o outh2o.gro

Reading solute configuration
Go Rough, Oppose Many Angry Chinese Serial killers
Containing 1440 atoms in 89 residues
Initialising van der waals distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
 based on residue and atom names, since they could not be
 definitively assigned from the information in your input
 files. These guessed numbers might deviate from the mass
 and radius of the atom type. Please check the output
 files if necessary.

Reading solvent configuration
216H2O,WATJP01,SPC216,SPC-
MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 18x18x13 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL (   3 atoms): 909792 residues
Calculating Overlap...
box_margin = 0.315
Removed 324522 atoms that were outside the box
Neighborsearching with a cut-off of 0.48
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
System total charge: 0.000
Grid: 73 x 73 x 51 cells
Successfully made neighbourlist
nri = 3007232, nrj = 82473964
Checking Protein-Solvent overlap: tested 36005 pairs, removed 1653 atoms.
Checking Solvent-Solvent overlap: tested 7152003 pairs, removed 73182 atoms.
Added 776673 molecules
Generated solvent containing 2330019 atoms in 776673 residues
Writing generated configuration to outh2o.gro

Back Off! I just backed up outh2o.gro to ./#outh2o.gro.1#
Go Rough, Oppose Many Angry Chinese Serial killers

Output configuration contains 2331459 atoms in 776762 residues
Volume : 23276.3 (nm^3)
Density: 1001.32 (g/l)
Number of SOL molecules:  776673

Processing topology
Adding line for 776673 solvent molecules to topology file (topol.top)


Later on, I used -d 0.5. I still get around 71 water molecules in the
system.

Then, I used g_mindist for both cases (d 1.0 and d 0.5). It is around 9 A
and 8.4 A respectively.

I need to know if I have done something wrong in setting up the system. Is
there any way to get feasible number of solvent molecules?

Thanks
Nikunj
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RE: [gmx-users] Large number of solvent molecules

2013-05-13 Thread Dallas Warren

From the box volume printed in the script output it appears you have a box 
that is approximately a 28nm cube.  And that size box requires a significant 
number of water molecules to fill up, so that number you have in there 
(~770,000) seems about correct.

If you want to have less water molecules, then you will need to make the 
simulation cell smaller.  Whether that is possible or not depends on what you 
are looking to observe, how big the molecule you are solvating is etc.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 


 -Original Message-
 From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
 boun...@gromacs.org] On Behalf Of Nikunj Maheshwari
 Sent: Tuesday, 14 May 2013 3:04 PM
 To: Discussion list for GROMACS users
 Subject: [gmx-users] Large number of solvent molecules
 
 Dear all,
 
 I am trying to see the folding of a 89 aa peptide. So I am setting up
 the
 system from linear conformation.
 I gave the following commands to build the box and add the solvent
 molecules.
 
 editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro
 
 genbox -cp outbox.gro -cs spc216.gro -p topol.top -o outh2o.gro
 
 Reading solute configuration
 Go Rough, Oppose Many Angry Chinese Serial killers
 Containing 1440 atoms in 89 residues
 Initialising van der waals distances...
 
 WARNING: Masses and atomic (Van der Waals) radii will be guessed
  based on residue and atom names, since they could not be
  definitively assigned from the information in your input
  files. These guessed numbers might deviate from the mass
  and radius of the atom type. Please check the output
  files if necessary.
 
 Reading solvent configuration
 216H2O,WATJP01,SPC216,SPC-
 MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
 solvent configuration contains 648 atoms in 216 residues
 
 Initialising van der waals distances...
 Will generate new solvent configuration of 18x18x13 boxes
 Generating configuration
 Sorting configuration
 Found 1 molecule type:
 SOL (   3 atoms): 909792 residues
 Calculating Overlap...
 box_margin = 0.315
 Removed 324522 atoms that were outside the box
 Neighborsearching with a cut-off of 0.48
 Table routines are used for coulomb: FALSE
 Table routines are used for vdw: FALSE
 Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
 System total charge: 0.000
 Grid: 73 x 73 x 51 cells
 Successfully made neighbourlist
 nri = 3007232, nrj = 82473964
 Checking Protein-Solvent overlap: tested 36005 pairs, removed 1653
 atoms.
 Checking Solvent-Solvent overlap: tested 7152003 pairs, removed 73182
 atoms.
 Added 776673 molecules
 Generated solvent containing 2330019 atoms in 776673 residues
 Writing generated configuration to outh2o.gro
 
 Back Off! I just backed up outh2o.gro to ./#outh2o.gro.1#
 Go Rough, Oppose Many Angry Chinese Serial killers
 
 Output configuration contains 2331459 atoms in 776762 residues
 Volume : 23276.3 (nm^3)
 Density: 1001.32 (g/l)
 Number of SOL molecules:  776673
 
 Processing topology
 Adding line for 776673 solvent molecules to topology file (topol.top)
 
 
 Later on, I used -d 0.5. I still get around 71 water molecules in
 the
 system.
 
 Then, I used g_mindist for both cases (d 1.0 and d 0.5). It is around 9
 A
 and 8.4 A respectively.
 
 I need to know if I have done something wrong in setting up the system.
 Is
 there any way to get feasible number of solvent molecules?
 
 Thanks
 Nikunj
 --
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 http://lists.gromacs.org/mailman/listinfo/gmx-users
 * Please search the archive at
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Re: [gmx-users] Large number of solvent molecules

2013-05-13 Thread Nikunj Maheshwari

Thank you Dr. Dallas. Yes I think the issue is that the starting
conformation is linear, as I want to study its folding properties. I tried
the same with helical starting conformation, and got around 11 water
molecules, which is still ok.
I am trying to find a way to simulate a 89 aa peptide in linear starting
conformation such that the simulation is practically feasible.

On Tue, May 14, 2013 at 10:45 AM, Dallas Warren dallas.war...@monash.eduwrote:

 From the box volume printed in the script output it appears you have a
 box that is approximately a 28nm cube.  And that size box requires a
 significant number of water molecules to fill up, so that number you have
 in there (~770,000) seems about correct.

 If you want to have less water molecules, then you will need to make the
 simulation cell smaller.  Whether that is possible or not depends on what
 you are looking to observe, how big the molecule you are solvating is etc.

 Catch ya,

 Dr. Dallas Warren
 Drug Discovery Biology
 Monash Institute of Pharmaceutical Sciences, Monash University
 381 Royal Parade, Parkville VIC 3052
 dallas.war...@monash.edu
 +61 3 9903 9304
 -
 When the only tool you own is a hammer, every problem begins to resemble a
 nail.


  -Original Message-
  From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
  boun...@gromacs.org] On Behalf Of Nikunj Maheshwari
  Sent: Tuesday, 14 May 2013 3:04 PM
  To: Discussion list for GROMACS users
  Subject: [gmx-users] Large number of solvent molecules
 
  Dear all,
 
  I am trying to see the folding of a 89 aa peptide. So I am setting up
  the
  system from linear conformation.
  I gave the following commands to build the box and add the solvent
  molecules.
 
  editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro
 
  genbox -cp outbox.gro -cs spc216.gro -p topol.top -o outh2o.gro
 
  Reading solute configuration
  Go Rough, Oppose Many Angry Chinese Serial killers
  Containing 1440 atoms in 89 residues
  Initialising van der waals distances...
 
  WARNING: Masses and atomic (Van der Waals) radii will be guessed
   based on residue and atom names, since they could not be
   definitively assigned from the information in your input
   files. These guessed numbers might deviate from the mass
   and radius of the atom type. Please check the output
   files if necessary.
 
  Reading solvent configuration
  216H2O,WATJP01,SPC216,SPC-
  MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
  solvent configuration contains 648 atoms in 216 residues
 
  Initialising van der waals distances...
  Will generate new solvent configuration of 18x18x13 boxes
  Generating configuration
  Sorting configuration
  Found 1 molecule type:
  SOL (   3 atoms): 909792 residues
  Calculating Overlap...
  box_margin = 0.315
  Removed 324522 atoms that were outside the box
  Neighborsearching with a cut-off of 0.48
  Table routines are used for coulomb: FALSE
  Table routines are used for vdw: FALSE
  Cut-off's:   NS: 0.48   Coulomb: 0.48   LJ: 0.48
  System total charge: 0.000
  Grid: 73 x 73 x 51 cells
  Successfully made neighbourlist
  nri = 3007232, nrj = 82473964
  Checking Protein-Solvent overlap: tested 36005 pairs, removed 1653
  atoms.
  Checking Solvent-Solvent overlap: tested 7152003 pairs, removed 73182
  atoms.
  Added 776673 molecules
  Generated solvent containing 2330019 atoms in 776673 residues
  Writing generated configuration to outh2o.gro
 
  Back Off! I just backed up outh2o.gro to ./#outh2o.gro.1#
  Go Rough, Oppose Many Angry Chinese Serial killers
 
  Output configuration contains 2331459 atoms in 776762 residues
  Volume : 23276.3 (nm^3)
  Density: 1001.32 (g/l)
  Number of SOL molecules:  776673
 
  Processing topology
  Adding line for 776673 solvent molecules to topology file (topol.top)
 
 
  Later on, I used -d 0.5. I still get around 71 water molecules in
  the
  system.
 
  Then, I used g_mindist for both cases (d 1.0 and d 0.5). It is around 9
  A
  and 8.4 A respectively.
 
  I need to know if I have done something wrong in setting up the system.
  Is
  there any way to get feasible number of solvent molecules?
 
  Thanks
  Nikunj
  --
  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.
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 --
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