[gmx-users] Energy analysis

2017-11-18 Thread Amir Zeb
Hi gromacs users,

I want to calculate the energy for comparative analysis of protein with and
without metal ion, wherein I would like to determine the influence of metal
on protein structural stability. I have used gromacs for simulation. Please
suggest me how to do this kind of analysis? Should i follow a specific
tutorial?

Amir
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[gmx-users] Turning off electrostatics between protein and water, then protein and protein

2017-11-18 Thread Aram Davtyan
Hello,

I am running simulations of two protein domains in tip4p water and 0.15M
salt concentration that contain up to 650,000 atoms total. The protein
domains are separated from each other at the start of each simulation and I
am measuring how the distance between them changes over time.

Now, I need to do the same simulations, but with electrostatics between
proteins and water turned off (with water-water, protein-protein,
ion-water, ion-protein electrostatics remaining). Then I need to repeat
that, but additionally turning off electrostatics between the two domains.
Water-water, ion-water, ion-protein, intra-domain electrostatics should
remain on.

What will be the best way to do this?

I am using CHARMM27 force field and the following settings to run the
production simulations:

integrator  = md
dt  = 0.002
nsteps  = 100 ; 2ns
nstlog  = 1000
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstcalcenergy   = 100
nstenergy   = 1000
;
cutoff-scheme   = Verlet
nstlist = 20
rlist   = 1.2
coulombtype = pme
rcoulomb= 1.2
vdwtype = Cut-off
vdw-modifier= Force-switch
rvdw_switch = 1.0
rvdw= 1.2
;
tcoupl  = Nose-Hoover
tc_grps = Protein Non-Protein
tau_t   = 1.0 1.0
ref_t   = 300.0   300.0
;
pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 5.0
compressibility = 4.5e-5
ref_p   = 1.0
;
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
nstcomm = 100
comm_mode   = linear
comm_grps   = Protein Non-Protein
;
refcoord_scaling= com


I have tried to use the energy groups (energygrp-table) to specify
interaction tables between water and protein, where I would set the
electrostatic potential to zero. However, given that energygrp-table and
Varlet cutoff-scheme are incompatible, I could not make it work. But it is
possible that I did something wrong.

Thank you in advance,

Aram
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Re: [gmx-users] Determining the cut offs more than half of the box

2017-11-18 Thread Mark Abraham
Hi,

I don't understand what you think you want long cutoffs for. They are baked
into the force field and you should not change those without reason to
believe it already works.

Mark

On Sat, 18 Nov 2017 18:08 Iman Ahmadabadi 
wrote:

> Dear Gromacs Users,
>
> I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box
> that its height along z direction is too small (for example 2.0 nm)  but
> the error will arise for me and I couldn't use the cut off more than 1.0 nm
> because of the box size. What should I do in this regard?
>
> Best,
> --
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Re: [gmx-users] virtual site, dummy massive site

2017-11-18 Thread Mark Abraham
Hi,

Yes those will affect what configurations are sampled, but not the LJ
component of the energy of the configurations.

Mark

On Sat, 18 Nov 2017 23:54 Alex  wrote:

> And the things that affect the motion of the things with LJ interactions.
> :)
>
> Alex
>
>
> On 11/18/2017 3:49 PM, Mark Abraham wrote:
> > Hi,
> >
> > Only things with LJ interactions can influence the LJ energy.
> >
> > Mark
> >
> > On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh  wrote:
> >
> >> I have 2 questions please. They seem evident, but I need to be sure to
> >> solve my simulation problem:
> >>
> >> 1- Does being a virtual site (charge, no mass) or a normal atom,
> effects on
> >> its LJ interaction energies with rest of system?
> >>
> >> 2-  Does adding a dummy massive site (no charge, only mass) to atoms of
> >> mono-atomic system, influences on the LJ energy of whole system?
> >>
> >> Best regards
> >> --
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> >> posting!
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> >>
>
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Re: [gmx-users] Restarting crashed simulation

2017-11-18 Thread Mark Abraham
Hi,

Looks like you made a typo with state.cpt and that you perhaps have
multiple mdrun processes running such that the actual output file is in one
of the backup files labelled with # characters.

Mark

On Fri, 17 Nov 2017 19:37 Ali Ahmed  wrote:

> Hello GROMACS users
> My MD simulation was crashed then I restarted the simulation from the point
> when the point was written using this command on 64 processors: mpirun -np
> 64  mdrun_mpi -s md.tpr -cpi stat.cpt
>
> After few days I got nothing in the folder usch as output.gro and I got the
> following
> ___
> Command line:
>   mdrun_mpi -s md.tpr -cpi stat.cpt
>
> Warning: No checkpoint file found with -cpi option. Assuming this is a new
> run.
>
>
> Back Off! I just backed up md.log to ./#md.log.2#
>
> Running on 4 nodes with total 64 cores, 64 logical cores
>   Cores per node:   16
>   Logical cores per node:   16
> Hardware detected on host compute-2-27.local (the node of MPI rank 0):
>   CPU info:
> Vendor: Intel
> Brand:  Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz
> SIMD instructions most likely to fit this hardware: AVX_256
> SIMD instructions selected at GROMACS compile time: AVX_256
>
>   Hardware topology: Basic
>
> Reading file md.tpr, VERSION 2016.3 (single precision)
> Changing nstlist from 10 to 40, rlist from 1 to 1.003
>
> Will use 48 particle-particle and 16 PME only ranks
> This is a guess, check the performance at the end of the log file
> Using 64 MPI processes
> Using 1 OpenMP thread per MPI process
>
> Non-default thread affinity set probably by the OpenMP library,
> disabling internal thread affinity
> WARNING: This run will generate roughly 50657 Mb of data
>
> starting mdrun 'Molecular Dynamics'
> 2500 steps,  5.0 ps.
>
> step 888000 Turning on dynamic load balancing, because the performance loss
> due to load imbalance is 8.7 %.
> step 930400 Turning off dynamic load balancing, because it is degrading
> performance.
> step 1328000 Turning on dynamic load balancing, because the performance
> loss due to load imbalance is 3.4 %.
> step 1328800 Turning off dynamic load balancing, because it is degrading
> performance.
> step 1336000 Turning on dynamic load balancing, because the performance
> loss due to load imbalance is 3.4 %.
> step 1338400 Turning off dynamic load balancing, because it is degrading
> performance.
> step 134 Will no longer try dynamic load balancing, as it degraded
> performance.
> Writing final coordinates.
>  Average load imbalance: 13.2 %
>  Part of the total run time spent waiting due to load imbalance: 7.5 %
>  Average PME mesh/force load: 1.077
>  Part of the total run time spent waiting due to PP/PME imbalance: 4.1 %
>
> NOTE: 7.5 % of the available CPU time was lost due to load imbalance
>   in the domain decomposition.
>   You might want to use dynamic load balancing (option -dlb.)
>
>
>Core t (s)   Wall t (s)(%)
>Time: 26331875.601   411435.556 6400.0
>  4d18h17:15
>  (ns/day)(hour/ns)
> Performance:   10.5002.286
> _
>
> Any advise or suggestion will be helpful.
>
> Thanks in advance
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Re: [gmx-users] virtual site, dummy massive site

2017-11-18 Thread Alex

And the things that affect the motion of the things with LJ interactions. :)

Alex


On 11/18/2017 3:49 PM, Mark Abraham wrote:

Hi,

Only things with LJ interactions can influence the LJ energy.

Mark

On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh  wrote:


I have 2 questions please. They seem evident, but I need to be sure to
solve my simulation problem:

1- Does being a virtual site (charge, no mass) or a normal atom, effects on
its LJ interaction energies with rest of system?

2-  Does adding a dummy massive site (no charge, only mass) to atoms of
mono-atomic system, influences on the LJ energy of whole system?

Best regards
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Re: [gmx-users] (no subject)

2017-11-18 Thread Mark Abraham
Hi,

Yes, modulo any exclusions you used.

Mark

On Fri, 17 Nov 2017 18:50 Faezeh Pousaneh  wrote:

> Hi,
>
> I have a simple system of non-charged diatomic molecule, (A-B).
>
> I expect total LJ interaction energy in such system when we put LJ
> parameters of atom B zero (c6 and c12=0)  should be equal with total LJ
> energy of a system containing only atom A.
> Am I right?
>
> Best regards
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Re: [gmx-users] virtual site, dummy massive site

2017-11-18 Thread Mark Abraham
Hi,

Only things with LJ interactions can influence the LJ energy.

Mark

On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh  wrote:

> I have 2 questions please. They seem evident, but I need to be sure to
> solve my simulation problem:
>
> 1- Does being a virtual site (charge, no mass) or a normal atom, effects on
> its LJ interaction energies with rest of system?
>
> 2-  Does adding a dummy massive site (no charge, only mass) to atoms of
> mono-atomic system, influences on the LJ energy of whole system?
>
> Best regards
> --
> Gromacs Users mailing list
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> * Please search the archive at
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[gmx-users] Determining the cut offs more than half of the box

2017-11-18 Thread Iman Ahmadabadi
Dear Gromacs Users,

I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box
that its height along z direction is too small (for example 2.0 nm)  but
the error will arise for me and I couldn't use the cut off more than 1.0 nm
because of the box size. What should I do in this regard?

Best,
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[gmx-users] c_6 and c_12 to zero

2017-11-18 Thread Faezeh Pousaneh
Hi,

I have a simple system of non-charged diatomic molecule, (A-B).

I expect total LJ interaction energy in such system when we put LJ
parameters of atom B zero (c6 and c12=0)  should be equal with total LJ
energy of a system containing only atom A.
Am I right?

Best regards
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[gmx-users] virtual site, dummy massive site LJ interactions

2017-11-18 Thread Faezeh Pousaneh
Hi,

I have 2 questions please. They seem evident, but I need to be sure to
solve my simulation problem:

1- Does being a virtual site (charge, no mass) or a normal atom, effects on
its LJ interaction energies with rest of system?

2-  Does adding a dummy massive site (no charge, only mass) to atoms of
mono-atomic system, influences on the LJ energy of whole system?

Best regards
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