[gmx-users] gromacs.org_gmx-users Digest, Vol 143, Issue 78
Sana Saeed
bioinformatic.lady at yahoo.com
Thu Mar 17 04:18:46 CET 2016
I am sending my message again because my mdp options were looking a little weird:
hi
I am performing protein ligand (pdb:4HBV)binding free energy calculations, I am done with complex simulation , now stuck in ligand simulation since last 2 weeks. first i was getting zero energy, and when I changed some of parameters and position restraint my ligand , now i am getting LINCS warnings sometimes with NPT and sometimes during production md. the strange part is that some of the lambdas are perfectly running while some of them crashes due to LINCS warnings, I know how to fix LINCS warnings (extending table size, decreasing step size, properly minimizing structure etc) but in this case some of lambdas are running perfectly, which means the structure and parameters are fine. I decreased step size to 1 fs and got the same result, bow i decreased it to 0.0001 ps. if someone ever got this kind of problem , please share your views.
my second question is that the simple simulation for solvation free energy of small molecule and the ligand simulation in binding free energy system are same? i mean can i use the solvation free energy parameters from BEVAN lab's tutorial in this situation? in some of tutorials they use position restraints for ligand simulation in water, that is the reason I used the same.
I provide npt and md.mdp parameters. if something is wrong kindly give comments. ignore the stepsize , I know its too small, I tried 0.001, 0.002, and this is the recent one, but couldn't see any difference.
thanks in advance
NPT.mdp
define = -DPOSRES
integrator = sd
tinit = 0
dt = 0.0001
nsteps = 500000 ; 100 ps
nstcomm = 100
; Boundary conditions
pbc = xyz
; Output
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 100 ; 10 ps
nstenergy = 100 ; 10 ps
nstcalcenergy = 20
nstxtcout = 100 ; 10 ps
xtc-precision = 1000
energygrps = System
; Neighbour searching
cutoff-scheme = Verlet
nstlist = 10 ; 20 fs
ns-type = grid
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Constraints
constraints = none
constraint-algorithm = lincs
lincs_iter = 1 ; accuracy of LINCS (1 is default)
lincs_order = 12 ; also related to accuracy (4 is default)
lincs-warnangle = 30 ; maximum angle that a bond can rotate before LINCS will complain
^M
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme-order = 6
fourierspacing = 0.10 ; grid spacing for FFT
ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb
optimize-fft = no
ewald_geometry = 3d
; van der Waal's
vdwtype = Switch
rvdw-switch = 0.9
DispCorr = EnerPres
;Temperature Coupling (SD integrator => Langevin dynamics)
tc_grps = System
tau_t = 1.0
ref_t = 298.15
; Pressure coupling
Pcoupl = Berendsen
pcoupltype = isotropic
tau_p = 2
compressibility = 4.5e-05
ref_p = 1.0
; Generate velocities
gen_vel = yes
gen_seed = -1
gen_temp = 298.15
continuation = no
; Free energy control stuff =
free-energy = yes
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
init-lambda-state = 0
coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0
vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0
couple-moltype = 15E
couple-intramol = no
couple-lambda0 = none
couple-lambda1 = vdw-q
nstdhdl = 100
calc-lambda-neighbors = -1
refcoord-scaling = com
PRODUCTION MD:
md.mdp
; Production MD
;
title = production
; Run parameters
integrator = sd ; stochastic leap-frog integrator
nsteps = 2500000
dt = 0.0001
nstcalcenergy = 100
energygrps = System
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Output control
nstvout = 500 ; save velocities to .trr file every 200 ps
nstfout = 500 ; save forces to .trr file every 100 ps
nstxout = 500 ; save coordinates every 5 ps
nstxtcout = 500 ; xtc compressed trajectory output every 2 ps
nstenergy = 500 ; save energies every 2 ps
nstlog = 500 ; update log file every 2 ps
; Bond parameters
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS (1 is default)
lincs_order = 6 ; also related to accuracy (4 is default)
lincs-warnangle = 30 ; maximum angle that a bond can rotate before LINCS will complain (30 is default)
; Neighbor searching
ns-type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme-order = 6
fourierspacing = 0.10 ; grid spacing for FFT
ewald-rtol = 1e-6 ; relative strength of the Ewald-shifted direct potential at rcoulomb
; Van der Waals
vdwtype = Switch
rvdw-switch = 0.9
DispCorr = EnerPres ; account for cut-off vdW scheme
;Temperature Coupling (SD integrator => Langevin dynamics)
tc_grps = System
tau_t = 1.0^M
ref_t = 298.15
; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-05 ; isothermal compressibility of water, bar^-1
; Velocity generation
gen_vel = no ; Velocity generation is on
gen_seed = -1 ; Use random seed
gen_temp = 298.15
continuation = yes ; Restarting after NPT
; Free energy control stuff
free-energy = yes
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
sc-coul = no
init-lambda-state = 0
coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0
vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0
couple-moltype = 15E
couple-intramol = no
couple-lambda0 = none
couple-lambda1 = vdw-q
nstdhdl = 100
dhdl-print-energy = yes
calc-lambda-neighbors = -1
Sana Saeed Khan,
Research Assistant
Chemoinformatics Lab
Graduate Student, MS bioinfo
Department of Bioinformatics
Soongsil University, Seoul, South Korea.
On Thursday, March 17, 2016 11:19 AM, "gromacs.org_gmx-users-request at maillist.sys.kth.se" <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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Today's Topics:
1. Re: Optimal hardware for running Gromacs (Szil?rd P?ll)
2. LINCS warnings for some lambdas. (Sana Saeed)
3. Using FFTK generated parameter file for Protein-Ligand
simulations (Soumya Lipsa Rath)
----------------------------------------------------------------------
Message: 1
Date: Wed, 16 Mar 2016 23:49:31 +0100
From: Szil?rd P?ll <pall.szilard at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: Discussion list for GROMACS users
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Optimal hardware for running Gromacs
Message-ID:
<CANnYEw5W9FZ-8B2dRhbgPNC3GZ0G61iGaZpJVZO3J6CwK7chKA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi David,
If seem to be interested in details so please do check the paper Carsten
linked (further papers can be found here
http://www.gromacs.org/Gromacs_papers). I also recommend you to look up
discussions on the mailing list form the past. Many of your questions have
been thoroughly answered before, hence the selective answers below.
On Sat, Mar 12, 2016 at 2:52 AM, David Berquist <berquist at buffalo.edu>
wrote:
> I'm looking into building a desktop computer for running Gromacs
> simulations. I'd like to know how I should configure it to get the best
> performance possible for the price.
>
> One example of something I might run on this system would be: simulate an
> ionic polymer of approximately 100k atoms for 1 millisecond. Coarse
> grained atoms, using Martini force field.
>
Will you typically not use PME? In that case your runs will be more
GPU-bound than usual which is relevant because many of the benchmarks out
there may not give you an accurate idea about the ideal CPU/GPU ratio.
>
> I would be planning to spend something under $1500 on this system.
>
When? FYI: both NVIDIA and AMD are expected to launch new GPUs that will be
substantially faster.
>
>
> In regards to the graphics card, what factors are important? I assume that
> the single precision Flop/s are a big factor, but what about memory
> bandwidth(on the card itself)?
>
This is a recurring question, I won't get into details, but in short:
(main) memory speed has little effect.
> I've noticed that Gromacs pages on GPUs tend to recommend nVidia cards,
> specifically those with CUDA Compute Capability 5.2. But, AMD Radeon cards
> appear to offer the same processing power for far lower prices(or
> alternatively, significantly more processing power for the same price).
5.1 is the first release with OpenCL support and the performance with AMD
GPUs is good, but there was room for improvement. We have been working on
optimizations and in the next release AMD Fiji cards are going to be _very_
good in terms of both raw performance and even better in perf/$ metric.
> For example, the nVidia GTX 970 offers 3494 GFlop/s of single precision,
> and 109 GFlop/s of double precision. It currently costs $290 at Newegg.
> On the other hand, the AMD Radeon R9 380 provides 3476.5 GFlop/s single
> precision, and 217.3 GFlop/s of double precision. It currently costs $150
> on Newegg.
>
> That's practically the same single precision, and nearly double the
> double-precision for around half the price.
>
> Or, for about the same price as the nVidia GTX 970 I could get an AMD
> Radeon R9 390. It provides 5120 GFlop/s of single precision and 640
> GFlop/s of double precision. That costs $310 on Newegg.
>
> That is, on paper, 46.5% more single precision performance, and 487% more
> double precision performance(nearly 5 times as much) for only a 6.9% higher
> price.
>
MD is not LINPACK, so while the SP throughput is (for now) a good indicator
of the GROMACS GPU (kernel) performance, you can only use the relative SP
flop rate to estimate performance only within an architectural family; e.g.
given the GTX 960 performance you can guesstimate what you'd get on the 980.
>
> So, does Gromacs run a lot faster on nVidia GPUs? Would the nVidia GTX 970
> provide similar or better performance than the AMD Radeon R9 390?
>
Based on quick extrapolation from the 980 and R290X numbers I had around,
those should perform similar, but results will greatly depend on the actual
stable clocks the cards run at.
However, does you 1.5k budget really not allow getting the next category of
cards? I'd recommend considering Fiji, especially the R9 Nano, or the GTX
980 / 980 Ti are good options.
> One more GPU Question; does Gromacs scale linearly across multiple graphics
> cards? So, if I have two identical cards which offer 2000 GFlop/s
> performance each, would they both together perform about the same as a
> more-expensive single card which provides 4000GFlop/s(provided you have a
> fast enough CPU, of course)?
>
Define "scaling". Assuming you mean strong scaling, no you won't get linear
scaling, especially not from one to two GPUs.
>
> Now, how about the CPU performance?
Typically it matters quite a bit. For your Martini run not so much.
Read the paper and do some test runs if you can.
> Would it be better to spend a lot of
> my budget on a high-end GPU, and then go for a low cost CPU? Something
> like an AMD Athlon X4 860K Kaveri Quad-Core 3.7 GHz CPU? Or would
> something like that bottleneck the performance of an nVidia GTX 970 or GTX
> 980? Maybe a AMD FX-6300 Vishera 6-Core 3.5 GHz? AMD FX-8300 Vishera
> 8-Core 3.3GHz?
> Does Intel vs AMD make any significant difference? When running Gromacs on
> a system with GPU compute turned on, what sort of computing load does
> Gromacs put on the CPU? Is there any commonly used CPU benchmark that can
> be used to approximate relative Gromacs performance between CPUs?
>
AMD CPUs are is sadly far far slower than Intel. Get a 4-core Haswell or
Skylake or the 6-core Hawell-E if you can afford.
>
>
> How important is the system RAM speed? Should I spend more of my budget
> building a DDR4 system(more expensive CPU, motherboard, and RAM modules),
> or would that not make a significant difference over DDR3?
>
It is not. Bio-mol MD runs mostly in cache. If it does not it will run so
slow that you won't get much in terms of results.
>
> Would you happen to know what quantity of memory should be sufficient for
> common Gromacs simulation runs, or runs such as the example I included
> above?
>
Typically? It depends on the system size. For 100k ~0.5 Gb should be
enough, though.
>
> Finally, does the speed of the hard drive impact Gromacs performance? The
> options are a cheap spinning-platter hard drive(100-200MB/s sequential
> write), a low-cost SSD(400-500MB/s sequential write), or a high-speed PCI-E
> SSD(1000-1500MB/s sequential write). Would writing out the data(.xtc,
> .trr, .edr) to a slower hard drive(100-200MB/s sequential write speed)
> cause the Gromacs simulation to slow down?
>
No, but depending on the type of analysis an SSD may matter a lot (and as
opposed to the MD run itself the you may need non-trivial amount of memory
too).
> I don't see any reason that a cheap spinning platter hard drive would slow
> Gromacs simulations down, but I want to make sure I'm not missing
> anything.
>
> Thank you for your time. I'd be very grateful for any information you can
> give me, or direct me to.
>
> David Berquist
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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>
------------------------------
Message: 2
Date: Thu, 17 Mar 2016 01:14:25 +0000 (UTC)
From: Sana Saeed <bioinformatic.lady at yahoo.com>
To: Discussion List for GROMACS Users <gmx-users at gromacs.org>
Subject: [gmx-users] LINCS warnings for some lambdas.
Message-ID:
<612231336.1498217.1458177265398.JavaMail.yahoo at mail.yahoo.com>
Content-Type: text/plain; charset=UTF-8
hii am performing protein ligand (pdb:4HBV)binding free energy calculations, i am done with complex simulation , now stuck in ligand simulation since last 2 weeks. first i was getting zero energy, and when i changed some of parameters and position restraint my ligand , now i am getting LINCS warnings sometimes with NPT ?and sometimes during production md. the strange part is that some of the lambdas are perfectly running while some of them crashes due to LINCS warnings, i know how to fix LINCS warnings (extending table size, decreasing stepsize, properly minimizing structure etc) but in ?this case some of lambdas are running perfectly, which means the structure and parameters are fine. i decresed step size to 1 fs and got the same result, bow i decreased it to 0.0001 ps. if someone ever got this kind of problem , please share your views.?my second question is that the simple simulation for solvation free energy of small molecule and the ligand simulation in binding free energ
y system are same? i mean can i use the solvation free energy parameters from BEVAN lab's tutorial in this situation? in some of tutorials they use position restraints for ligand simulation in water, that is the reason i used the same.?i provide npt and md.mdp parameters. if something is wrong kindly give comments. ignore the stepsize , i know its too small, i tried 0.001, 0.002, and this is the recent one, but couldnt see any difference.thanks in advance?
NPT.mdp
define ? ? ? ? ? ? ?= ?-DPOSRESintegrator ? ? ? ? ?= ?sdtinit ? ? ? ? ? ? ? = ?0dt ? ? ? ? ? ? ? ? ?= ?0.0001 ??nsteps ? ? ? ? ? ? ?= ?500000 ?; 100 psnstcomm ? ? ? ? ? ? = ?100
; Boundary conditionspbc ? ? ? ? ? ? ? ? = ?xyz
; Outputnstxout ? ? ? ? ? ? = ?0nstvout ? ? ? ? ? ? = ?0nstfout ? ? ? ? ? ? = ?0nstlog ? ? ? ? ? ? ?= ?100 ? ; 10 psnstenergy ? ? ? ? ? = ?100 ? ; 10 psnstcalcenergy ? ? ? = ?20nstxtcout ? ? ? ? ? = ?100 ? ; 10 psxtc-precision ? ? ? = ?1000energygrps ? ? ? ? ?= ?System
; Neighbour searchingcutoff-scheme ? ? ? = Verletnstlist ? ? ? ? ? ? = 10 ? ? ?; 20 fsns-type ? ? ? ? ? ? = gridrlist ? ? ? ? ? ? ? = 1.2 ? ? ? ? ? ? ? ; short-range neighborlist cutoff (in nm)rcoulomb ? ? ? ? ? ?= 1.2 ? ? ? ? ? ? ? ; short-range electrostatic cutoff (in nm)rvdw ? ? ? ? ? ? ? ?= 1.2 ? ? ? ? ? ? ? ; short-range van der Waals cutoff (in nm)
; Constraintsconstraints ? ? ? ? = ?noneconstraint-algorithm = lincslincs_iter ? ? ? ? ?= 1 ? ? ? ? ; accuracy of LINCS (1 is default)lincs_order ? ? ? ? = 12 ? ? ? ?; also related to accuracy (4 is default)lincs-warnangle ? ? = 30 ? ? ? ?; maximum angle that a bond can rotate before LINCS will complain^M; Electrostaticscoulombtype ? ? = PME ? ? ? ? ? ; Particle Mesh Ewald for long-range electrostaticspme-order ? ? ? = 6 ? ? ? ? ? ??fourierspacing ?= 0.10 ? ? ? ? ?; grid spacing for FFTewald-rtol ? ? ?= 1e-6 ? ? ? ? ?; relative strength of the Ewald-shifted direct potential at rcoulomboptimize-fft ? ?= noewald_geometry ? = 3d ?
; van der Waal'svdwtype ? ? ? ? ? ?= ?Switchrvdw-switch ? ? ? ? = ?0.9DispCorr ? ? ? ? ? ?= ?EnerPres
;Temperature Coupling (SD integrator => Langevin dynamics)tc_grps ? ? ? ? ? ? = ?Systemtau_t ? ? ? ? ? ? ? = ?1.0ref_t ? ? ? ? ? ? ? = ?298.15
; Pressure couplingPcoupl ? ? ? ? ? ? ?= ?Berendsenpcoupltype ? ? ? ? ?= ?isotropictau_p ? ? ? ? ? ? ? = ?2compressibility ? ? = ?4.5e-05ref_p ? ? ? ? ? ? ? = ?1.0
; Generate velocitiesgen_vel ? ? ? ? ? ? = yesgen_seed ? ? ? ? ? ?= -1gen_temp ? ? ? ? ? ?= 298.15
continuation ? ? ? ?= no?
; Free energy control stuff =?free-energy ? ? ? ? ? ? ?= yessc-alpha ? ? ? ? ? ? ? ? = 0.5sc-power ? ? ? ? ? ? ? ? = 1sc-sigma ? ? ? ? ? ? ? ? = 0.3init-lambda-state ? ? ? ?= 0coul-lambdas ? ? ? ? ? ? = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0vdw-lambdas ? ? ? ? ? ? ?= 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0??couple-moltype ? ? ? ? ?= 15E?couple-intramol ? ? ? ? = no?couple-lambda0 ? ? ? ? ?= none?couple-lambda1 ? ? ? ? ?= vdw-qnstdhdl ? ? ? ? ? ? ? ? ?= 100calc-lambda-neighbors ? ?= -1refcoord-scaling ? ? ? ? = com
PRODUCTION MD:md.mdp
; Production MD;title ? ? ? ? ? = production
; Run parametersintegrator ? ? ?= sd ? ? ? ? ? ?; stochastic leap-frog integratornsteps ? ? ? ? ?= 2500000 ? ? ??dt ? ? ? ? ? ? ?= 0.0001 ? ? ? ? ? ? ? ?nstcalcenergy ? = ?100energygrps ? ? ?= ?System
; Periodic boundary conditionspbc ? ? ? ? ? ? = xyz ? ? ? ? ? ; 3-D PBC
; Output controlnstvout ? ? ? ? = 500 ? ? ? ?; save velocities to .trr file every 200 psnstfout ? ? ? ? = 500 ? ? ? ?; save forces to .trr file every 100 psnstxout ? ? ? ? = 500 ? ? ? ? ? ; save coordinates every 5 psnstxtcout ? ? ? = 500 ? ? ? ? ? ; xtc compressed trajectory output every 2 psnstenergy ? ? ? = 500 ? ? ? ? ? ; save energies every 2 psnstlog ? ? ? ? ?= 500 ? ? ? ? ? ; update log file every 2 ps
; Bond parametersconstraint_algorithm = lincs ? ?; holonomic constraints?constraints ? ? = h-bonds ? ? ? ; all bonds (even heavy atom-H bonds) constrainedlincs_iter ? ? ?= 1 ? ? ? ? ? ? ; accuracy of LINCS (1 is default)lincs_order ? ? = 6 ? ? ? ? ? ? ; also related to accuracy (4 is default)lincs-warnangle = 30 ? ? ? ? ? ?; maximum angle that a bond can rotate before LINCS will complain (30 is default)
; Neighbor searchingns-type ? ? ? ? = grid ? ? ? ? ?; search neighboring grid cellsnstlist ? ? ? ? = 5 ? ? ? ? ? ? ; 10 fsrlist ? ? ? ? ? = 1.2 ? ? ? ? ? ; short-range neighborlist cutoff (in nm)rcoulomb ? ? ? ?= 1.2 ? ? ? ? ? ; short-range electrostatic cutoff (in nm)rvdw ? ? ? ? ? ?= 1.2 ? ? ? ? ? ; short-range van der Waals cutoff (in nm)
; Electrostaticscoulombtype ? ? = PME ? ? ? ? ? ; Particle Mesh Ewald for long-range electrostaticspme-order ? ? ? = 6 ? ? ? ? ? ?fourierspacing ?= 0.10 ? ? ? ? ?; grid spacing for FFTewald-rtol ? ? ?= 1e-6 ? ? ? ? ?; relative strength of the Ewald-shifted direct potential at rcoulomb; Van der Waalsvdwtype ? ? ? ?= ?Switchrvdw-switch ? ? = ?0.9DispCorr ? ? ? ?= ?EnerPres ? ? ; account for cut-off vdW scheme
;Temperature Coupling (SD integrator => Langevin dynamics)
tc_grps ? ? ? ? ? ? = ?Systemtau_t ? ? ? ? ? ? ? = ?1.0^Mref_t ? ? ? ? ? ? ? = ?298.15
; Pressure coupling is onpcoupl ? ? ? ? ?= Parrinello-Rahmanpcoupltype ? ? ?= isotropic ? ? ; uniform scaling of box vectorstau_p ? ? ? ? ? = 2 ? ? ? ? ? ? ; time constant, in psref_p ? ? ? ? ? = 1.0 ? ? ? ? ? ; reference pressure, in barcompressibility = 4.5e-05 ? ? ? ; isothermal compressibility of water, bar^-1 ?
; Velocity generationgen_vel ? ? ? ? = no ? ? ? ? ? ?; Velocity generation is ongen_seed ? ? ? ?= -1 ? ? ? ? ? ?; Use random seedgen_temp ? ? ? ?= 298.15
continuation ? ?= yes ? ? ? ? ? ; Restarting after NPT
; Free energy control stuff?free-energy ? ? ? ? ? ? ?= yessc-alpha ? ? ? ? ? ? ? ? = 0.5sc-power ? ? ? ? ? ? ? ? = 1sc-sigma ? ? ? ? ? ? ? ? = 0.3sc-coul ? ? ? ? ? ? ? ? ?= noinit-lambda-state ? ? ? ?= 0coul-lambdas ? ? ? ? ? ? = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0vdw-lambdas ? ? ? ? ? ? ?= 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0?couple-moltype ? ? ? ? ?= 15E?couple-intramol ? ? ? ? = no?couple-lambda0 ? ? ? ? ?= none?couple-lambda1 ? ? ? ? ?= vdw-qnstdhdl ? ? ? ? ? ? ? ? ?= 100dhdl-print-energy ? ? ? ?= yescalc-lambda-neighbors ? ?= -1
?Sana Saeed Khan,Research AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of BioinformaticsSoongsil University, Seoul, South Korea.
------------------------------
Message: 3
Date: Thu, 17 Mar 2016 11:18:43 +0900
From: Soumya Lipsa Rath <soumyalipsabt at gmail.com>
To: gmx-users at gromacs.org
Subject: [gmx-users] Using FFTK generated parameter file for
Protein-Ligand simulations
Message-ID:
<CAA3RoxbLG67g9Z657PBT0fu5RHa5n=7LbAXfyo1ZvfAjPewmVA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear Gromacs Users,
I have to run a protein-ligand system. I am using CHARMM36 ff for the
simulation. For generating the parameters for the ligand molecule I used
the forcefield development toolkit of vmd, which gives CHARMM compatible
parameters.
But, I am unable to understand how should I include the parameters I had
obtained. I went through the tutorial files which shows an example of
PRODRG server for generating the itp file, but my ligand contains metal
atoms. I would appreciate if somebody could suggest me how to solve this.
Thanks,
Soumya
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