[gmx-users] some question about REMD

saber naderi sbrnaderi at gmail.com
Wed Oct 17 18:18:05 CEST 2012


I am no expert in implicit solvent simulations but I think for these
simulations it is better to use stochastic dynamic integrators with no
pbc (instead of NVT) and infinite (or very large) cut-off distances because
there is no actual water molecule in your simulation box and [normally] you
do not have to worry about the boundary effects.

For finding appropriate parameters, you should have a look at the Gromacs
manual and read the literature but if you need a quick example see below
(please note that this is just an example).

Cheers,
Saber

; RUN CONTROL PARAMETERS
integrator               = sd
tinit                    = 0       ; Starting time
dt                       = 0.002   ; 2 femtosecond time step for integration
nsteps                   = 50000

; OUTPUT CONTROL OPTIONS
nstxout                  = 50000 ; Writing full precision coordinates every
nanosecond
nstvout                  = 50000 ; Writing velocities every nanosecond
nstfout                  = 0     ; Not writing forces
nstlog                   = 2500  ; Writing to the log file every step
nstenergy                = 2500  ; Writing out energy information every step
nstxtcout                = 2500  ; Writing coordinates every 5 ps
energygrps               = System

; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 0
ns-type                  = simple
pbc                      = no
rlist                    = 0

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype = cut-off
rvdw = 0
rcoulomb = 0

; Temperature coupling
tc-grps                  = System
tau_t                    = 10
ref_t                    = 300
ld_seed    = 123

;implicit solvent

implicit_solvent    = GBSA
gb_algorithm = OBC
rgbradii   = 0
gb_epsilon_solvent = 80

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = yes
gen_temp = 300
comm_mode = Angular

; OPTIONS FOR BONDS
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = yes
lincs-order              = 4
lincs-iter               = 1
lincs-warnangle          = 30

On 17 October 2012 17:51, Albert <mailmd2011 at gmail.com> wrote:

> Hi Saber:
>
>  thanks a lot for such kind reply.
>  How about the second question? I don't find any tutorial for the GBSA
> solvent simulation in Gromacs website and I am not sure what kind of
> parameters we should use for GBSA.
>
>
> thank you very much
> best
> Albert
>
> On 10/17/2012 05:48 PM, saber naderi wrote:
>
>> Hi Albert,
>>
>> Regarding you first question, your protein is relatively big and in my
>> opinion 28 replicas is not much for a protein made of 290 AA with the
>> temperature range of 280-530. One thing that you can do is to use a lower
>> value for exchange probability to have less replicas. By doing this the
>> average time interval between exchanges becomes longer (assuming that you
>> keep the exchange attempt interval fixed). This is not necessarily a bad
>> thing because in case of large proteins the dynamics is slow anyway and it
>> is useful if you let the system relax between exchanges.
>>
>> Cheers,
>> Saber
>>
>> On 17 October 2012 17:32, Albert <mailmd2011 at gmail.com> wrote:
>>
>>  hello:
>>>
>>>   I am going to perform replica exchange MD with Gromacs and I found some
>>> problems there:
>>>
>>> 1. my protein have around 290 aa with 4680 atoms. If I would like to
>>> perform with implicite solvent with exchange probability 0.2, I found
>>> from
>>> http://folding.bmc.uu.se/remd/ that I will have to generate around 28
>>> different replica between 280 and 530. However, I seldom see someone
>>> perform so much round of replicas......If I perform with explicit solvent
>>> with 8000 water molecules, the number of replica goes up to 112.... That'
>>> unbelievable a lot. My protein is a normal size and when we read the
>>> paper,
>>> usually people will produce no more than 12 replica. Why it is so much
>>> round for my case?
>>>
>>> 2. If I would like to perform in NVT with implicit solvent, shall I
>>> change
>>> something in the .mdp file? If the following (from Justine's tutorial)
>>> all
>>> right for the GBSA solvent?
>>>
>>> title       = Protein-ligand complex NVT equilibration
>>> define      = -DPOSRES  ; position restrain the protein and ligand
>>> ; Run parameters
>>> integrator  = md        ; leap-frog integrator
>>> nsteps      = 50000     ; 2 * 50000 = 100 ps
>>> dt          = 0.002     ; 2 fs
>>> ; Output control
>>> nstxout     = 100       ; save coordinates every 0.2 ps
>>> nstvout     = 100       ; save velocities every 0.2 ps
>>> nstenergy   = 100       ; save energies every 0.2 ps
>>> nstlog      = 100       ; update log file every 0.2 ps
>>> energygrps  = Protein JZ4
>>> ; Bond parameters
>>> continuation    = no            ; first dynamics run
>>> constraint_algorithm = lincs    ; holonomic constraints
>>> constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
>>> constrained
>>> lincs_iter      = 1             ; accuracy of LINCS
>>> lincs_order     = 4             ; also related to accuracy
>>> ; Neighborsearching
>>> ns_type     = grid      ; search neighboring grid cells
>>> nstlist     = 5         ; 10 fs
>>> rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
>>> rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
>>> rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)
>>> ; Electrostatics
>>> coulombtype     = PME       ; Particle Mesh Ewald for long-range
>>> electrostatics
>>> pme_order       = 4         ; cubic interpolation
>>> fourierspacing  = 0.16      ; grid spacing for FFT
>>> ; Temperature coupling
>>> tcoupl      = V-rescale                     ; modified Berendsen
>>> thermostat
>>> tc-grps     = Protein_JZ4 Water_and_ions    ; two coupling groups - more
>>> accurate
>>> tau_t       = 0.1   0.1                     ; time constant, in ps
>>> ref_t       = 300   300                     ; reference temperature, one
>>> for each group, in K
>>> ; Pressure coupling
>>> pcoupl      = no        ; no pressure coupling in NVT
>>> ; Periodic boundary conditions
>>> pbc         = xyz       ; 3-D PBC
>>> ; Dispersion correction
>>> DispCorr    = EnerPres  ; account for cut-off vdW scheme
>>> ; Velocity generation
>>> gen_vel     = yes       ; assign velocities from Maxwell distribution
>>> gen_temp    = 300       ; temperature for Maxwell distribution
>>> gen_seed    = -1        ; generate a random seed
>>>
>>>
>>> thank you very much
>>> best
>>> Albert
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>> Mailing_Lists/Search<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-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>> >
>>>
>>>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<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-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>



More information about the gromacs.org_gmx-users mailing list