Re: [gmx-users] .mdp file for calculating surface tension of water

[Rana Ali]

Dear David Sir
Thanks a lot for your help

Sincerely
Rana

On Tue, Jun 19, 2018 at 7:18 PM, David van der Spoel 
wrote:

> Den 2018-06-19 kl. 14:52, skrev Rana Ali:
>
>> Dear expert users
>> It will be of great help if somebody share the .mdp file for calculating
>> the surface tension of  water
>> using NVT ensemble
>>
>> Thank in advance
>>
>> Regards
>>
>> Rana
>>
>> Check: http://virtualchemistry.org/ff.php
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] .mdp file for calculating surface tension of water

[David van der Spoel]

Den 2018-06-19 kl. 14:52, skrev Rana Ali:

Dear expert users
It will be of great help if somebody share the .mdp file for calculating
the surface tension of  water
using NVT ensemble

Thank in advance

Regards

Rana


Check: http://virtualchemistry.org/ff.php

--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] .mdp file for calculating surface tension of water

[Rana Ali]

Dear expert users
It will be of great help if somebody share the .mdp file for calculating
the surface tension of  water
using NVT ensemble

Thank in advance

Regards

Rana
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial

[Justin Lemkul]

On 5/22/17 6:47 AM, ZHANG Cheng wrote:

Dear Joao,
Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that 
true that NVT needs to change two lines, while NPT and production run only need 
to change one line?




Yes.

-Justin


Yours sincerely
Cheng


1) In the NVT:
ref_t = 370  370   ; reference temperature, one for each group, in K
gen_temp = 370 ; temperature for Maxwell distribution



2)  In the NPT:
ref_t = 370  370; reference temperature, one for each group, in K


3) In the production run:
ref_t   = 370 370   ; reference temperature, one for each 
group, in K



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial

[ZHANG Cheng]

Dear Joao,
Sorry, I forgot. Thank you for reminding me. Is that all right now? Is that 
true that NVT needs to change two lines, while NPT and production run only need 
to change one line?


Yours sincerely
Cheng


1) In the NVT:
ref_t = 370  370   ; reference temperature, one for each group, in K
gen_temp = 370 ; temperature for Maxwell distribution



2)  In the NPT:
ref_t = 370  370; reference temperature, one for each group, in K


3) In the production run:
ref_t   = 370 370   ; reference temperature, one for each 
group, in K
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file for 370 K MD based on Justin's tutorial

[João Henriques]

You haven't adjusted the temperature on the production mdp file, it's still
300 K.

J

On Mon, May 22, 2017 at 12:37 PM, ZHANG Cheng <272699...@qq.com> wrote:

> Dear Gromacs,
> I am performing 370 K MD based on Justin's tutorial.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> gmx-tutorials/lysozyme/index.html
>
>
> After "Step Five: Energy Minimization", I need to do NVT, NPT and a
> production run.
>
>
> I think I need to change 300 K to 370 K in three mdp files. Specifically,
>
>
> 1) In the NVT:
> ref_t = 370  370   ; reference temperature, one for each group, in
> K
> gen_temp = 370 ; temperature for Maxwell distribution
>
>
>
> 2)  In the NPT:
> ref_t = 370  370; reference temperature, one for each group, in K
>
>
> 3) In the production run:
> ref_t   = 300 300   ; reference temperature, one for
> each group, in K
>
>
> Can I ask if these are the adjustments I need to do, and if there are
> something else I need? Thank you.
>
>
> Yours sincerely
> Cheng
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] mdp file for 370 K MD based on Justin's tutorial

[ZHANG Cheng]

Dear Gromacs,
I am performing 370 K MD based on Justin's tutorial. 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html


After "Step Five: Energy Minimization", I need to do NVT, NPT and a production 
run.


I think I need to change 300 K to 370 K in three mdp files. Specifically,


1) In the NVT:
ref_t = 370  370   ; reference temperature, one for each group, in K
gen_temp = 370 ; temperature for Maxwell distribution



2)  In the NPT:
ref_t = 370  370; reference temperature, one for each group, in K


3) In the production run:
ref_t   = 300 300   ; reference temperature, one for each 
group, in K


Can I ask if these are the adjustments I need to do, and if there are something 
else I need? Thank you.


Yours sincerely
Cheng
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] .mdp file settings for thermodynamic integration

[deepak bapat]

Dear Gromacs users

I had a doubt regarding .mdp options for free energy using constrained
dynamics.

If i wish to change a bond length from l_A to l_B (say for example from 0.5
nm to 5 nm.  this bond will be used in the form of constraints type 2.
something similar to what is shown in manual of gromacs v 5.1.2 in
section *5.8.5
page no 151-152*) for doing thermodynamic integration instead of BAR.

I would be only varying this bond length and no other parameters such as
charge, mass.

would the following settings which i have shown in *case 1* and *case 2* in
mdp options yield same results?

*Case 1 mdp settings:*

init-lambda = 0.4 ; (i.e. for separation of (0.4*0.5+(1-0.4)*5=3.2 nm)
delta_lambda = 0
nstdhdl = 10
and
*case 2 mdp optoins:*

init-lambda-state = 4 ; column corresponding to 0.4 in bonded lambdas
;col0   col1   col2col3col4
bonded-lambdas =  0 0.1  0.2  0.3 0.4 . 1.0
delta_lambda = 0
; all other lambda such as mass lambda, coul lambda being set to 0 for all
coumns

Is case1 identical to case 2?

Regards

-- 
Deepak U. Bapat
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] .mdp file for Enthalpy of Vaporization calculation

[Justin Lemkul]

On 4/4/17 6:21 AM, Matteo Busato wrote:

Goodmorning to everyone,


I'm writing here because I'm trying to perform a calculation about the Enthalpy 
of Vaporization of a system with 434 molecules of an ionic liquid. I've already 
read all the previous posts in the forum about this subject and it has come 
clear to me how to perform the calculation, however I'm having problems with my 
.mdp file when trying to perform the NVT equilibration.

I've read that for such calculation cutoffs must be set = 0 and pbc=none, 
however with such parameters I'm forced to use cutoff-scheme=group instead of 
Verlet, so the first problem is that 'group' is not configured for GPU 
acceleration and I can use just 1 MPI rank (which slows the job time a lot). Is 
there a way to perform this calculation with Verlet?

The second problem is that if I set rvdw=0, gromacs gives me an error saying that 
(obviously), vdw-switch must be < rvdw. How can I solve this issue?



There's nothing to switch; you're using a plain cutoff.

There's no point trying to use a GPU to simulate one molecule.  This simulation 
should run in a matter of seconds on a single CPU.


-Justin


I'll post the mdp I'm using here. Thank you in advance.


; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.001
nsteps   = 100; 1000 ps
nstcomm  = 100
; Output control
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy= 500
nstxout-compressed   = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= group
nstlist  = 0
ns_type  = grid
pbc  = no
rlist= 0
; Electrostatics
coulombtype  = cutoff
rcoulomb = 0
; van der Waals
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw = 0
rvdw-switch  =0
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 298.15
; Pressure coupling is off for NVT
Pcoupl   = No
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0
; Generate velocities to start
gen_vel  = yes
gen_temp = 300
gen_seed = -1
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12
dispcorr=no


Matteo Busato



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] .mdp file for Enthalpy of Vaporization calculation

[Matteo Busato]

Goodmorning to everyone,


I'm writing here because I'm trying to perform a calculation about the Enthalpy 
of Vaporization of a system with 434 molecules of an ionic liquid. I've already 
read all the previous posts in the forum about this subject and it has come 
clear to me how to perform the calculation, however I'm having problems with my 
.mdp file when trying to perform the NVT equilibration.

I've read that for such calculation cutoffs must be set = 0 and pbc=none, 
however with such parameters I'm forced to use cutoff-scheme=group instead of 
Verlet, so the first problem is that 'group' is not configured for GPU 
acceleration and I can use just 1 MPI rank (which slows the job time a lot). Is 
there a way to perform this calculation with Verlet?

The second problem is that if I set rvdw=0, gromacs gives me an error saying 
that (obviously), vdw-switch must be < rvdw. How can I solve this issue?

I'll post the mdp I'm using here. Thank you in advance.


; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.001
nsteps   = 100; 1000 ps
nstcomm  = 100
; Output control
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy= 500
nstxout-compressed   = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= group
nstlist  = 0
ns_type  = grid
pbc  = no
rlist= 0
; Electrostatics
coulombtype  = cutoff
rcoulomb = 0
; van der Waals
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw = 0
rvdw-switch  =0
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 298.15
; Pressure coupling is off for NVT
Pcoupl   = No
tau_p= 0.5
compressibility  = 4.5e-05
ref_p= 1.0
; Generate velocities to start
gen_vel  = yes
gen_temp = 300
gen_seed = -1
; options for bonds
constraints  = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm = lincs
; Do not constrain the starting configuration
continuation = no
; Highest order in the expansion of the constraint coupling matrix
lincs-order  = 12
dispcorr=no


Matteo Busato
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] mdp file for slow-growth free energy calculation

[Matteo Busato]

Good morning to everyone,


I am trying to perform a very simple calculation of the free energy of 
hydration of a Zinc ion in a box of water, using the slow-growth method and the 
gmx_bar program with GROMACS 5.0.4. I've taken the LJ paramethers for Zn2+ from 
the Stote and Karplus article dated 1995 (sigma=0.195nm and 
epsilon=1.046KJ/mol), but I've obtained a DG of just 1500 KJ/mol more on less 
against the experimental value of more than 2000 KJ/mol. The fact is that the 
VdW contribute results just 2.92KJ/mol, and the Coulomb more or less 1500KJ/mol.

I can't figure out where the error is, but I think it can just be the .mdp 
file, so I'll post here the mpd I've used, for example for the dynamics. Both 
the method and the mdp are based on Dr. Justin Lemkul tutorial for the DG of 
methane in water, I've just added the Coulombs growth as recommended in the 
last page of the tutorial and then obtained 40 values of lambdas. This is the 
mdp I'm using (lambda=32):


; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.002
nsteps   = 50   ; 1 ns
nstcomm  = 100
; Output control
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy= 500
nstxout-compressed   = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
nstlist  = 20
ns_type  = grid
pbc  = xyz
rlist= 1.2
; Electrostatics
coulombtype  = PME
rcoulomb = 1.2
; van der Waals
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw-switch  = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 300
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
tau_p= 1.0
compressibility  = 4.5e-05
ref_p= 1.0
; Free energy control stuff
free_energy  = yes
init_lambda_state= 32
delta_lambda = 0
calc_lambda_neighbors= 1; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for 
each simulation
; init_lambda_state012345678910 
  11   12   13   14   15   16   17   18   19   20   21   22   23   24   25   26 
  27   28   29   29   30   31   32   33   34   35   36   37   38   39
vdw_lambdas  = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.45 
0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 1.00 1.00 1.00 
1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 0.15 0.20 0.25 
0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
; We are not transforming any bonded or restrained interactions
bonded_lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Masses are not changing (particle identities are the same at lambda = 0 and 
lambda = 1)
mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Not doing simulated temperting here
temperature_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Options for the decoupling
sc-alpha = 0.5
sc-coul  = no   ; linear interpolation of Coulomb (none in 
this case)
sc-power = 1.0
sc-sigma = 0.3
couple-moltype   = ZN   ; name of moleculetype to decouple
couple-lambda0   = none ; no interactions at lambda=0
couple-lambda1   =

Re: [gmx-users] mdp file of membrane simulation

[Mijiddorj Batsaikhan]

Dear Justin,

Thank you very much.

Best regards,

Mijiddorj



On 10/20/16 11:47 AM, Mijiddorj Batsaikhan wrote:
> Thank you very much.
>
> *(1)*
> Which one is suitable the following 2 examples for energy groups in my mdp
> file?
>
> *Example 1*
>
> energygrps = Protein Membrane
> energy grps = r_1 Membrane
> energygrps = r_2 Membrane
> ...
> energygrps = r_N Membrane
>
> *Example 2*
> energygrps = Protein Membrane r_1 r_2 ... r_N
>

This is correct.  As with any .mdp keyword, it can only appear once.

>
> *(2)* -mdrerun is how faster than original md simulation?
>

In general, it takes a few minutes.  Don't waste time with energygrps for
the
original run (if there are many, your run can slow down a lot!) and just
treat
the pairwise energy decomposition as simply analysis.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file of membrane simulation

[Justin Lemkul]

On 10/20/16 11:47 AM, Mijiddorj Batsaikhan wrote:

Thank you very much.

*(1)*
Which one is suitable the following 2 examples for energy groups in my mdp
file?

*Example 1*

energygrps = Protein Membrane
energy grps = r_1 Membrane
energygrps = r_2 Membrane
...
energygrps = r_N Membrane

*Example 2*
energygrps = Protein Membrane r_1 r_2 ... r_N



This is correct.  As with any .mdp keyword, it can only appear once.



*(2)* -mdrerun is how faster than original md simulation?



In general, it takes a few minutes.  Don't waste time with energygrps for the 
original run (if there are many, your run can slow down a lot!) and just treat 
the pairwise energy decomposition as simply analysis.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file of membrane simulation

[Mijiddorj Batsaikhan]

Thank you very much.

*(1)*
Which one is suitable the following 2 examples for energy groups in my mdp
file?

*Example 1*

energygrps = Protein Membrane
energy grps = r_1 Membrane
energygrps = r_2 Membrane
...
energygrps = r_N Membrane

*Example 2*
energygrps = Protein Membrane r_1 r_2 ... r_N


*(2)* -mdrerun is how faster than original md simulation?

Best regards,

Mijiddorj


> --
>
> Message: 1
> Date: Wed, 12 Oct 2016 11:07:46 +0530
> From: Nikhil Maroli 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] mdp file of membrane simulation
> Message-ID:
>  gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
> You need to find the resname/index name for the individual component,it
> depends on your system. add those names in energygps and do mdrerun
> You can find for
>
> PROT-LIPID
> PROT-MOLECULE
> PROT-REST/WATER
> LIPID-MOLECULE
> so on
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] mdp file

[Mouri Ahmed]

Hi

I want to use no constraint in my MD simulation. What will I write in my
mdp file?

Best Regards
Mouri
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file of membrane simulation

[Nikhil Maroli]

Hi,
You need to find the resname/index name for the individual component,it
depends on your system. add those names in energygps and do mdrerun
You can find for

PROT-LIPID
PROT-MOLECULE
PROT-REST/WATER
LIPID-MOLECULE
so on
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] mdp file of membrane simulation

[Mijiddorj Batsaikhan]

Dear users,

I would like to simulate a system that consists of 3 different types of
membrane models, peptides (they contain modified amino acid) and small
molecule. In this case, I would like to know peptide-peptide, peptide-small
molecule, peptide-lipid, and modified amino acid-small molecule
interactions. I prepared the system using Charmm-gui tool. How can I set
gromacs input mdp file? such as energygps tems. Please, can you suggest and
advice me?


Best regards,

Mijiddorj
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file

[Sotirios Dionysios I. Papadatos]

Thanks for your quick reply. Up till now all the simulations I have performed 
are with the OPLS force field, because the software I used in the past 
supported only that in the academic version. 
Anyway, to sum it up for non bonded from the literature about a particular 
force field and try some tutorials. Got it.
Thank you so much


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Justin Lemkul 

Sent: Wednesday, September 2, 2015 12:26 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] mdp file

On 9/1/15 12:50 PM, Sotirios Dionysios I. Papadatos wrote:
> Hi,
>
> I am having some trouble defining a proper mdp file for minimization and 
> production runs. I am aware of the manual's - site's reference to this 
> matter, it is pretty thourough.
>
> My question is: How do I know which parameters to use for each simulation? Is 
> there a publication, book etc to guide the user through this? I mean for 
> example if I want to simulate a protein, which parameters do I have to use??
>

Try some tutorials.

http://www.gromacs.org/Documentation/Tutorials

Most settings (output, thermostats, etc) are pretty boilerplate.  The nonbonded
setup (cutoffs) depend on the force field, which you will learn about by reading
the primary literature for the force field you've chosen for your work.  Because
you've scrutinized the literature and know about why you've chosen that
particular force field, right?

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file

[Justin Lemkul]

On 9/1/15 12:50 PM, Sotirios Dionysios I. Papadatos wrote:

Hi,

I am having some trouble defining a proper mdp file for minimization and 
production runs. I am aware of the manual's - site's reference to this matter, 
it is pretty thourough.

My question is: How do I know which parameters to use for each simulation? Is 
there a publication, book etc to guide the user through this? I mean for 
example if I want to simulate a protein, which parameters do I have to use??



Try some tutorials.

http://www.gromacs.org/Documentation/Tutorials

Most settings (output, thermostats, etc) are pretty boilerplate.  The nonbonded 
setup (cutoffs) depend on the force field, which you will learn about by reading 
the primary literature for the force field you've chosen for your work.  Because 
you've scrutinized the literature and know about why you've chosen that 
particular force field, right?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] mdp file

[Sotirios Dionysios I. Papadatos]

Hi,

I am having some trouble defining a proper mdp file for minimization and 
production runs. I am aware of the manual's - site's reference to this matter, 
it is pretty thourough.

My question is: How do I know which parameters to use for each simulation? Is 
there a publication, book etc to guide the user through this? I mean for 
example if I want to simulate a protein, which parameters do I have to use??

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] mdp file for slab geometry

[anu chandra]

Dear gromacs users,

I am planing to run a membrane protein simulation with implementation of a
slab geometry, due to ion asymmetry. Below, I just copied the mdp file that
I will be using for NPT equilibration and later, for production run. Can
you please have a look and let me know if there is a need of any
modifications.

**
define  = -DPORSE -DEQ
integrator  = md
dt  = 0.001
nsteps  = 25000
nstlog  = 1000
nstxout = 1000
nstvout = 1000
nstfout = 1000
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
;
ewald-geometry  = 3dc  ;slab geometry
pbc = xyz
;
tcoupl  = V-rescale
tc_grps = Protein POPC Cal_CL_SOL
tau_t   = 0.50.5 0.5
ref_t   = 305.0305.0305.0
;
pcoupl  = Parrinello-Rahman
pcoupltype  = semiisotropic
tau_p   = 5.0 5.0
compressibility = 4.5e-5  0  ;0 for z-direction due to vaccum
slab
ref_p   = 1.0 1.0
;
constraints = h-bonds
constraint_algorithm= LINCS
continuation= yes
;
nstcomm = 100
comm_mode   = linear
comm_grps   = Protein_POPC Cal_CL_SOL
;
refcoord_scaling= com

*

Many thanks in advance

Best regards
Anu
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file for system without charges

[Alex]

I'd try

coulombtype = cut-off
rcoulomb = [whatever your vdw cutoff is]

It is my understanding that no grid-based PME will be done and for
(nonexistent in your case) electrostatics, the system will rely on the neighbor 
lists created for
your van der Waals interactions. The Gurus will be here soon. :)

Alex

MS> Dear gmx-users,

MS> Could you give me an advice.
MS> I have a system of uncharged LJ particles. How should the
MS> electrostatic part of the mdp file look like for the best
MS> performance. Is it possible to tell GROMACS that it should forget
MS> about electrostatics at all? Or it understands this
MS> by itself and thus the performance is independent on
MS> corresponding parameters set in mdp file?
MS> (I am planning to use GROMACS 5.0.4)

MS> Thank you very much in advance.

MS> Mikhail


MS> Mikhail Stukan, Ph.D.
MS> Senior Research Scientist
MS> Schlumberger Moscow Research
MS> 13, Pudovkina st.
MS> Moscow, 119285
MS> Russia
MS> Tel: +7 495 9358200 ext 24017
MS> Fax: +7 495 9358780
MS> mstu...@slb.com




-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file for system without charges

[Kutzner, Carsten]

Hi,

> On 08 Apr 2015, at 16:28, Mikhail Stukan  wrote:
> 
> Dear gmx-users,
> 
> Could you give me an advice.
> I have a system of uncharged LJ particles. How should the electrostatic part 
> of the mdp file look like for the best performance. Is it possible to tell 
> GROMACS that it should forget about electrostatics at all? Or it understands 
> this by itself and thus the performance is independent on corresponding 
> parameters set in mdp file?
> (I am planning to use GROMACS 5.0.4)
I think as long as you do not specify PME for the treatment of the
electrostatics potential and forces, there should be no superfluous
calculations, since Gromacs checks which interactions there are
for each particle pair. So using coulombtype = Cut-off should do the
trick. 

Carsten


> 
> Thank you very much in advance.
> 
> Mikhail
> 
> 
> Mikhail Stukan, Ph.D.
> Senior Research Scientist
> Schlumberger Moscow Research
> 13, Pudovkina st.
> Moscow, 119285
> Russia
> Tel: +7 495 9358200 ext 24017
> Fax: +7 495 9358780
> mstu...@slb.com
> 
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] mdp file for system without charges

[Mikhail Stukan]

Dear gmx-users,

Could you give me an advice.
I have a system of uncharged LJ particles. How should the electrostatic part of 
the mdp file look like for the best performance. Is it possible to tell GROMACS 
that it should forget about electrostatics at all? Or it understands this by 
itself and thus the performance is independent on corresponding parameters set 
in mdp file?
(I am planning to use GROMACS 5.0.4)

Thank you very much in advance.

Mikhail


Mikhail Stukan, Ph.D.
Senior Research Scientist
Schlumberger Moscow Research
13, Pudovkina st.
Moscow, 119285
Russia
Tel: +7 495 9358200 ext 24017
Fax: +7 495 9358780
mstu...@slb.com

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file coarse grained simulation with cutoff-scheme = Verlet

[Mark Abraham]

On Sun, Dec 14, 2014 at 8:11 PM, Carlos Navarro Retamal 
wrote:
>
> Dear Mark,
> Thanks for your quick reply.
> I used this one as a template (provided by one of the tutorials of martini)
>

Tutorials are generally not normative. Some people's tutorials are
deliberately cut down so that they run quickly. Read the real literature
from the authors of the force field - both the original work and the things
they've published later.

> dt = 0.02 nsteps = 100 nstxout = 0 nstvout = 0 nstlog = 1
> nstxtcout = 1000 xtc-precision = 10 rlist = 1.4 coulombtype = shift
> rcoulomb = 1.2 epsilon_r = 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2
> tcoupl = v-rescale tc-grps = Protein W tau-t = 1.0 1.0 ref-t = 300 300
> Pcoupl = parrinello-rahman Pcoupltype = isotropic tau-p = 12.0
> compressibility = 3e-4 ref-p = 1.0 refcoord_scaling = all
> >
> >
> >
> >
>
> and i add cutoff-scheme = Verlet, but i got the following errors:
>
> > ERROR 1 [file dynamic.mdp]:
> >   With Verlet lists only cut-off LJ interactions are supported
> >
> >
> > ERROR 2 [file dynamic.mdp]:
> >   With Verlet lists only cut-off, reaction-field, PME and Ewald
> >   electrostatics are supported
>

These kinds of things are available in Gromacs 5.

so my question is. For a system consisting in a protein and a membrane,
> which options are the correct ones for the vdw and the electrostatic
> interactions? I read on another topic that for the electrostatic
> interactions the PME approximation is the best, but i don’t know which one
> would be the best for the vdw term.
>

The answer to this question starts with reading the literature :-) For a
membrane system, I think PME for both Coulomb and LJ is appropriate, but
Martini was not parameterized that way, so you should follow the
parameterization they used, unless you can see they've changed their mind
later for systems relevant to yours.

Mark


> Kind regards,
> Carlos
>
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
> On Sunday, December 14, 2014 at 3:58 PM, Mark Abraham wrote:
>
> > Hi,
> >
> > In one sense, there's nothing to do. Set the cut-off scheme to Verlet,
> and
> > choose your non-bonded and/or integrator setup according to the
> > recommendations for your model physics. mdrun's job is to implement it
> > faithfully, but it's your job to choose it ;-)
> >
> > Mark
> >
> > On Sun, Dec 14, 2014 at 7:41 PM, Carlos Navarro Retamal <
> cnava...@utalca.cl (mailto:cnava...@utalca.cl)>
> > wrote:
> > >
> > >
> > > Dear gromacs users,
> > > I’mt trying to improve the performance of some CG simulations by using
> GPU
> > > (with cutoff-scheme = Verlet). So i’m trying to create an specific mdp
> file
> > > for my simulations (4.6.3 version for now) without luck so far.
> > > Could someone provide me a parameters file? i'll be appreciated for
> your
> > > help.
> > > Have a nice day,
> > > Carlos
> > > --
> > > Carlos Navarro Retamal
> > > Bioinformatic engineer
> > > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > > Center of Bioinformatics and Molecular Simulations (CBSM)
> > > Universidad de Talca
> > > 2 Norte 685, Casilla 721, Talca - Chile
> > > Teléfono: 56-71-201 798,
> > > Fax: 56-71-201 561
> > > Email: carlos.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com)
> or cnava...@utalca.cl (mailto:cnava...@utalca.cl)
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org (mailto:
> gmx-users-requ...@gromacs.org).
> > >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org (mailto:
> gmx-users-requ...@gromacs.org).
> >
> >
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromac

Re: [gmx-users] mdp file coarse grained simulation with cutoff-scheme = Verlet

[Carlos Navarro Retamal]

Dear Mark,
Thanks for your quick reply.
I used this one as a template (provided by one of the tutorials of martini)



> dt = 0.02 nsteps = 100 nstxout = 0 nstvout = 0 nstlog = 1 nstxtcout = 
> 1000 xtc-precision = 10 rlist = 1.4 coulombtype = shift rcoulomb = 1.2 
> epsilon_r = 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = 
> v-rescale tc-grps = Protein W tau-t = 1.0 1.0 ref-t = 300 300 Pcoupl = 
> parrinello-rahman Pcoupltype = isotropic tau-p = 12.0 compressibility = 3e-4 
> ref-p = 1.0 refcoord_scaling = all
>  
>  
>  
>  

and i add cutoff-scheme = Verlet, but i got the following errors:

> ERROR 1 [file dynamic.mdp]:
>   With Verlet lists only cut-off LJ interactions are supported
>  
>  
> ERROR 2 [file dynamic.mdp]:
>   With Verlet lists only cut-off, reaction-field, PME and Ewald
>   electrostatics are supported



so my question is. For a system consisting in a protein and a membrane, which 
options are the correct ones for the vdw and the electrostatic interactions? I 
read on another topic that for the electrostatic interactions the PME 
approximation is the best, but i don’t know which one would be the best for the 
vdw term.
Kind regards,
Carlos

--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


On Sunday, December 14, 2014 at 3:58 PM, Mark Abraham wrote:

> Hi,
>  
> In one sense, there's nothing to do. Set the cut-off scheme to Verlet, and
> choose your non-bonded and/or integrator setup according to the
> recommendations for your model physics. mdrun's job is to implement it
> faithfully, but it's your job to choose it ;-)
>  
> Mark
>  
> On Sun, Dec 14, 2014 at 7:41 PM, Carlos Navarro Retamal  (mailto:cnava...@utalca.cl)>
> wrote:
> >  
> >  
> > Dear gromacs users,
> > I’mt trying to improve the performance of some CG simulations by using GPU
> > (with cutoff-scheme = Verlet). So i’m trying to create an specific mdp file
> > for my simulations (4.6.3 version for now) without luck so far.
> > Could someone provide me a parameters file? i'll be appreciated for your
> > help.
> > Have a nice day,
> > Carlos
> > --
> > Carlos Navarro Retamal
> > Bioinformatic engineer
> > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > Center of Bioinformatics and Molecular Simulations (CBSM)
> > Universidad de Talca
> > 2 Norte 685, Casilla 721, Talca - Chile
> > Teléfono: 56-71-201 798,
> > Fax: 56-71-201 561
> > Email: carlos.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com) or 
> > cnava...@utalca.cl (mailto:cnava...@utalca.cl)
> >  
> > --
> > Gromacs Users mailing list
> >  
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >  
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >  
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org 
> > (mailto:gmx-users-requ...@gromacs.org).
> >  
>  
> --  
> Gromacs Users mailing list
>  
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>  
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org (mailto:gmx-users-requ...@gromacs.org).
>  
>  


-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] mdp file coarse grained simulation with cutoff-scheme = Verlet

[Mark Abraham]

Hi,

In one sense, there's nothing to do. Set the cut-off scheme to Verlet, and
choose your non-bonded and/or integrator setup according to the
recommendations for your model physics. mdrun's job is to implement it
faithfully, but it's your job to choose it ;-)

Mark

On Sun, Dec 14, 2014 at 7:41 PM, Carlos Navarro Retamal 
wrote:
>
>
> Dear gromacs users,
> I’mt trying to improve the performance of some CG simulations by using GPU
> (with cutoff-scheme = Verlet). So i’m trying to create an specific mdp file
> for my simulations (4.6.3 version for now) without luck so far.
> Could someone provide me a parameters file? i'll be appreciated for your
> help.
> Have a nice day,
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] mdp file coarse grained simulation with cutoff-scheme = Verlet

[Carlos Navarro Retamal]

Dear gromacs users,
I’mt trying to improve the performance of some CG simulations by using GPU 
(with cutoff-scheme = Verlet). So i’m trying to create an specific mdp file for 
my simulations (4.6.3 version for now) without luck so far.
Could someone provide me a parameters file? i'll be appreciated for your help.
Have a nice day,
Carlos
--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.