Re: [gmx-users] Equilibration Problem.

[Dallas Warren]

Did you visualise the system? What would you expect the density of the
system to be?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 17 Sep 2019 at 19:17, Navneet Kumar Singh 
wrote:

> Hello Everyone!
>
> Trying to simulate a system build in PACKMOL having peptides, water and
> small molecules. Energy minimization and other process for setting up md
> simulation went fine.
>
> NVT AND NPT FOR 1000PS BUT system didn't Equilibrated.
> Average required temperature maintained.
>
>
>
>
>
> *Energy  Average   Err.Est. RMSD
>
> Tot-Drift---Pressure
>   0.261272 0.49  49.10611.55678  (bar)*
>
>
> *Density213.361   0.58   1.18799
>4.08348 (kg/m^3)*
>
>
> *Temperature   300.002   0.04  2.38265
> -0.0854606  (K)*
>
>
> *---*
>
> *Temperature 300k is fine. But the density of the system is 213.361 and
> attached graph (https://fil.email/ic2yZ4x3 )
> shows unstable system. I extended it to 10 ns but still follows same
> pattern. What can be the problem with this? Using TIP3P water model with
> CHARMM36 force field to simulate the system.*
>
>
>  Thanks & Regards
> ___
>
> [image: photo]
> *NAVNEET KUMAR*
>
> Doctoral Student
> Dept. of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research, Sector 67,
> S.A.S. Nagar - 160062, Punjab (INDIA)
> P +918017967647  <+918017967647> |
> E navneet...@gmail.com  
>
> 
>  
>
> Please consider your environmental responsibility. Before printing this
> e-mail message, ask yourself whether you really need a hard copy.
> --
> 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] Equilibration Problem.

[Navneet Kumar Singh]

Hello Everyone!

Trying to simulate a system build in PACKMOL having peptides, water and
small molecules. Energy minimization and other process for setting up md
simulation went fine.

NVT AND NPT FOR 1000PS BUT system didn't Equilibrated.
Average required temperature maintained.





*Energy  Average   Err.Est. RMSD
Tot-Drift---Pressure
  0.261272 0.49  49.10611.55678  (bar)*


*Density213.361   0.58   1.18799
   4.08348 (kg/m^3)*


*Temperature   300.002   0.04  2.38265
-0.0854606  (K)*

*---*

*Temperature 300k is fine. But the density of the system is 213.361 and
attached graph (https://fil.email/ic2yZ4x3 )
shows unstable system. I extended it to 10 ns but still follows same
pattern. What can be the problem with this? Using TIP3P water model with
CHARMM36 force field to simulate the system.*


 Thanks & Regards
___

[image: photo]
*NAVNEET KUMAR*

Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
S.A.S. Nagar - 160062, Punjab (INDIA)
P +918017967647  <+918017967647> |
E navneet...@gmail.com  


 

Please consider your environmental responsibility. Before printing this
e-mail message, ask yourself whether you really need a hard copy.
-- 
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] Equilibration Error, Skew Factor

[Hemant Khoba]

Hello,

I am working on a coarse-grained polymer system having various chain length
(20 & 62), dissolved in water with different counter-ion concentrations.
While equilibrating the systems I am consistently facing an error.

For chain Length 20;
Fatal error:
The X-size of the box (6.716921) times the triclinic skew factor (1.00)
is
smaller than the number of DD cells (4) times the smallest allowed cell size
(1.68)

For chain length 62;
Fatal error:
The X-size of the box (11.840870) times the triclinic skew factor (1.00)
is smaller than the number of DD cells (8) times the smallest allowed cell
size (1.48)

I have accurately calculated the box size to maintain a particular ion
concentration. 9.8 cubic box for chain length 20 and 18 nm cubic box for
chain length 62.

attached are the .mdp's for temperature and pressure equilibration. Any
suggestions would be highly appreciated.

Thanking you in advance.


Regards,
Hemant Khoba


[image: Mailtrack]

Sender
notified by
Mailtrack

08/01/19,
05:42:21 PM
; minim.mdp - used as input into grompp to generate em.tpr
;
; Run parameters
integrator   = steep; Algorithm (steep = steepest 
descent minimization)
tinit= 0
dt   = 0.002
init-step= 0
comm-mode= Linear
nstcomm  = 100
comm-grps= system
emtol= 1000.0   ; Stop 
minimization when the maximum force < 1000.0 kJ/mol/nm
emstep   = 0.002; Energy step size
nsteps   = 5; Maximum number of 
(minimization) steps to perform
;
; Output control
nstxout   = 500 ; save coordinates every 1 ps
nstvout   = 500 ; save velocities every 1 ps
nstenergy = 500 ; save energies every 1 ps
nstxtcout = 500 ; co-ordinates to xtc
nstlog= 500 ; update log file every 1.0 ps
nstfout   = 500
nstcalcenergy = 100 ; calculate energies
nstcheckpoint = 1000
xtc-precision = 1000
xtc_grps  = system
;
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric  = 0
ld-seed  = -1
;
; Max number of iterations in relax_shells
niter= 20
;
; NEIGHBOR SEARCHING
cutoff-scheme= Verlet
ns-type  = grid ; Method to determine 
neighbor list (simple, grid)
nstlist  = 10   ; Frequency to update the 
neighbor list and long range forces
rlist= 1.0
rvdw = 1.0  ; Short-range 
Van der Waals cut-off
verlet-buffer-tolerance  = 0.005
pbc  = xyz  ; Periodic 
Boundary Conditions (yes/no)
periodic_molecules   = no
;
; ELECTROSTATICS
coulombtype  = PME  ; Treatment of 
long range electrostatic interactions
pme-order= 8
rcoulomb = 1.2  ; Short-range 
electrostatic cut-off
rcoulomb-switch  = 0
epsilon-r= 1; 2.5 (with polarizable water)
epsilon-rf   = 1
;
; VAN DER WAALS
vdwtype  = Cut-off
vdw-modifier = Potential-shift-verlet
;
; CUT-OFF LENGHTS   
rvdw-switch  = 0
;
; Ewald
DispCorr = EnerPres ;Apply long range dispersion 
corrections for Energy and Pressure
table-extension  = 1
energygrp-table  = 
fourierspacing   = 0.15
fourier-nx   = 0
fourier-ny   = 0
fourier-nz   = 0
ewald-rtol   = 1e-05
ewald-rtol-lj= 1e-3
ewald-geometry   = 3d
lj-pme-comb-rule = Geometric
epsilon-surface  = 0
optimize_fft = yes
;
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
tcoupl   = No
tc-grps  = 
tau-t= 
ref-t= 
pcoupl   = No
pcoupltype   = Isotropic
tau-p= 1
ref-p= 
refcoord_scaling = No
andersen_seed= 815131
;
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel  = no
gen-temp = 300
gen_seed = -1   ;173529
;
; OPTIONS FOR BONDS
constraints  = none
constraint-algorithm = LINCS
continuation = no
Shake-SOR= no
shake-tol= 0.0001
lincs-order  = 8
lincs-iter   = 1
lincs-warnangle  = 30
morse= notitle   = 

Re: [gmx-users] Equilibration step not moving forward

[Kevin Boyd]

Hi,

We can't help you unless you're more specific. What error is occurring?

Kevin

On Tue, Feb 5, 2019 at 1:30 AM Deepanshi  wrote:

> Hello,
> I am trying to equilibrate a bilayer vesicle which I have prepared using
> martini maker of charmm-GUI. The vesicle is made up of POPC and has around
> 3000 lipids. I am trying to equilibrate the system but steps are not
> moving forward and I am stuck at this point. Here are the details of the
> .mdp file which I am using for this step:
> define   = -DVESICLE_LIPIDTAIL_R=2.00
> integrator   = sd
> tinit= 0.0
> dt   = 0.010
> nsteps   = 100
>
> nstlog   = 1000
> nstenergy= 1000
> nstxout-compressed   = 1000
> compressed-x-precision   = 100
>
> cutoff-scheme= Verlet
> nstlist  = 20
> ns_type  = grid
> pbc  = xyz
> verlet-buffer-tolerance  = 0.005
>
> epsilon_r= 15
> coulombtype  = reaction-field
> rcoulomb = 1.1
> vdw_type = cutoff
> vdw-modifier = Potential-shift-verlet
> rvdw = 1.1
>
> tc-grps  = system
> tau_t= 4.0
> ref_t= 310
>
> ; Pressure coupling:
> Pcoupl   = no
>
> ; GENERATE VELOCITIES FOR STARTUP RUN:
> gen_vel  = yes
> gen_temp = 310
> gen_seed = 1549004057
>
> refcoord_scaling = all
>
> Thank you.
>
> Best Regards.
> Zara.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Ckevin.boyd%40uconn.edu%7Cf6ede7bca2d84c47840108d68b336af7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636849450295340905sdata=kaBvdvNNgGjDa3gAV%2FdLDHZwaUZGYA22qH9CX%2F7S0jg%3Dreserved=0
> before posting!
>
> * Can't post? Read
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=02%7C01%7Ckevin.boyd%40uconn.edu%7Cf6ede7bca2d84c47840108d68b336af7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636849450295340905sdata=T2MVpXdE06n1d8ouBz3c7udbIMQ%2BKyDVCM9zH%2BpegA8%3Dreserved=0
>
> * For (un)subscribe requests visit
>
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=02%7C01%7Ckevin.boyd%40uconn.edu%7Cf6ede7bca2d84c47840108d68b336af7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636849450295340905sdata=13ZbBiacpXWW22C9XE0pWQ9tQsPxbac3HghFRk%2B1Asc%3Dreserved=0
> 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] Equilibration step not moving forward

[Deepanshi]

Hello,
I am trying to equilibrate a bilayer vesicle which I have prepared using
martini maker of charmm-GUI. The vesicle is made up of POPC and has around
3000 lipids. I am trying to equilibrate the system but steps are not
moving forward and I am stuck at this point. Here are the details of the
.mdp file which I am using for this step:
define   = -DVESICLE_LIPIDTAIL_R=2.00
integrator   = sd
tinit= 0.0
dt   = 0.010
nsteps   = 100

nstlog   = 1000
nstenergy= 1000
nstxout-compressed   = 1000
compressed-x-precision   = 100

cutoff-scheme= Verlet
nstlist  = 20
ns_type  = grid
pbc  = xyz
verlet-buffer-tolerance  = 0.005

epsilon_r= 15
coulombtype  = reaction-field
rcoulomb = 1.1
vdw_type = cutoff
vdw-modifier = Potential-shift-verlet
rvdw = 1.1

tc-grps  = system
tau_t= 4.0
ref_t= 310

; Pressure coupling:
Pcoupl   = no

; GENERATE VELOCITIES FOR STARTUP RUN:
gen_vel  = yes
gen_temp = 310
gen_seed = 1549004057

refcoord_scaling = all

Thank you.

Best Regards.
Zara.
-- 
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] equilibration error

[Dallas Warren]

What is actually different in the mdp file between each of these
steps?  What about the cluster run on, or mdrun command used for each
of the steps?

How have you determined that each step in the process is long enough
i.e. what are you looking at to see if things have stabilised
sufficiently?

There is a recent discussion about this on the emailing list, but no
real solution was suggested …

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-June/120979.html

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On Thu, 11 Oct 2018 at 16:16, Stephani Macalino
 wrote:
>
> Hello,
> I am planing to do MD of a membrane protein bound to a ligand.
> I already have my files and I am doing my 6 step equilibration with
> reducing force constants.
> However, in the 5th step, it gave an error saying that the previous system
> (4th step) was not well equilibrated:
>
> Fatal error:
> 5 particles communicated to PME rank 0 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
>
> I'm a newbie to this and don't completely understand the error.
> Since it says the previous system is not well equilibrated, should I
> increase the steps for equilibration?
>
> I am wary to change the force constant values since I did 100ns MD for apo
> WT and mutant structures for the same protein that I am now doing with the
> ligand.
>
> Hope you can suggest some ways to solve this problem. Thanks in advance!
>
> Regards,
> Stephani
> --
> 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] equilibration error

[Stephani Macalino]

Hello,
I am planing to do MD of a membrane protein bound to a ligand.
I already have my files and I am doing my 6 step equilibration with
reducing force constants.
However, in the 5th step, it gave an error saying that the previous system
(4th step) was not well equilibrated:

Fatal error:
5 particles communicated to PME rank 0 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.

I'm a newbie to this and don't completely understand the error.
Since it says the previous system is not well equilibrated, should I
increase the steps for equilibration?

I am wary to change the force constant values since I did 100ns MD for apo
WT and mutant structures for the same protein that I am now doing with the
ligand.

Hope you can suggest some ways to solve this problem. Thanks in advance!

Regards,
Stephani
-- 
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] Equilibration step in MD

[SHYANTANI MAITI]

Dear all,
The rmsd obtained after equilibration of protein-protein complex at 1atm
pressure is quite high(5times) but the rmsd obtained for only 100ps
simulatrion of equilibration is quite stable. Which rmsd should be
considered?

-- 
Best regards,
*Shyantani Maiti*
-- 
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] Equilibration

[Justin Lemkul]

On 2/28/18 6:38 AM, Amin Rouy wrote:

Thanks Justin, however,


I run a simulation of a solute in water. I have 2 question please:

1- After NVT equilibrium, I see that all quantities like
energies and
temperature become stable, except pressure. Should I continue
till pressure
also goes stable? or can I move forward and do it in
production run?


Pressure isn't a conserved quantity in NVT. It is in NPT (hence
the P).

Yes, but if a system goes to equilibrium in NVT, pressure should be 
fluctuating around a stable value.  For any system with defined N, T, 
V there should be one value for pressure, is not it?


Pressure fluctuates pretty wildly, and in NVT there is no barostat 
regulating it, so no, you should not expect to see any sort of stable 
value in this quantity.


-Justin


2- My interest production run is NVT, should I run
2th-step-equilibrium
with NPT also? or only NVT equilibration is enough?


Model whatever conditions are relevant to you; even with NVT, you
may want to simulate at a fixed density, which requires NPT
equilibration to stabilize the pressure/density and then continue
with NVT. Rarely is the initial configuration ideal.

-Justin

-- 
==


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu  | (540) 231-3129

http://www.biochem.vt.edu/people/faculty/JustinLemkul.html


==

-- 
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
.




--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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] Equilibration

[Amin Rouy]

Thanks Justin, however,

>
>> I run a simulation of a solute in water. I have 2 question please:
>>
>> 1- After NVT equilibrium, I see that all quantities like energies and
>> temperature become stable, except pressure. Should I continue till
>> pressure
>> also goes stable? or can I move forward and do it in production run?
>>
>
> Pressure isn't a conserved quantity in NVT. It is in NPT (hence the P).
>
> Yes, but if a system goes to equilibrium in NVT, pressure should be
fluctuating around a stable value.  For any system with defined N, T, V
there should be one value for pressure, is not it?

> 2- My interest production run is NVT, should I run 2th-step-equilibrium
>> with NPT also? or only NVT equilibration is enough?
>>
>
> Model whatever conditions are relevant to you; even with NVT, you may want
> to simulate at a fixed density, which requires NPT equilibration to
> stabilize the pressure/density and then continue with NVT. Rarely is the
> initial configuration ideal.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> 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] Equilibration

[Amin Rouy]

sorry but I did not get my answer.
In NVT equilibration, the pressure is not equilibrated yet, can I move
forward to production run? (I see that I have no blow up when I run
production)

On Wed, Feb 28, 2018 at 10:38 AM, Quyen V. Vu  wrote:

> No matter how many steps of equilibration you want to run.
> You need to run production run when your configuration is reasonable and in
> which condition, which ensemble you want to mimic
>
> On Wed, Feb 28, 2018 at 3:54 PM, Amin Rouy  wrote:
>
> > Hi,
> >
> >
> > I run a simulation of a solute in water. I have 2 questions please:
> >
> >
> > 1- After NVT equilibrium, I see that all quantities like energies and
> > temperature become stable, except pressure. Should I continue untill
> > pressure becomes stable too? or can I move forward and do it in
> > production run?
> >
> > 2- My interest production run is NVT, should I run
> > 2th-step-equilibrium with NPT also? or only NVT equilibration is
> > enough?
> >
> >
> > Thanks for answer
> > --
> > 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.
>
-- 
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] Equilibration

[Quyen V. Vu]

No matter how many steps of equilibration you want to run.
You need to run production run when your configuration is reasonable and in
which condition, which ensemble you want to mimic

On Wed, Feb 28, 2018 at 3:54 PM, Amin Rouy  wrote:

> Hi,
>
>
> I run a simulation of a solute in water. I have 2 questions please:
>
>
> 1- After NVT equilibrium, I see that all quantities like energies and
> temperature become stable, except pressure. Should I continue untill
> pressure becomes stable too? or can I move forward and do it in
> production run?
>
> 2- My interest production run is NVT, should I run
> 2th-step-equilibrium with NPT also? or only NVT equilibration is
> enough?
>
>
> Thanks for answer
> --
> 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] Equilibration

[Amin Rouy]

Hi,


I run a simulation of a solute in water. I have 2 questions please:


1- After NVT equilibrium, I see that all quantities like energies and
temperature become stable, except pressure. Should I continue untill
pressure becomes stable too? or can I move forward and do it in
production run?

2- My interest production run is NVT, should I run
2th-step-equilibrium with NPT also? or only NVT equilibration is
enough?


Thanks for answer
-- 
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] Equilibration

[Dallas Warren]

Not sure about with constant volume, as I don't tend to run under
those conditions, but with constant pressure the pressure will always
fluctuate quite substantially.

How big the fluctuation is depends on the size of the system, the
later the system is, the smaller the fluctuations.

Small system (6k): https://twitter.com/dr_dbw/status/968624615063937025

Larger system (300k): https://twitter.com/dr_dbw/status/968625462959210496

You really should run a component with NPT, so that the system reaches
the correct box size and pressure.  It is unlikely that the box you
set has the exact right dimensions and number of molecules to give the
correct pressure/density.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 28 February 2018 at 02:05, Amin Rouy  wrote:
> Hi,
>
> I run a simulation of a solute in water. I have 2 question please:
>
> 1- After NVT equilibrium, I see that all quantities like energies and
> temperature become stable, except pressure. Should I continue till pressure
> also goes stable? or can I move forward and do it in production run?
>
> 2- My interest production run is NVT, should I run 2th-step-equilibrium
> with NPT also? or only NVT equilibration is enough?
> --
> 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] Equilibration

[Justin Lemkul]

On 2/27/18 10:05 AM, Amin Rouy wrote:

Hi,

I run a simulation of a solute in water. I have 2 question please:

1- After NVT equilibrium, I see that all quantities like energies and
temperature become stable, except pressure. Should I continue till pressure
also goes stable? or can I move forward and do it in production run?


Pressure isn't a conserved quantity in NVT. It is in NPT (hence the P).


2- My interest production run is NVT, should I run 2th-step-equilibrium
with NPT also? or only NVT equilibration is enough?


Model whatever conditions are relevant to you; even with NVT, you may 
want to simulate at a fixed density, which requires NPT equilibration to 
stabilize the pressure/density and then continue with NVT. Rarely is the 
initial configuration ideal.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

--
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] Equilibration

[Amin Rouy]

Hi,

I run a simulation of a solute in water. I have 2 question please:

1- After NVT equilibrium, I see that all quantities like energies and
temperature become stable, except pressure. Should I continue till pressure
also goes stable? or can I move forward and do it in production run?

2- My interest production run is NVT, should I run 2th-step-equilibrium
with NPT also? or only NVT equilibration is enough?
-- 
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] Equilibration using position restraints in NPT

[Mark Abraham]

On Sun, Oct 8, 2017 at 11:30 PM Neha Gandhi  wrote:

> Thank you Mark.
>
> The nanotube is 2x2x13 nm long. Then I use editconf with -c  and -d  2 and
> solvate using spc216.gro.
>

Please visualize that result. Such a command would put solvent all around
your nanotube, so it could not have an infinite topology and be stable.

How can I calculate box size after NVT so that I get density of 1 or 0.99
> when using pressure coupling?
>

Your z dimension is chosen by the size of the nanotube. Your x and y might
be chosen by whatever the above procedure suggests, but you can't actually
use the box that it produced.

Mark
-- 
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] Equilibration using position restraints in NPT

[Alex]

In addition, the CNT edges have to be periodically commensurate.


On 10/8/2017 3:36 PM, Alex wrote:
PBC for crystals are not set this way, this is why the simulator is 
turning the CNT into a pogo stick.


Prior to any simulations, please calculate the correct PBC-compatible 
axial length using crystallographic considerations and CNT chirality, 
-box properly, generate topology with PBC, then proceed with EM, etc.


Alex


On 10/8/2017 3:29 PM, Neha Gandhi wrote:

Thank you Mark.

The nanotube is 2x2x13 nm long. Then I use editconf with -c  and -d  
2 and

solvate using spc216.gro.

How can I calculate box size after NVT so that I get density of 1 or 
0.99

when using pressure coupling?






Message: 1
Date: Sun, 8 Oct 2017 23:38:58 +1000
From: Neha Gandhi <n.gandh...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Equilibration using position restraints in NPT
Message-ID:
<CA+Hq8HyXsHSXfNAe5AmBmy3ArxS-=aZHJckdJSC4yqWUMJDbmA@mail.
gmail.com>
Content-Type: text/plain; charset="UTF-8"

This is a very common post on previous mailing list however, I am 
still not

able to fix the problem of position restraints during NPT.

I have a carbon nanotube aligned to z-direction. I am trying to 
simulate
infinite nanotube using periodic conditions. It is common to use 
position
restraints for nanotube (most papers report this). I have imposed 
position
restraints on nanotube and in doing so, the coordinates fluctuates 
by 0.5-1

nm. This is not an issue with NVT simulation (Berendsen thermostat and
barostat). I tried different thermostats and barostats, they deform the
nanotube as previously discussed on gromacs mailing list.

How do I equilibrate nanotube system with position restraints when used
together with pressure coupling? Should I play with the box size after
first NVT run?
The force field is opls based on gromacs guideline on CNTs and GROMACS
version is 5.1.4. The mdp parameters are below:

Thank you in advance,

Sincerely,
Neha



title    = OPLS Lysozyme NPT equilibration
define    = -DPOSRES_CNT    ; position restrain the protein
; Run parameters
integrator    = md    ; leap-frog integrator
nsteps    = 50    ; 2
dt    = 0.001    ; 2 fs
; Output control
nstxout    = 5000    ; save coordinates every 1.0 ps
nstvout    = 5000    ; save velocities every 1.0 ps
nstenergy    = 5000    ; save energies every 1.0 ps
nstlog    = 5000    ; update log file every 1.0 ps
;energygrps   = Protein  CNT Water NA
; Bond parameters
continuation    = yes    ; Restarting after NVT
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
cutoff-scheme   = Verlet
ns_type    = grid    ; search neighboring grid cells
nstlist    = 10    ; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb    = 1.0    ; short-range electrostatic cutoff (in nm)
rvdw    = 1.0    ; 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 is on
tcoupl    = Berendsen    ; modified Berendsen
thermostat
tc-grps    = CNT Water    ; two coupling groups - more accurate
tau_t    = 0.2  0.2    ; time constant, in ps
ref_t    = 310   310   ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl    = Berendsen    ; Pressure coupling on in NPT
pcoupltype    = isotropic    ; uniform scaling 
of box

vectors
tau_p    = 5.0    ; 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
; Periodic boundary conditions
pbc    = xyz    ; 3-D PBC
periodic_molecules = yes
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
gen_vel    = no    ; Velocity generation is off

--
Regards,
Dr. Neha S. Gandhi,


--

Message: 2
Date: Sun, 8 Oct 2017 22:34:21 +0530
From: Dilip H N <cy16f01.di...@nitk.edu.in>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding charges for atoms in a molecule
Message-ID:
<CAD6GXy07bfJ8BMOdi68a6rjkvf-tTF9kWF_VroK9nKfVdDQ-wA@mail.
gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hello,
I have an amino-acid (eg. glycine) and water mixture, and by using 
charmm36
ff

Re: [gmx-users] Equilibration using position restraints in NPT

[Alex]

PBC for crystals are not set this way, this is why the simulator is 
turning the CNT into a pogo stick.


Prior to any simulations, please calculate the correct PBC-compatible 
axial length using crystallographic considerations and CNT chirality, 
-box properly, generate topology with PBC, then proceed with EM, etc.


Alex


On 10/8/2017 3:29 PM, Neha Gandhi wrote:

Thank you Mark.

The nanotube is 2x2x13 nm long. Then I use editconf with -c  and -d  2 and
solvate using spc216.gro.

How can I calculate box size after NVT so that I get density of 1 or 0.99
when using pressure coupling?






Message: 1
Date: Sun, 8 Oct 2017 23:38:58 +1000
From: Neha Gandhi <n.gandh...@gmail.com>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Equilibration using position restraints in NPT
Message-ID:
 <CA+Hq8HyXsHSXfNAe5AmBmy3ArxS-=aZHJckdJSC4yqWUMJDbmA@mail.
gmail.com>
Content-Type: text/plain; charset="UTF-8"

This is a very common post on previous mailing list however, I am still not
able to fix the problem of position restraints during NPT.

I have a carbon nanotube aligned to z-direction. I am trying to simulate
infinite nanotube using periodic conditions. It is common to use position
restraints for nanotube (most papers report this). I have imposed position
restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
nm. This is not an issue with NVT simulation (Berendsen thermostat and
barostat). I tried different thermostats and barostats, they deform the
nanotube as previously discussed on gromacs mailing list.

How do I equilibrate nanotube system with position restraints when used
together with pressure coupling? Should I play with the box size after
first NVT run?
The force field is opls based on gromacs guideline on CNTs and GROMACS
version is 5.1.4. The mdp parameters are below:

Thank you in advance,

Sincerely,
Neha



title= OPLS Lysozyme NPT equilibration
define= -DPOSRES_CNT; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 50; 2
dt= 0.001; 2 fs
; Output control
nstxout= 5000; save coordinates every 1.0 ps
nstvout= 5000; save velocities every 1.0 ps
nstenergy= 5000; save energies every 1.0 ps
nstlog= 5000; update log file every 1.0 ps
;energygrps   = Protein  CNT Water NA
; Bond parameters
continuation= yes; Restarting after NVT
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
cutoff-scheme   = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; 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 is on
tcoupl= Berendsen; modified Berendsen
thermostat
tc-grps= CNT Water; two coupling groups - more accurate
tau_t= 0.2  0.2; time constant, in ps
ref_t= 310   310   ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl= Berendsen; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box
vectors
tau_p= 5.0; 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
; Periodic boundary conditions
pbc= xyz; 3-D PBC
periodic_molecules = yes
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off

--
Regards,
Dr. Neha S. Gandhi,


--

Message: 2
Date: Sun, 8 Oct 2017 22:34:21 +0530
From: Dilip H N <cy16f01.di...@nitk.edu.in>
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Regarding charges for atoms in a molecule
Message-ID:
 <CAD6GXy07bfJ8BMOdi68a6rjkvf-tTF9kWF_VroK9nKfVdDQ-wA@mail.
gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hello,
I have an amino-acid (eg. glycine) and water mixture, and by using charmm36
ff forcefield, I got the topology file through gmx pdb2gmx -f abc.pdb -o
abc.gro command.
1] In 

[gmx-users] Equilibration using position restraints in NPT

[Neha Gandhi]

Thank you Mark.

The nanotube is 2x2x13 nm long. Then I use editconf with -c  and -d  2 and
solvate using spc216.gro.

How can I calculate box size after NVT so that I get density of 1 or 0.99
when using pressure coupling?





> Message: 1
> Date: Sun, 8 Oct 2017 23:38:58 +1000
> From: Neha Gandhi <n.gandh...@gmail.com>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Equilibration using position restraints in NPT
> Message-ID:
> <CA+Hq8HyXsHSXfNAe5AmBmy3ArxS-=aZHJckdJSC4yqWUMJDbmA@mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> This is a very common post on previous mailing list however, I am still not
> able to fix the problem of position restraints during NPT.
>
> I have a carbon nanotube aligned to z-direction. I am trying to simulate
> infinite nanotube using periodic conditions. It is common to use position
> restraints for nanotube (most papers report this). I have imposed position
> restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
> nm. This is not an issue with NVT simulation (Berendsen thermostat and
> barostat). I tried different thermostats and barostats, they deform the
> nanotube as previously discussed on gromacs mailing list.
>
> How do I equilibrate nanotube system with position restraints when used
> together with pressure coupling? Should I play with the box size after
> first NVT run?
> The force field is opls based on gromacs guideline on CNTs and GROMACS
> version is 5.1.4. The mdp parameters are below:
>
> Thank you in advance,
>
> Sincerely,
> Neha
>
>
>
> title= OPLS Lysozyme NPT equilibration
> define= -DPOSRES_CNT; position restrain the protein
> ; Run parameters
> integrator= md; leap-frog integrator
> nsteps= 50; 2
> dt= 0.001; 2 fs
> ; Output control
> nstxout= 5000; save coordinates every 1.0 ps
> nstvout= 5000; save velocities every 1.0 ps
> nstenergy= 5000; save energies every 1.0 ps
> nstlog= 5000; update log file every 1.0 ps
> ;energygrps   = Protein  CNT Water NA
> ; Bond parameters
> continuation= yes; Restarting after NVT
> 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
> cutoff-scheme   = Verlet
> ns_type= grid; search neighboring grid cells
> nstlist= 10; 20 fs, largely irrelevant with Verlet
> scheme
> rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
> rvdw= 1.0; 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 is on
> tcoupl= Berendsen; modified Berendsen
> thermostat
> tc-grps= CNT Water; two coupling groups - more accurate
> tau_t= 0.2  0.2; time constant, in ps
> ref_t= 310   310   ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl= Berendsen; Pressure coupling on in NPT
> pcoupltype= isotropic; uniform scaling of box
> vectors
> tau_p= 5.0; 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
> ; Periodic boundary conditions
> pbc= xyz; 3-D PBC
> periodic_molecules = yes
> ; Dispersion correction
> DispCorr= EnerPres; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel= no; Velocity generation is off
>
> --
> Regards,
> Dr. Neha S. Gandhi,
>
>
> --
>
> Message: 2
> Date: Sun, 8 Oct 2017 22:34:21 +0530
> From: Dilip H N <cy16f01.di...@nitk.edu.in>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Regarding charges for atoms in a molecule
> Message-ID:
> <CAD6GXy07bfJ8BMOdi68a6rjkvf-tTF9kWF_VroK9nKfVdDQ-wA@mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hello,
> I have an amino-aci

Re: [gmx-users] Equilibration using position restraints in NPT

[Mark Abraham]

Hi,

The simplest explanation is that your box size is inappropriate for the
contents. If the box wants to change size but the nanotube is restrained to
fixed positions then you have an invalid model.

Mark

On Sun, 8 Oct 2017 15:39 Neha Gandhi  wrote:

> This is a very common post on previous mailing list however, I am still not
> able to fix the problem of position restraints during NPT.
>
> I have a carbon nanotube aligned to z-direction. I am trying to simulate
> infinite nanotube using periodic conditions. It is common to use position
> restraints for nanotube (most papers report this). I have imposed position
> restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
> nm. This is not an issue with NVT simulation (Berendsen thermostat and
> barostat). I tried different thermostats and barostats, they deform the
> nanotube as previously discussed on gromacs mailing list.
>
> How do I equilibrate nanotube system with position restraints when used
> together with pressure coupling? Should I play with the box size after
> first NVT run?
> The force field is opls based on gromacs guideline on CNTs and GROMACS
> version is 5.1.4. The mdp parameters are below:
>
> Thank you in advance,
>
> Sincerely,
> Neha
>
>
>
> title= OPLS Lysozyme NPT equilibration
> define= -DPOSRES_CNT; position restrain the protein
> ; Run parameters
> integrator= md; leap-frog integrator
> nsteps= 50; 2
> dt= 0.001; 2 fs
> ; Output control
> nstxout= 5000; save coordinates every 1.0 ps
> nstvout= 5000; save velocities every 1.0 ps
> nstenergy= 5000; save energies every 1.0 ps
> nstlog= 5000; update log file every 1.0 ps
> ;energygrps   = Protein  CNT Water NA
> ; Bond parameters
> continuation= yes; Restarting after NVT
> 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
> cutoff-scheme   = Verlet
> ns_type= grid; search neighboring grid cells
> nstlist= 10; 20 fs, largely irrelevant with Verlet
> scheme
> rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
> rvdw= 1.0; 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 is on
> tcoupl= Berendsen; modified Berendsen
> thermostat
> tc-grps= CNT Water; two coupling groups - more accurate
> tau_t= 0.2  0.2; time constant, in ps
> ref_t= 310   310   ; reference temperature, one for
> each group, in K
> ; Pressure coupling is on
> pcoupl= Berendsen; Pressure coupling on in NPT
> pcoupltype= isotropic; uniform scaling of box
> vectors
> tau_p= 5.0; 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
> ; Periodic boundary conditions
> pbc= xyz; 3-D PBC
> periodic_molecules = yes
> ; Dispersion correction
> DispCorr= EnerPres; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel= no; Velocity generation is off
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> --
> 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] Equilibration using position restraints in NPT

[Neha Gandhi]

This is a very common post on previous mailing list however, I am still not
able to fix the problem of position restraints during NPT.

I have a carbon nanotube aligned to z-direction. I am trying to simulate
infinite nanotube using periodic conditions. It is common to use position
restraints for nanotube (most papers report this). I have imposed position
restraints on nanotube and in doing so, the coordinates fluctuates by 0.5-1
nm. This is not an issue with NVT simulation (Berendsen thermostat and
barostat). I tried different thermostats and barostats, they deform the
nanotube as previously discussed on gromacs mailing list.

How do I equilibrate nanotube system with position restraints when used
together with pressure coupling? Should I play with the box size after
first NVT run?
The force field is opls based on gromacs guideline on CNTs and GROMACS
version is 5.1.4. The mdp parameters are below:

Thank you in advance,

Sincerely,
Neha



title= OPLS Lysozyme NPT equilibration
define= -DPOSRES_CNT; position restrain the protein
; Run parameters
integrator= md; leap-frog integrator
nsteps= 50; 2
dt= 0.001; 2 fs
; Output control
nstxout= 5000; save coordinates every 1.0 ps
nstvout= 5000; save velocities every 1.0 ps
nstenergy= 5000; save energies every 1.0 ps
nstlog= 5000; update log file every 1.0 ps
;energygrps   = Protein  CNT Water NA
; Bond parameters
continuation= yes; Restarting after NVT
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
cutoff-scheme   = Verlet
ns_type= grid; search neighboring grid cells
nstlist= 10; 20 fs, largely irrelevant with Verlet
scheme
rcoulomb= 1.0; short-range electrostatic cutoff (in nm)
rvdw= 1.0; 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 is on
tcoupl= Berendsen; modified Berendsen thermostat
tc-grps= CNT Water; two coupling groups - more accurate
tau_t= 0.2  0.2; time constant, in ps
ref_t= 310   310   ; reference temperature, one for
each group, in K
; Pressure coupling is on
pcoupl= Berendsen; Pressure coupling on in NPT
pcoupltype= isotropic; uniform scaling of box
vectors
tau_p= 5.0; 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
; Periodic boundary conditions
pbc= xyz; 3-D PBC
periodic_molecules = yes
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off

-- 
Regards,
Dr. Neha S. Gandhi,
-- 
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] Equilibration at each temperature in simmulated annealing

[Mark Abraham]

Hi,

That's still not going to have any effect. You're probably referring to
ref-t, which is exactly what simulated annealing is documented to replace.

Mark

On Tue, Sep 26, 2017 at 3:15 PM lan hoa Trinh  wrote:

> Thanks! sorry for the spelling error, I just meant tcoupl.
>
> Sent from my iPhone
>
> > On Sep 26, 2017, at 6:30 AM, Mark Abraham 
> wrote:
> >
> > Hi,
> >
> > It'll equilibrate if you leave it alone long enough at an annealing
> point,
> > as normal. See
> >
> http://manual.gromacs.org/documentation/2016.4/user-guide/mdp-options.html#simulated-annealing
> .
> > I don't know what you mean by referring to the non-existent t_couple
> >
> > Mark
> >
> >> On Tue, Sep 26, 2017 at 8:49 AM Hoa Trinh 
> wrote:
> >>
> >> Hi all,
> >> I would like to cool my system from 200K to 100K via multiple
> intermediate
> >> temperatures and at each temperature, the system is equilibrated for a
> >> while before decreasing temperature.
> >> I am thinking of doing something like this:
> >> annealing_temp = 200 150 150 100 100
> >> But I am afraid this is not going to equilibrate my system at 150K
> since I
> >> only have one value of t_couple in mdp file. That means I can only
> choose
> >> to equilibrate my system at either 150K or 100K.
> >> So how can I equilibrate my system at each temperature in simulated
> >> annealing?
> >> I am looking forward to hearing from you.
> >> Thanks in advance!
> >> Best regards,
> >> *Lan Hoa*
> >> --
> >> 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.
> --
> 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] Equilibration at each temperature in simmulated annealing

[Mark Abraham]

Hi,

It'll equilibrate if you leave it alone long enough at an annealing point,
as normal. See
http://manual.gromacs.org/documentation/2016.4/user-guide/mdp-options.html#simulated-annealing.
I don't know what you mean by referring to the non-existent t_couple

Mark

On Tue, Sep 26, 2017 at 8:49 AM Hoa Trinh  wrote:

> Hi all,
> I would like to cool my system from 200K to 100K via multiple intermediate
> temperatures and at each temperature, the system is equilibrated for a
> while before decreasing temperature.
> I am thinking of doing something like this:
> annealing_temp = 200 150 150 100 100
> But I am afraid this is not going to equilibrate my system at 150K since I
> only have one value of t_couple in mdp file. That means I can only choose
> to equilibrate my system at either 150K or 100K.
> So how can I equilibrate my system at each temperature in simulated
> annealing?
> I am looking forward to hearing from you.
> Thanks in advance!
> Best regards,
> *Lan Hoa*
> --
> 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] Equilibration at each temperature in simmulated annealing

[Hoa Trinh]

Hi all,
I would like to cool my system from 200K to 100K via multiple intermediate
temperatures and at each temperature, the system is equilibrated for a
while before decreasing temperature.
I am thinking of doing something like this:
annealing_temp = 200 150 150 100 100
But I am afraid this is not going to equilibrate my system at 150K since I
only have one value of t_couple in mdp file. That means I can only choose
to equilibrate my system at either 150K or 100K.
So how can I equilibrate my system at each temperature in simulated
annealing?
I am looking forward to hearing from you.
Thanks in advance!
Best regards,
*Lan Hoa*
-- 
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] Equilibration

[Dallas Warren]

That ultimately depends on what physical property you are hoping to
show is at "equilibrium".  For example, see
https://twitter.com/dr_dbw/status/907735156382777344 for how
temperature, total energy, volume, density and pressure change with
time for an example system.  Pressure and temperature you don't see
any trends, since those happen in rapid time frames so they have
reached equilibrium very rapidly, <<1ns.  You can see that
density/volume have a change during first 10ns, then things settle
down, so they have reached equilibrium within 10ns.  Total energy has
a slight downward trend, but it is difficult to see for sure. Then if
you look at a different property, say solvent accessible surface area,
see https://twitter.com/dr_dbw/status/907736554939891712, then you can
see that by the end of the 50ns it may have reach equilibrium, but
there is insufficient data to say for sure.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 13 September 2017 at 05:15, ÁLVARO RODRIGO RUIZ FERNÁNDEZ
 wrote:
> Dear users,
>
> I need to demonstrate that my box is in equilibrium. What is the maximum
> slope of the energy or the volume in function of time to demosntrate it? .
> Or exist anothe parameter to follow. Thank you very much.
>
> --
>
> *Dr. Álvaro  Ruiz  *
>
>
>
> *Physicochemical Molecular LaboratoryDepartamento de QuímicaFacultad de
> CienciasUniversidad de Chile*Mobile: +56-9-51178101
> Office: +56-2-9787443
> arr...@ug.uchile.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] Equilibration

[ÁLVARO RODRIGO RUIZ FERNÁNDEZ]

Dear users,

I need to demonstrate that my box is in equilibrium. What is the maximum
slope of the energy or the volume in function of time to demosntrate it? .
Or exist anothe parameter to follow. Thank you very much.

-- 

*Dr. Álvaro  Ruiz  *



*Physicochemical Molecular LaboratoryDepartamento de QuímicaFacultad de
CienciasUniversidad de Chile*Mobile: +56-9-51178101
Office: +56-2-9787443
arr...@ug.uchile.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.

Re: [gmx-users] Equilibration of Lipid Bilayers created through charmm-gui

[Justin Lemkul]

On 7/17/17 2:14 PM, Nidhin Thomas wrote:

Hello  everyone,

I have created an 'alpha-helix protein embedded in a lipid bilayer’ system 
using charmm-gui.

I used the mdp files provided by charmm-gui directly without changing the 
number of steps or constraints for equilibration. I ran final simulation for 
200 ns without any constraints and obtained a system in which there was no 
water penetration into the bilayer.



I'm assuming you mean restraints?  You certainly should be using constraints.


I compared my results against a research paper and I see water penetration into 
the bilayer for that system. They didn’t use charm-gui for modeling and they 
had frozen the protein during the initial equilibration compared to my system.



Freezing is a very severe and artificial perturbation.  It's entirely possible 
that water leaked in as an artifact of having an immobile protein.



Should we always freeze the protein during the initial equilibration time and 
let lipids settle before starting the equilibration with constraints to protein?



Not necessarily.  I rarely find freezing necessary or appropriate.


When I used the mdp files obtained from charmm-gui directly, I checked the RMSD 
values of the protein and it’s within 3 Angstrom which I think is within the 
acceptable range. Also average protein tilt within the lipids is also constant. 
Could you please tell me what else I can check to confirm if my system is fully 
equilibrated ?



Check convergence by looking at the time-dependence of any relevant property.

-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] Equilibration of Lipid Bilayers created through charmm-gui

[Nidhin Thomas]

Hello  everyone,

I have created an 'alpha-helix protein embedded in a lipid bilayer’ system 
using charmm-gui.

I used the mdp files provided by charmm-gui directly without changing the 
number of steps or constraints for equilibration. I ran final simulation for 
200 ns without any constraints and obtained a system in which there was no 
water penetration into the bilayer.

I compared my results against a research paper and I see water penetration into 
the bilayer for that system. They didn’t use charm-gui for modeling and they 
had frozen the protein during the initial equilibration compared to my system.

Should we always freeze the protein during the initial equilibration time and 
let lipids settle before starting the equilibration with constraints to protein?

When I used the mdp files obtained from charmm-gui directly, I checked the RMSD 
values of the protein and it’s within 3 Angstrom which I think is within the 
acceptable range. Also average protein tilt within the lipids is also constant. 
Could you please tell me what else I can check to confirm if my system is fully 
equilibrated ?

Thanks everyone,

Nidhin Thomas

-- 
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] equilibration

[Justin Lemkul]

On 7/14/17 7:43 AM, ‪farial tavakoli‬ ‪ wrote:

Hi justin
  Thank you for reply and sorry for sending in another email, because when i wanted to reply, it was rejected.Actually, since i am a new gromacs user, i used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial in gromacs. And did all the steps and issued all commands that said in this tuturial . I also generated my ligand topology by PRODRG and edited the charges and charge groups . To edit atome charge, according to aminoacids.rtp file, i considered what my atomes are bonded to , in order to best give their charge. Then , regarding to the article : Practical considerations for building GROMOS-compatible 


Parametrization by analogy is only a starting point.  In some cases it is 
straightforward and works well.  In others, it requires more effort.


small-molecule topologiesEditted the charge groups , but i think , maybe i was 
wrong in specifying charg groups. In addition, i noticed that there was a wrong 
bond in the gromacs topology ang gromacs cordinate files, so i


Wrong bond?  How so?  Also, there are no bonds in coordinate files; if you're 
visualizing the coordinates and something funny shows up, that's a problem with 
the viewing program, not the topology itself.


corrected them but i dont know if i did right?  These are all that i did. I dont 
know more about generating ligand topology but informatin that said in this 
tuturial. If you let me, send my ligand topology file to you?


Sorry, I do not have time to check your work here.

-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] equilibration

[‪farial tavakoli‬ ‪]

Hi justin
 Thank you for reply and sorry for sending in another email, because when i 
wanted to reply, it was rejected.Actually, since i am a new gromacs user, i 
used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 
4 ) tuturial in gromacs. And did all the steps and issued all commands that 
said in this tuturial . I also generated my ligand topology by PRODRG and 
edited the charges and charge groups . To edit atome charge, according to 
aminoacids.rtp file, i considered what my atomes are bonded to , in order to 
best give their charge. Then , regarding to the article : Practical 
considerations for building GROMOS-compatible small-molecule topologiesEditted 
the charge groups , but i think , maybe i was wrong in specifying charg groups. 
In addition, i noticed that there was a wrong bond in the gromacs topology ang 
gromacs cordinate files, so i corrected them but i dont know if i did right?  
These are all that i did. I dont know more about generating ligand topology but 
informatin that said in this tuturial. If you let me, send my ligand topology 
file to you? 
With best regardsFarial
-- 
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] Equilibration

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  Hi justin
 Thank you for replyActually, since i am a new gromacs user, i used all .mdp 
files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial 
in gromacs. And did all the steps and issued all commands that said in this 
tuturial . I also generated my ligand topology by PRODRG and edited the charges 
and charge groups . To edit atome charge, according to aminoacids.rtp file, i 
considered what my atomes are bonded to , in order to best give their charge. 
Then , regarding to the article : Practical considerations for building 
GROMOS-compatible small-molecule topologiesEditted the charge groups , but i 
think , maybe i was wrong in specifying charg groups. In addition, i noticed 
that there was a wrong bond in the gromacs topology ang gromacs cordinate 
files, so i corrected them but i dont know if i did right?  These are all that 
i did. I dont know more about generating ligand topology but informatin that 
said in this tuturial. If you let me, send my ligand topology file to you? 
With best regardsFarial

Sent from Yahoo Mail for iPhone


On Friday, July 14, 2017, 2:59 PM, Justin Lemkul  wrote:



On 7/13/17 11:21 AM, ‪farial tavakoli‬ ‪ wrote:
> Hi Justin
> Thank you so much for your reply about minimize ligand in vacuoaccording to 
> :http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>  I minimized my protein and ligand alone to fix the problem (  LINCS warning, 
>( one or more water molecules can not to be settled . check for bad contacts 
>or reduce time step))I checked my protein in desired solvent as i noticed in 
>the previous mail, and it was stable. i minimized my ligand too in vacuo with 
>the .mdp file which you advised me, it was minimized well and monitored by 
>pymol, its configuration was ok.
> In addition, I reduced the time step from 0,002 to 0.001 , but got the same 
> error in 2 steps.then, reduced the temperature to 100 k , but the same error 
> displayed again.
> Actually, I cant understand some advices and causes in this site. like:
> I dont understand  some of causes and advices in this site, include:1) you 
> are doing particle insertion in free energy calculations without using soft 
> core2) your position restraints are to coordinates too different from those 
> present in the system3) Make sure the forces don't get that large

None of those are relevant.

> How can i make sure the forces dont get that large? I dont know what these 3 
> causes are.
>  I have not recognized where the problem is and fixed it yet. It is wasting 
>my time a lot. My protein and ligand were intact . so what is its 
>problem?would you please help me? and introduce me an appropriate reference to 
>be expert in GROMACS?

Your protein in water works, but when you add the ligand it doesn't.  There's 
your problem.  The ligand minimizing in vacuo just means there's nothing 
catastrophically wrong with its topology, but it doesn't mean that topology is 
actually of suitable quality for an MD simulation.  How did you generate its 
parameters and in what ways did you validate it before trying to use it?

-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] Equilibration

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }Hi justin
 Thank you for replyActually, since i am a new gromacs user, i used all .mdp 
files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial 
in gromacs. And did all the steps and issued all commands that said in this 
tuturial . I also generated my ligand topology by PRODRG and edited the charges 
and charge groups . To edit atome charge, according to aminoacids.rtp file, i 
considered what my atomes are bonded to , in order to best give their charge. 
Then , regarding to the article : Practical considerations for building 
GROMOS-compatible small-molecule topologiesEditted the charge groups , but i 
think , maybe i was wrong in specifying charg groups. In addition, i noticed 
that there was a wrong bond in the gromacs topology ang gromacs cordinate 
files, so i corrected them but i dont know if i did right?  These are all that 
i did. I dont know more about generating ligand topology but informatin that 
said in this tuturial. If you let me, send my ligand topology file to you? 
With best regardsFarial

Sent from Yahoo Mail for iPhone


On Friday, July 14, 2017, 2:59 PM, Justin Lemkul  wrote:



On 7/13/17 11:21 AM, ‪farial tavakoli‬ ‪ wrote:
> Hi Justin
> Thank you so much for your reply about minimize ligand in vacuoaccording to 
> :http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>  I minimized my protein and ligand alone to fix the problem (  LINCS warning, 
>( one or more water molecules can not to be settled . check for bad contacts 
>or reduce time step))I checked my protein in desired solvent as i noticed in 
>the previous mail, and it was stable. i minimized my ligand too in vacuo with 
>the .mdp file which you advised me, it was minimized well and monitored by 
>pymol, its configuration was ok.
> In addition, I reduced the time step from 0,002 to 0.001 , but got the same 
> error in 2 steps.then, reduced the temperature to 100 k , but the same error 
> displayed again.
> Actually, I cant understand some advices and causes in this site. like:
> I dont understand  some of causes and advices in this site, include:1) you 
> are doing particle insertion in free energy calculations without using soft 
> core2) your position restraints are to coordinates too different from those 
> present in the system3) Make sure the forces don't get that large

None of those are relevant.

> How can i make sure the forces dont get that large? I dont know what these 3 
> causes are.
>  I have not recognized where the problem is and fixed it yet. It is wasting 
>my time a lot. My protein and ligand were intact . so what is its 
>problem?would you please help me? and introduce me an appropriate reference to 
>be expert in GROMACS?

Your protein in water works, but when you add the ligand it doesn't.  There's 
your problem.  The ligand minimizing in vacuo just means there's nothing 
catastrophically wrong with its topology, but it doesn't mean that topology is 
actually of suitable quality for an MD simulation.  How did you generate its 
parameters and in what ways did you validate it before trying to use it?

-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] Equilibration

[Justin Lemkul]

On 7/13/17 11:21 AM, ‪farial tavakoli‬ ‪ wrote:

Hi Justin
Thank you so much for your reply about minimize ligand in vacuoaccording to 
:http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
  I minimized my protein and ligand alone to fix the problem (  LINCS warning, 
( one or more water molecules can not to be settled . check for bad contacts or 
reduce time step))I checked my protein in desired solvent as i noticed in the 
previous mail, and it was stable. i minimized my ligand too in vacuo with the 
.mdp file which you advised me, it was minimized well and monitored by pymol, 
its configuration was ok.
In addition, I reduced the time step from 0,002 to 0.001 , but got the same 
error in 2 steps.then, reduced the temperature to 100 k , but the same error 
displayed again.
Actually, I cant understand some advices and causes in this site. like:
I dont understand  some of causes and advices in this site, include:1) you are 
doing particle insertion in free energy calculations without using soft core2) 
your position restraints are to coordinates too different from those present in 
the system3) Make sure the forces don't get that large


None of those are relevant.


How can i make sure the forces dont get that large? I dont know what these 3 
causes are.
  I have not recognized where the problem is and fixed it yet. It is wasting my 
time a lot. My protein and ligand were intact . so what is its problem?would 
you please help me? and introduce me an appropriate reference to be expert in 
GROMACS?


Your protein in water works, but when you add the ligand it doesn't.  There's 
your problem.  The ligand minimizing in vacuo just means there's nothing 
catastrophically wrong with its topology, but it doesn't mean that topology is 
actually of suitable quality for an MD simulation.  How did you generate its 
parameters and in what ways did you validate it before trying to use it?


-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] Equilibration

[‪farial tavakoli‬ ‪]

Hi Justin
Thank you so much for your reply about minimize ligand in vacuoaccording to 
:http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
 I minimized my protein and ligand alone to fix the problem (  LINCS warning, ( 
one or more water molecules can not to be settled . check for bad contacts or 
reduce time step))I checked my protein in desired solvent as i noticed in the 
previous mail, and it was stable. i minimized my ligand too in vacuo with the 
.mdp file which you advised me, it was minimized well and monitored by pymol, 
its configuration was ok.
In addition, I reduced the time step from 0,002 to 0.001 , but got the same 
error in 2 steps.then, reduced the temperature to 100 k , but the same error 
displayed again. 
Actually, I cant understand some advices and causes in this site. like:
I dont understand  some of causes and advices in this site, include:1) you are 
doing particle insertion in free energy calculations without using soft core2) 
your position restraints are to coordinates too different from those present in 
the system3) Make sure the forces don't get that large
How can i make sure the forces dont get that large? I dont know what these 3 
causes are.
 I have not recognized where the problem is and fixed it yet. It is wasting my 
time a lot. My protein and ligand were intact . so what is its problem?would 
you please help me? and introduce me an appropriate reference to be expert in 
GROMACS?
Thanks in advanceFarial

-- 
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] Equilibration

[farial tavakoli]

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  HiI am a new GROMACS user and i am trying to run a 
simulation on 4LY1 protein and my designed drug to check their interaction I 
used gromos 43a1 force field and when i performed equilibration with NVT.mdp 
file , I faced this error: step 1: One or more water molecules can not be 
settled. Check for bad contacts and/or reduce the timestep if appropriateI 
really appropriate if anybody can help meThanks alotFarialI typed this command  
gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
gmx mdrun -deffnm nvtThe nvt. Mdp file which i used:
title   = Protein-ligand complex NVT equilibration 
define  = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 500   ; save coordinates every 1.0 ps
nstvout = 500   ; save velocities every 1.0 ps
nstenergy   = 500   ; save energies every 1.0 ps
nstlog  = 500   ; update log file every 1.0 ps
energygrps  = Protein DRG
; 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
cutoff-scheme   = Verlet
ns_type = grid  ; search neighboring grid cells
nstlist = 10; 20 fs, largely irrelevant with Verlet
rcoulomb= 1.4   ; 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_DRG 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

Sent from Yahoo Mail for iPhone
  
-- 
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] EQUILIBRATION

[‪farial tavakoli‬ ‪]

HiI am a new GROMACS user and trying to run md on HDAC2 with PDB ID: 4LY1.  but 
when I wanted to performance equilibration , i got this ERROR:  
step 1: One or more water molecules can not be settled.
  Check for bad contacts and/or reduce the timestep if 
appropriate

Would you please help me to fix this problem?
These are all stages which I did:
I took 4LY1.pdb file from PDB site and removed B and C chains and all ligands 
and water molecules from it and left just chain A and HETATM ZN A . 
I constructed my protein topology by using gromos 43a1 and this command:pdb2gmx 
-f 4LY1.pdb -o 4LY1.gro -water spc
then made a complex.gro file which include 4LY1.gro and DRG.gro which i got 
from PRODRG site. I also copy paste ; Include ligand topology
#include "DRG.itp"

in the topology file and added DRG as a ligand in [ molecules ] directive. 
Then I defined box by using this command :
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0

then defined solvate by :
gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

then used grommp to assemble a .tpr file by using a .mdp file and this command :
gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

that was my .mdp afile :
integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform
energygrps  = system; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list 
and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions

and added 2 CL ions since my total charge was 2.00 because of zn ion. 

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 2

then for minimization, i replaced energygroups from system to protein DRG in 
em_real.mdp. that was my em_real.mdp file:

integrator  = steep ; Algorithm (steep = steepest descent 
minimization)
emtol   = 1000.0; Stop minimization when the maximum force < 
10.0 kJ/mol 
emstep  = 0.01  ; Energy step size
nsteps  = 5 ; Maximum number of (minimization) steps to 
perform
energygrps  = protein DRG   ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to 
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list 
and long range forces
cutoff-scheme   = Verlet
ns_type = grid  ; Method to determine neighbor list 
(simple, grid)
rlist   = 1.0   ; Cut-off for making neighbor list 
(short range forces)
coulombtype = PME   ; Treatment of long range electrostatic 
interactions
rcoulomb= 1.0   ; long range electrostatic cut-off
rvdw= 1.0   ; long range Van der Waals cut-off
pbc = xyz   ; Periodic Boundary Conditions

and typed these command: gmx grompp -f em_real.mdp -c solv_ions.gro -p 
topol.top -o em.tprand
gmx mdrun -v -deffnm em

GROMACS replies:
Steepest Descents converged to Fmax < 1000 in 1833 steps
Potential Energy  = -5.6356275e+05
Maximum force =  9.7815100e+02 on atom 3452
Norm of force =  3.1465845e+01

Simulation ended prematurely, no performance report will be written.
Is there any problem that simulation ended prematurely?

Then for equilibriation i typed gmx genrestr -f jz4.gro -o posre_jz4.itp -fc 
1000 1000 1000

and in order to restrain both the protein and the ligand simultaneously, I 
specify define = -DPOSRES -DPOSRES_LIG in the .mdp file. 
then typed   gmx make_ndx -f em.gro -o index.ndx

to merge the protein and DRG. and selected protein and DRG by :
> 1 | 14
> qthen set tc_grps = Protein_DRG Water_and_ions in NVT.mdp file to achieve my 
> desired "Protein Non-Protein" effect. that was my NVT.mdp file:

title = Protein-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG 
; position restrain the protein and ligand
integrator = md ; leap-frog integratornsteps = 5 ; 2 * 5 = 100 psdt 

[gmx-users] equilibration and production run

[Neha Gupta]

Hi gromacs users,

I intend to do the following steps for protein ligand simulations (for
linear interaction energy)

(1) Energy minimization
(2) NVT equilibration (with restraints on protein  and ligand)
(3) NPT equilibration (with restraints on protein  and ligand)
(4) NPT production

During NVT and NPT equilibration run can we use brendsen method in pcoupl
and Parrinello -Rahman in production run?

Will it yield correct results?

Or should we use the same kind of pcoupl through equilibration and
production?


Thanks,
Neha
-- 
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] Equilibration problem

[Justin Lemkul]

On 8/4/16 6:09 AM, amitbe...@chemeng.iisc.ernet.in wrote:

Hello everyone,
I prepared a bilayer using PACKMOL. Then ran energy minimisation. Till
this point the structure completely intact. Then I ran nvt on the
structure. At this point GROMACS-5.1.2 is giving back more than one pdb
files (named step**.pdb) instead of usual .gro file.


Your simulation crashed.


Does anyone know how to solve this issue.



http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-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] Equilibration problem

[amitbehra]

Hello everyone,
I prepared a bilayer using PACKMOL. Then ran energy minimisation. Till
this point the structure completely intact. Then I ran nvt on the
structure. At this point GROMACS-5.1.2 is giving back more than one pdb
files (named step**.pdb) instead of usual .gro file.
Does anyone know how to solve this issue.

Thanks
Amit Behera

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

-- 
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] Equilibration error

[Abid Channa]

Hi gromacs users,
I have found error in equalibration step  in my simulation. Kindly give your 
valuable suggestions.

Fatal error:
2 particles communicated to PME rank 5 are more than 2/3 times the cut-off out 
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
 Thanks,
Regards,

Abid Ali Channa,
Junior Research Fellow,
Lab No.  P-133, Computational Chemistry Unit,
 Dr .Panjwani Center for Molecular Medicine and Drug Research (PCMD),
 International Center for Chemical and Biological Sciences  (ICCBS),
 University of Karachi-75270.Karachi-Pakistan.UAN # (92-21) 111-222-292 Ext. 
(309)
 Cell # +923013553051.
http://www.iccs.edu/
-- 
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] Equilibration error

[Justin Lemkul]

On 2/8/16 5:22 AM, Abid Channa wrote:

Hi gromacs users,
I have found error in equalibration step  in my simulation. Kindly give your 
valuable suggestions.

Fatal error:
2 particles communicated to PME rank 5 are more than 2/3 times the cut-off out 
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.


http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Google is useful, too.  This is probably the most commonly asked question on 
this mailing list.


-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] Equilibration fails only when run from script

[Justin Lemkul]

On 12/1/15 6:39 AM, R Corey wrote:

Hello

I am running a series of FEP MD simulations using Gromacs 5.0.4, for each a
steepest descents minimization, NVT equil, NPT equil and production run,
all controlled by a central script. However, only about 50% of the runs get
through the NVT equilibration without crashing - crash error as below:

Fatal error:
3 particles communicated to PME rank 0 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.

However, the weird thing is that if I re-run the script the next day,
choosing only failed jobs to rerun, some of them now work fine. And if I
simply mdrun each tpr from the command line it runs fine too.

Is this expected, that a tpr file for an NVT equilibration will crash one
day but run fine the next?



This suggests transient instability that arises due to differences in order of 
operations, inherent chaos in MD, etc. If it's that difficult to get running, 
you probably have a larger issue that only shows up transiently. In any case, 
you can always try running with the latest version (5.1.1) in case of a bug.


-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] Equilibration fails only when run from script

[R Corey]

Hello

I am running a series of FEP MD simulations using Gromacs 5.0.4, for each a
steepest descents minimization, NVT equil, NPT equil and production run,
all controlled by a central script. However, only about 50% of the runs get
through the NVT equilibration without crashing - crash error as below:

Fatal error:
3 particles communicated to PME rank 0 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.

However, the weird thing is that if I re-run the script the next day,
choosing only failed jobs to rerun, some of them now work fine. And if I
simply mdrun each tpr from the command line it runs fine too.

Is this expected, that a tpr file for an NVT equilibration will crash one
day but run fine the next?

Cheers

Robin

-- 
*Robin Corey*
PhD Student
School of Biochemistry
University of Bristol
University Walk
Bristol BS8 1TD
UK
r.co...@bristol.ac.uk
-- 
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] Equilibration from Non-shifted to Shifted Potential

[Johnny Lu]

I guess I get the idea now. F = -dV(x)/dx. So no time derivative is
involved. So shifting the potential would not cause a suddenly impulse on
the system.

By the way, is Potential-shift the default vdw and coulomb-modifier (so
that is used even if i didn't specify a modifier) for gromacs 4.6.7?
I didn't see the default value when I searched for vdw-modifier (p.214) of
gromacs manual 4.6.7, or when I look at the online manual.

   coulomb-modifier = Potential-shift
   rcoulomb-switch  = 0
   rcoulomb = 1
   vdwtype  = Cut-off
   vdw-modifier = Potential-shift


On Fri, Nov 14, 2014 at 9:31 AM, Mark Abraham mark.j.abra...@gmail.com
wrote:

 Hi,

 Try it and see ;-)

 mdrun -nsteps 10 -reprod -deffnm shifted
 mdrun -nsteps 10 -reprod -deffnm not-shifted
 gmx check -f shifted -f2 not-shifted
 gmx check -e shifted -e2 not-shifted

 Alternatively, given that the forces are not computed from the energies
 (e.g. by central difference or some such), what role does the potential
 energy play in the integration scheme? :-)

 Mark


 On Fri, Nov 14, 2014 at 3:19 PM, Johnny Lu johnny.lu...@gmail.com wrote:

  Hi.
 
  If I change my potential from non-shifted to shift, will the sudden
 change
  of energy from non-shifted to shifted potential at step 0 completely mess
  up the equilibration?
 
  Thanks again.
  --
  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.

-- 
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.