[gmx-users] Error while running free energy simulation.

[vivek sharma]

Dear Users,
I am trying to replicate the free energy tutorial by Dr Justin. In my
attempt I have calculated the OPLS-AA FF parameters for my molecules of
interest using acpype. I made the system in water and 1-octanol, While
running the independent lambda simulation for both the systems, I got an
error while running the simulation for 1-octanol system whereas the
simulation for water system were successful.

Following is the error message reported in failed simulation for 1-octanol
system
--
WARNING: Listed nonbonded interaction between particles 842 and 851
at distance 427.422 which is larger than the table limit 2.200 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

-

I tried running the same system without free energy option ( free_energy
   = no), which was successful. It has narrowed the reason for
error to be the free energy code.
It will be really helpful if anybody can help me in understanding the
probable reason for error and any directions for handling this error.

Pasting below the mdp options for one of the independent lambda simulation
for reference.
---
; Run control
integrator   = sd   ; Langevin dynamics
tinit= 0
dt   = 0.002
nsteps   = 250   ; 5 ns
nstcomm  = 100
; Output control
nstxout  = 500
nstvout  = 500
nstfout  = 0
nstlog   = 500
nstenergy= 500
nstxout-compressed   = 0
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme= verlet
nstlist  = 20
ns_type  = grid
pbc  = xyz
rlist= 1.2
; Electrostatics
coulombtype  = PME
rcoulomb = 1.2
; van der Waals
vdwtype  = cutoff
vdw-modifier = potential-switch
rvdw-switch  = 1.0
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing   = 0.12
; EWALD/PME/PPPM parameters
pme_order= 6
ewald_rtol   = 1e-06
epsilon_surface  = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tc_grps  = system
tau_t= 1.0
ref_t= 300
; Pressure coupling is on for NPT
Pcoupl   = Parrinello-Rahman
tau_p= 1.0
compressibility  = 4.5e-05
ref_p= 1.0
; Free energy control stuff
free_energy  = yes
init_lambda_state= 0
delta_lambda = 0
calc_lambda_neighbors= 1; only immediate neighboring windows
; Vectors of lambda specified here
; Each combination is an index that is retrieved from init_lambda_state for
each simulation
; init_lambda_state0123456789
 10   11   12   13   14   15   16   17   18   19   20
vdw_lambdas  = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80
0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00
coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00
; We are not transforming any bonded or restrained interactions
bonded_lambdas   = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
restraint_lambdas= 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Masses are not changing (particle identities are the same at lambda = 0
and lambda = 1)
mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Not doing simulated temperting here
temperature_lambdas  = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
; Options for the decoupling
sc-alpha = 0.5
sc-coul  = no   ; linear interpolation of Coulomb (none
in this case)
sc-power = 1.0
sc-sigma = 0.3
couple-molt

[gmx-users] How much different run (with posre.itp) from no posre.itp?

[Batdorj Batsaikhan]

Dear gmx-users,

I run 3 different conformation of a protein. I run 2 of them no posre.itp and 
another one has posre.itp. How much different these two run? 


Sincerely,

Batsaikhan
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Re: [gmx-users] Problem - How to center a protein in a CG simulation

[Carlos Navarro Retamal]

Dear Justin,
It worked! :D
Thanks a lot.
I first preprocess  the whole trajectory,  
> trjconv -f dynamic-NO-Elastic.xtc -s equilibration.tpr -pbc mol  

And after that i center the protein  

> trjconv -f trajout.xtc -s equilibration.tpr -pbc mol -center -skip 50 -o 
> test.xtc
In order to extract the last frame i used the following command:

> trjconv -f test.xtc -sep -o LastFrame.gro

The only ‘issue’ was that the frames i saved with -sep content the description 
of each atom as follows:

>  
> 1LYS BB1   5.4   6.9   8.4
> 1LYSSC12   5.3   7.2   8.5
> 1LYSSC23   5.0   7.3   8.6
> 2ARG BB4   5.1   6.8   8.5
> 2ARGSC15   5.1   6.6   8.7
> 2ARGSC26   5.0   6.5   9.0
>  



so i got an error with initram. To avoid this i performed a minimisation of 
this lastFrame.gro file in order to obtain the correct description of each 
atom. After that, FINALLY, the backward process worked :D

Thanks to all of you :D

ps- During the CG simulation using Elastic-Network i saw big movements of the 
K2P protein, and when i compared it with respect to the inicial AA model i saw 
how a part of the CAP of the K2P channel is completely rotate to another side 
of the protein.
 I used 500 kj/mol^-1/nm^-2 as the tutorial suggest.  
Should i increase the elastic force constant to 1000 (or even more), or instead 
try ElNeDyn?  
I didn’t want to use this approximation, since the tutorial emphasise that 
using it will be huge change on the martini ff.
Best regards to all of you,
Carlos
--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


On Monday, November 10, 2014 at 8:45 PM, Justin Lemkul wrote:

>  
>  
> On 11/10/14 10:01 AM, Carlos Navarro Retamal wrote:
> > nobody?
> > if there is not a way to do this at this moment (after the simulation) is 
> > there a way to apply a restraint to maintain fix the protein in the middle 
> > of the POPC bilayer (other than elastic network) during the MD simulation 
> > in order to avoid this problem?
> >  
>  
>  
> I don't know why the -center option isn't working. That's precisely what it  
> does. Other things to try:
>  
> 1. Often I find that PBC routines do not work well when dealing with a single 
>  
> coordinate file. Processing the trajectory, then extracting the frame(s) of  
> interest works all the time.
>  
> 2. Try the -fit transxy option of trjconv. It's designed for interfacial and  
> membrane systems.
>  
> -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 (mailto:jalem...@outerbanks.umaryland.edu) 
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>  
> ==
> --  
> Gromacs Users mailing list
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> * Please search the archive at 
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>  
>  


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Re: [gmx-users] Question about "Lysozyme in Water" tutorial by Dr. Lemkul

[Justin Lemkul]

On 11/10/14 7:33 PM, Nima Soltani wrote:

Hi everyone
I am following excellent Gromacs tutorial that is provided by Dr. Justin
Lemkul, First of all i want to thank him for taking time to provide such an
excellent tutorial.
My Question is about final structure of protein and ions after runing final
Molecular Dynamic simulation of the last step
Here is link of my final structure that i get after simulation -after
converting it from .gro file to .pdb file (by Avogadro program):
https://www.dropbox.com/s/smabls57wj4pvtm/md_0_1.pdb?dl=0
i find out that all CL ions are in a strange position far away from protein
at edge of the box, well i suppose that negative Chlorine ions should be
away from each other (same charge) and close to protein which has positive
charge. which is not!
is my simulation is incorrect?
if not what cause this seemingly strange thing to happen?


You also have a line of waters doing the exact same thing.  The conversion of 
.gro to .pdb has totally botched the coordinates.  If you want .pdb format, just 
use editconf, rather than some external program which is clearly misformatting 
or misinterpreting the contents of the file.


-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

==
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[gmx-users] Question about "Lysozyme in Water" tutorial by Dr. Lemkul

[Nima Soltani]

Hi everyone
I am following excellent Gromacs tutorial that is provided by Dr. Justin
Lemkul, First of all i want to thank him for taking time to provide such an
excellent tutorial.
My Question is about final structure of protein and ions after runing final
Molecular Dynamic simulation of the last step
Here is link of my final structure that i get after simulation -after
converting it from .gro file to .pdb file (by Avogadro program):
https://www.dropbox.com/s/smabls57wj4pvtm/md_0_1.pdb?dl=0
i find out that all CL ions are in a strange position far away from protein
at edge of the box, well i suppose that negative Chlorine ions should be
away from each other (same charge) and close to protein which has positive
charge. which is not!
is my simulation is incorrect?
if not what cause this seemingly strange thing to happen?
Thanks in advance for any guidance


Best Regards,
Nima Soltani
---
Student of Physical Chemistry
Department of Chemistry,
Sharif University of Technology.
=
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Re: [gmx-users] Problem - How to center a protein in a CG simulation

[Justin Lemkul]

On 11/10/14 10:01 AM, Carlos Navarro Retamal wrote:

nobody?
if there is not a way to do this at this moment (after the simulation) is there 
a way to apply a restraint to maintain fix the protein in the middle of the 
POPC bilayer (other than elastic network) during the MD simulation in order to 
avoid this problem?


I don't know why the -center option isn't working.  That's precisely what it 
does.  Other things to try:


1. Often I find that PBC routines do not work well when dealing with a single 
coordinate file.  Processing the trajectory, then extracting the frame(s) of 
interest works all the time.


2. Try the -fit transxy option of trjconv.  It's designed for interfacial and 
membrane systems.


-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

==
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Re: [gmx-users] How to exclude atoms within the same molecule from an rdf.

[Stella Nickerson]

Thanks.

On Thu, Nov 6, 2014 at 2:34 PM, João M. Damas  wrote:

> It's fairly "simple": generate a .tpr file with a nrexcl big enough to
> exclude "self-counts" and give it to g_rdf through the -s flag.
>
> João
>
> On Thu, Nov 6, 2014 at 8:42 PM, Stella Nickerson <
> stella.nicker...@gmail.com
> > wrote:
>
> > I'm simulating a mixture of molecules (call them Molecules A, B, and C).
> > The rdf between A and B and between A and C both look fine, but the one
> > between A and A is crazy-looking. I assume this is because it's comparing
> > atoms within the same molecule. I can't figure out how to exclude atoms
> in
> > the same molecule from the rdf.
> >
> > Thanks,
> >
> > Stella
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
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Re: [gmx-users] Problem - How to center a protein in a CG simulation

[Carlos Navarro Retamal]

Dear Tsjerk,
I don’t understand what you mean.
Take a look at the next image.
http://cl.ly/262g2q2C2o3H

You say this is ok? Even when i open the file with vmd i got tons of warning 
message:

> Warning) Unusual bond between residues:  44 (protein) and 45 (none)
> Warning) Unusual bond between residues:  45 (none) and 46 (protein)
> Warning) Unusual bond between residues:  47 (protein) and 48 (none)
> Warning) Unusual bond between residues:  49 (none) and 50 (protein)
> Warning) Unusual bond between residues:  60 (none) and 61 (protein)
> Warning) Unusual bond between residues:  62 (protein) and 63 (none)
> Warning) Unusual bond between residues:  63 (none) and 64 (protein)
> Warning) Unusual bond between residues:  66 (protein) and 67 (none)
> Warning) Unusual bond between residues:  70 (protein) and 71 (none)
> Warning) Unusual bond between residues:  71 (none) and 72 (protein)
> Warning) Unusual bond between residues:  91 (none) and 92 (protein)
> Warning) Unusual bond between residues:  99 (protein) and 100 (none)
> Warning) Unusual bond between residues:  101 (none) and 102 (protein)
> Warning) Unusual bond between residues:  102 (protein) and 103 (none)
> Warning) Unusual bond between residues:  103 (none) and 104 (protein)
> Warning) Unusual bond between residues:  110 (protein) and 111 (none)
> Warning) Unusual bond between residues:  111 (none) and 112 (protein)
> Warning) Unusual bond between residues:  113 (protein) and 114 (none)
> Warning) Unusual bond between residues:  120 (none) and 121 (protein)
> Warning) Unusual bond between residues:  122 (protein) and 123 (none)
> Warning) Unusual bond between residues:  123 (none) and 124 (protein)
> Warning) Unusual bond between residues:  124 (protein) and 125 (none)
> Warning) Unusual bond between residues:  125 (none) and 126 (protein)
> Warning) Unusual bond between residues:  126 (protein) and 127 (none)
> Warning) Unusual bond between residues:  128 (none) and 129 (protein)
> Warning) Unusual bond between residues:  130 (protein) and 131 (none)
> Warning) Unusual bond between residues:  131 (none) and 132 (protein)
> Warning) Unusual bond between residues:  134 (protein) and 135 (none)
> Warning) Unusual bond between residues:  135 (none) and 136 (protein)
> Warning) Unusual bond between residues:  211 (protein) and 212 (none)
> Warning) Unusual bond between residues:  212 (none) and 213 (protein)
> Warning) Unusual bond between residues:  226 (protein) and 227 (none)
> Warning) Unusual bond between residues:  227 (none) and 228 (protein)
> Warning) Unusual bond between residues:  247 (protein) and 248 (none)
> Warning) Unusual bond between residues:  248 (none) and 249 (protein)
> Warning) Unusual bond between residues:  16 (protein) and 17 (none)
> Warning) Unusual bond between residues:  17 (none) and 18 (protein)
> Warning) Unusual bond between residues:  18 (protein) and 19 (none)
> Warning) Unusual bond between residues:  20 (none) and 21 (protein)
> Warning) Unusual bond between residues:  77 (protein) and 78 (none)
> Warning) Unusual bond between residues:  78 (none) and 79 (protein)
> Warning) Unusual bond between residues:  81 (protein) and 82 (none)
> Warning) Unusual bond between residues:  82 (none) and 83 (protein)
> Warning) Unusual bond between residues:  84 (protein) and 85 (none)
> Warning) Unusual bond between residues:  85 (none) and 86 (protein)
> Warning) Unusual bond between residues:  123 (protein) and 124 (none)
> Warning) Unusual bond between residues:  126 (none) and 127 (protein)
> Warning) Unusual bond between residues:  140 (protein) and 141 (none)
> Warning) Unusual bond between residues:  141 (none) and 142 (protein)
> Warning) Unusual bond between residues:  143 (protein) and 144 (none)
> Warning) Unusual bond between residues:  144 (none) and 145 (protein)
> Warning) Unusual bond between residues:  155 (protein) and 156 (none)
> Warning) Unusual bond between residues:  156 (none) and 157 (protein)
> Warning) Unusual bond between residues:  207 (none) and 208 (protein)
> Warning) Unusual bond between residues:  242 (protein) and 243 (none)
> Warning) Unusual bond between residues:  243 (none) and 244 (protein)
> Warning) Unusual bond between residues:  245 (protein) and 246 (none)
> Warning) Unusual bond between residues:  246 (none) and 247 (protein)

 sorry for asking to much stuffs, but this is my first time trying to convert a 
system form a CG-representation to an AA one.
Thanks for all of your help.
Best Regards,
Carlos

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


On Monday, November 10, 2014 at 2:11 PM, Tsjerk Wassenaar wrote:

> Hey :)
>  
> The protein is a dimer. Are you sure there is a real problem?
>  
> Cheers,
>  

Re: [gmx-users] Problem - How to center a protein in a CG simulation

[Tsjerk Wassenaar]

Hey :)

The protein is a dimer. Are you sure there is a real problem?

Cheers,

Tsjerk

On Mon, Nov 10, 2014 at 6:07 PM, Carlos Navarro Retamal 
wrote:

> Dear Tsjerk,
> I forgot to mention it, but indeed i used -pbc mol, as follows:
>
>
> > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol -o
> LastFrame.gro
> >
> >
> >
>
> And using this file (LastFrame.gro) i run initram, getting my protein
> split on different side of the box.
> What could it be?
> Best Regards,
> Carlos
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
> On Monday, November 10, 2014 at 1:35 PM, Tsjerk Wassenaar wrote:
>
> > Hi Carlos,
> >
> > You used -pbc nojump on the last frame with the .tpr as reference, which
> > means it removes the jumps with respect to the tpr, and that will give
> > rubbish. You should use -pbc mol and try again.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Mon, Nov 10, 2014 at 5:25 PM, Carlos Navarro Retamal <
> cnava...@utalca.cl (mailto:cnava...@utalca.cl)>
> > wrote:
> >
> > > Dear Erick,
> > > First of all thanks a lot for your reply.
> > > Your are correct. I know that there’s not a ‘middle’ part in the system
> > > (based on the PBC), i was just trying to say that i need a structure
> where
> > > the protein will be surrounded by the POPC membrane in order to have
> > > ‘valid’ structure to start the AA MD simulations.
> > >
> > > I run the following commands:
> > >
> > > > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc
> nojump
> > > -o LastFrame.gro
> > > >
> > >
> > >
> > >
> > > followed by:
> > >
> > > > trjconv -f LastFrame.gro -s dynamic-NO-Elastic.tpr -fit rot+trans -o
> > > conf.gro
> > > >
> > >
> > >
> > > without luck ( the proteins is not fix either with these commands).
> > > what should i do?
> > >
> > >
> > > Dear Tsjerk,
> > > Thanks for your kind reply.
> > > I did what you suggested, without luck:
> > > > ./initram.sh (http://initram.sh) -f LastFrame.gro -o
> aa_gromos54a7.gro -to gromos54a7 -p
> > >
> > > topol.top
> > > (in the input file the protein is intact)
> > > CG-model:
> > > http://cl.ly/3V3E1O2R0L31
> > > AA-model
> > > http://cl.ly/0U2r2n0F290i
> > >
> > >
> > > Thanks to both of you for all your help,
> > > Best Regards,
> > > Carlos
> > >
> > > --
> > > Carlos Navarro Retamal
> > > Bioinformatic engineer
> > > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > > Center of Bioinformatics and Molecular Simulations (CBSM)
> > > Universidad de Talca
> > > 2 Norte 685, Casilla 721, Talca - Chile
> > > Teléfono: 56-71-201 798,
> > > Fax: 56-71-201 561
> > > Email: carlos.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com)
> or cnava...@utalca.cl (mailto:cnava...@utalca.cl)
> > >
> > >
> > > On Monday, November 10, 2014 at 12:16 PM, Erik Marklund wrote:
> > >
> > > > Dear Carlos,
> > > >
> > > > I guess it's just not obvious to most of us why this is a problem at
> > > all. If the protein diffuses (as proteins do) you can just
> translate/rotate
> > > it back to where it was. Strictly speaking , there is no 'middle' in a
> > > periodic system. Or are we missing something?
> > > >
> > > > In any case, adding restraints can affect the dynamics and you can
> often
> > > use trjconv -nojump followed by trjconv -fit to get your protein sit
> > > steadily in the middle of your box, assuming the protein was where you
> > > wanted it to be in the first place.
> > > >
> > > > Kind regards,
> > > > Erik
> > > >
> > > >
> > > > Erik Marklund, PhD
> > > > Postdoctoral Research Fellow, Fulford JRF
> > > >
> > > > Department of Chemistry
> > > > Physical & Theoretical Chemistry Laboratory
> > > > University of Oxford
> > > > South Parks Road
> > > > Oxford
> > > > OX1 3QZ
> > > >
> > > > On 10 Nov 2014, at 15:01, Carlos Navarro Retamal  (mailto:cnava...@utalca.cl)
> > > > wrote:
> > > >
> > > > nobody?
> > > > if there is not a way to do this at this moment (after the
> simulation)
> > > >
> > >
> > > is there a way to apply a restraint to maintain fix the protein in the
> > > middle of the POPC bilayer (other than elastic network) during the MD
> > > simulation in order to avoid this problem?
> > > > Best regards,
> > > > Carlos
> > > >
> > > > --
> > > > Carlos Navarro Retamal
> > > > Bioinformatic engineer
> > > > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > > > Center of Bioinformatics and Molecular Simulations (CBSM)
> > > > Universidad de Talca
> > > > 2 Norte 685, Casilla 721, Talca - Chile
> > > > Teléfono: 56-71-201 798,
> > > > Fax: 56-71-201 561
> > > > Email: carlos.navarr...@gmail.com
> or
> > > >
> > >
> > > cnava...@utalca.cl
> > > >
>

Re: [gmx-users] Problem - How to center a protein in a CG simulation

[Carlos Navarro Retamal]

Dear Tsjerk,
I forgot to mention it, but indeed i used -pbc mol, as follows:


> trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol -o 
> LastFrame.gro
>  
>  
>  

And using this file (LastFrame.gro) i run initram, getting my protein split on 
different side of the box.
What could it be?
Best Regards,
Carlos
--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarr...@gmail.com or cnava...@utalca.cl


On Monday, November 10, 2014 at 1:35 PM, Tsjerk Wassenaar wrote:

> Hi Carlos,
>  
> You used -pbc nojump on the last frame with the .tpr as reference, which
> means it removes the jumps with respect to the tpr, and that will give
> rubbish. You should use -pbc mol and try again.
>  
> Cheers,
>  
> Tsjerk
>  
> On Mon, Nov 10, 2014 at 5:25 PM, Carlos Navarro Retamal  (mailto:cnava...@utalca.cl)>
> wrote:
>  
> > Dear Erick,
> > First of all thanks a lot for your reply.
> > Your are correct. I know that there’s not a ‘middle’ part in the system
> > (based on the PBC), i was just trying to say that i need a structure where
> > the protein will be surrounded by the POPC membrane in order to have
> > ‘valid’ structure to start the AA MD simulations.
> >  
> > I run the following commands:
> >  
> > > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc nojump
> > -o LastFrame.gro
> > >  
> >  
> >  
> >  
> > followed by:
> >  
> > > trjconv -f LastFrame.gro -s dynamic-NO-Elastic.tpr -fit rot+trans -o
> > conf.gro
> > >  
> >  
> >  
> > without luck ( the proteins is not fix either with these commands).
> > what should i do?
> >  
> >  
> > Dear Tsjerk,
> > Thanks for your kind reply.
> > I did what you suggested, without luck:
> > > ./initram.sh (http://initram.sh) -f LastFrame.gro -o aa_gromos54a7.gro 
> > > -to gromos54a7 -p
> >  
> > topol.top
> > (in the input file the protein is intact)
> > CG-model:
> > http://cl.ly/3V3E1O2R0L31
> > AA-model
> > http://cl.ly/0U2r2n0F290i
> >  
> >  
> > Thanks to both of you for all your help,
> > Best Regards,
> > Carlos
> >  
> > --
> > Carlos Navarro Retamal
> > Bioinformatic engineer
> > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > Center of Bioinformatics and Molecular Simulations (CBSM)
> > Universidad de Talca
> > 2 Norte 685, Casilla 721, Talca - Chile
> > Teléfono: 56-71-201 798,
> > Fax: 56-71-201 561
> > Email: carlos.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com) or 
> > cnava...@utalca.cl (mailto:cnava...@utalca.cl)
> >  
> >  
> > On Monday, November 10, 2014 at 12:16 PM, Erik Marklund wrote:
> >  
> > > Dear Carlos,
> > >  
> > > I guess it's just not obvious to most of us why this is a problem at
> > all. If the protein diffuses (as proteins do) you can just translate/rotate
> > it back to where it was. Strictly speaking , there is no 'middle' in a
> > periodic system. Or are we missing something?
> > >  
> > > In any case, adding restraints can affect the dynamics and you can often
> > use trjconv -nojump followed by trjconv -fit to get your protein sit
> > steadily in the middle of your box, assuming the protein was where you
> > wanted it to be in the first place.
> > >  
> > > Kind regards,
> > > Erik
> > >  
> > >  
> > > Erik Marklund, PhD
> > > Postdoctoral Research Fellow, Fulford JRF
> > >  
> > > Department of Chemistry
> > > Physical & Theoretical Chemistry Laboratory
> > > University of Oxford
> > > South Parks Road
> > > Oxford
> > > OX1 3QZ
> > >  
> > > On 10 Nov 2014, at 15:01, Carlos Navarro Retamal  > > (mailto:cnava...@utalca.cl)
> > > wrote:
> > >  
> > > nobody?
> > > if there is not a way to do this at this moment (after the simulation)
> > >  
> >  
> > is there a way to apply a restraint to maintain fix the protein in the
> > middle of the POPC bilayer (other than elastic network) during the MD
> > simulation in order to avoid this problem?
> > > Best regards,
> > > Carlos
> > >  
> > > --
> > > Carlos Navarro Retamal
> > > Bioinformatic engineer
> > > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > > Center of Bioinformatics and Molecular Simulations (CBSM)
> > > Universidad de Talca
> > > 2 Norte 685, Casilla 721, Talca - Chile
> > > Teléfono: 56-71-201 798,
> > > Fax: 56-71-201 561
> > > Email: carlos.navarr...@gmail.com or
> > >  
> >  
> > cnava...@utalca.cl
> > >  
> > >  
> > > On Monday, November 10, 2014 at 2:11 AM, Carlos Navarro Retamal wrote:
> > >  
> > > Dear gromacs users,
> > > I’m trying to replicate the following paper:
> > >  
> >  
> > http://www.nature.com/ncomms/2014/140708/ncomms5377/full/ncomms5377.html
> > >  
> > > On that way i:
> > > - Create a CG (two different ones, with and without elastic-network
> > >  
> >  
> >

Re: [gmx-users] Problem - How to center a protein in a CG simulation

[Tsjerk Wassenaar]

Hi Carlos,

You used -pbc nojump on the last frame with the .tpr as reference, which
means it removes the jumps with respect to the tpr, and that will give
rubbish. You should use -pbc mol and try again.

Cheers,

Tsjerk

On Mon, Nov 10, 2014 at 5:25 PM, Carlos Navarro Retamal 
wrote:

> Dear Erick,
> First of all thanks a lot for your reply.
> Your are correct. I know that there’s not a ‘middle’ part in the system
> (based on the PBC), i was just trying to say that i need a structure where
> the protein will be surrounded by the POPC membrane in order to have
> ‘valid’ structure to start the AA MD simulations.
>
> I run the following commands:
>
> > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc nojump
> -o LastFrame.gro
> >
>
>
> followed by:
>
> > trjconv -f LastFrame.gro -s dynamic-NO-Elastic.tpr -fit rot+trans -o
> conf.gro
> >
>
> without luck ( the proteins is not fix either with these commands).
> what should i do?
>
>
> Dear Tsjerk,
> Thanks for your kind reply.
> I did what you suggested, without luck:
> > ./initram.sh -f LastFrame.gro -o aa_gromos54a7.gro -to gromos54a7 -p
> topol.top
> (in the input file the protein is intact)
> CG-model:
> http://cl.ly/3V3E1O2R0L31
> AA-model
> http://cl.ly/0U2r2n0F290i
>
>
> Thanks to both of you for all your help,
> Best Regards,
> Carlos
>
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
> On Monday, November 10, 2014 at 12:16 PM, Erik Marklund wrote:
>
> > Dear Carlos,
> >
> > I guess it's just not obvious to most of us why this is a problem at
> all. If the protein diffuses (as proteins do) you can just translate/rotate
> it back to where it was. Strictly speaking , there is no 'middle' in a
> periodic system. Or are we missing something?
> >
> > In any case, adding restraints can affect the dynamics and you can often
> use trjconv -nojump followed by trjconv -fit to get your protein sit
> steadily in the middle of your box, assuming the protein was where you
> wanted it to be in the first place.
> >
> > Kind regards,
> > Erik
> >
> >
> > Erik Marklund, PhD
> > Postdoctoral Research Fellow, Fulford JRF
> >
> > Department of Chemistry
> > Physical & Theoretical Chemistry Laboratory
> > University of Oxford
> > South Parks Road
> > Oxford
> > OX1 3QZ
> >
> > On 10 Nov 2014, at 15:01, Carlos Navarro Retamal  > wrote:
> >
> > nobody?
> > if there is not a way to do this at this moment (after the simulation)
> is there a way to apply a restraint to maintain fix the protein in the
> middle of the POPC bilayer (other than elastic network) during the MD
> simulation in order to avoid this problem?
> > Best regards,
> > Carlos
> >
> > --
> > Carlos Navarro Retamal
> > Bioinformatic engineer
> > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > Center of Bioinformatics and Molecular Simulations (CBSM)
> > Universidad de Talca
> > 2 Norte 685, Casilla 721, Talca - Chile
> > Teléfono: 56-71-201 798,
> > Fax: 56-71-201 561
> > Email: carlos.navarr...@gmail.com or
> cnava...@utalca.cl
> >
> >
> > On Monday, November 10, 2014 at 2:11 AM, Carlos Navarro Retamal wrote:
> >
> > Dear gromacs users,
> > I’m trying to replicate the following paper:
> http://www.nature.com/ncomms/2014/140708/ncomms5377/full/ncomms5377.html
> >
> > On that way i:
> > - Create a CG (two different ones, with and without elastic-network
> restraints) representation of my K2P protein by using martinize.py
> > - I embedded it in a POPC bilayer membrane using insane.py
> > After some energy minimization and equilibration i run a 500ns MD of
> production.
> > The problem was that during both simulation the protein starts to move
> across the box to a different box.
> > By using tryconv as follows:
> > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol -o
> LastFrame.gro
> >
> >
> > i was able to ‘fix’ the protein (fix the pbc issue of the protein), but
> its remains out of the box.
> > I even used -center keyword without luck.
> > And since i need a structure where the protein remains in the middle of
> the POPC membrane in order to perform the ‘backward’ step to obtain an AA
> representation of my system and perform a new MD simulation i’m kind of
> stuck.
> > I don’t know what to do :/
> > Hope someone can help me.
> > Have a nice week,
> > Carlos
> >
> >
> > --
> > Carlos Navarro Retamal
> > Bioinformatic engineer
> > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > Center of Bioinformatics and Molecular Simulations (CBSM)
> > Universidad de Talca
> > 2 Norte 685, Casilla 721, Talca - Chile
> > Teléfono: 56-71-201 798,
> > Fax: 56-71-201 561
> > Email: carlos.na

Re: [gmx-users] Problem - How to center a protein in a CG simulation

[Carlos Navarro Retamal]

Dear Erick,
First of all thanks a lot for your reply.
Your are correct. I know that there’s not a ‘middle’ part in the system (based 
on the PBC), i was just trying to say that i need a structure where the protein 
will be surrounded by the POPC membrane in order to have ‘valid’ structure to 
start the AA MD simulations.

I run the following commands:

> trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc nojump -o 
> LastFrame.gro
>  


followed by:

> trjconv -f LastFrame.gro -s dynamic-NO-Elastic.tpr -fit rot+trans -o conf.gro
>  

without luck ( the proteins is not fix either with these commands).
what should i do?


Dear Tsjerk,
Thanks for your kind reply.
I did what you suggested, without luck:
> ./initram.sh -f LastFrame.gro -o aa_gromos54a7.gro -to gromos54a7 -p topol.top
(in the input file the protein is intact)
CG-model:
http://cl.ly/3V3E1O2R0L31
AA-model
http://cl.ly/0U2r2n0F290i

  
Thanks to both of you for all your help,
Best Regards,
Carlos

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


On Monday, November 10, 2014 at 12:16 PM, Erik Marklund wrote:

> Dear Carlos,
>  
> I guess it's just not obvious to most of us why this is a problem at all. If 
> the protein diffuses (as proteins do) you can just translate/rotate it back 
> to where it was. Strictly speaking , there is no 'middle' in a periodic 
> system. Or are we missing something?
>  
> In any case, adding restraints can affect the dynamics and you can often use 
> trjconv -nojump followed by trjconv -fit to get your protein sit steadily in 
> the middle of your box, assuming the protein was where you wanted it to be in 
> the first place.
>  
> Kind regards,
> Erik
>  
>  
> Erik Marklund, PhD
> Postdoctoral Research Fellow, Fulford JRF
>  
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
>  
> On 10 Nov 2014, at 15:01, Carlos Navarro Retamal 
> mailto:cnava...@utalca.cl>> wrote:
>  
> nobody?
> if there is not a way to do this at this moment (after the simulation) is 
> there a way to apply a restraint to maintain fix the protein in the middle of 
> the POPC bilayer (other than elastic network) during the MD simulation in 
> order to avoid this problem?
> Best regards,
> Carlos
>  
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarr...@gmail.com or 
> cnava...@utalca.cl
>  
>  
> On Monday, November 10, 2014 at 2:11 AM, Carlos Navarro Retamal wrote:
>  
> Dear gromacs users,
> I’m trying to replicate the following paper: 
> http://www.nature.com/ncomms/2014/140708/ncomms5377/full/ncomms5377.html
>  
> On that way i:
> - Create a CG (two different ones, with and without elastic-network 
> restraints) representation of my K2P protein by using martinize.py
> - I embedded it in a POPC bilayer membrane using insane.py
> After some energy minimization and equilibration i run a 500ns MD of 
> production.
> The problem was that during both simulation the protein starts to move across 
> the box to a different box.
> By using tryconv as follows:
> trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol -o 
> LastFrame.gro
>  
>  
> i was able to ‘fix’ the protein (fix the pbc issue of the protein), but its 
> remains out of the box.
> I even used -center keyword without luck.
> And since i need a structure where the protein remains in the middle of the 
> POPC membrane in order to perform the ‘backward’ step to obtain an AA 
> representation of my system and perform a new MD simulation i’m kind of stuck.
> I don’t know what to do :/
> Hope someone can help me.
> Have a nice week,
> Carlos
>  
>  
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarr...@gmail.com 
> (mailto:carlos.navarr...@gmail.com) or 
> cnava...@utalca.cl (mailto:cnava...@utalca.cl)
>  
> --
> Gromacs Users mailing list
>  
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>  
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  
> * For (un)subscribe requests visit
> https://maillist

Re: [gmx-users] Problem - How to center a protein in a CG simulation

[Tsjerk Wassenaar]

Hi Carlos,

Who says it needs to be in the center for backward? It needs to be in one
piece, but doesn't need to be in te center. Backward understands PBC. It's
not stupid ;)

Cheers,

Tsjerk


On Mon, Nov 10, 2014 at 4:01 PM, Carlos Navarro Retamal 
wrote:

> nobody?
> if there is not a way to do this at this moment (after the simulation) is
> there a way to apply a restraint to maintain fix the protein in the middle
> of the POPC bilayer (other than elastic network) during the MD simulation
> in order to avoid this problem?
> Best regards,
> Carlos
>
> --
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile
> Teléfono: 56-71-201 798,
> Fax: 56-71-201 561
> Email: carlos.navarr...@gmail.com or cnava...@utalca.cl
>
>
> On Monday, November 10, 2014 at 2:11 AM, Carlos Navarro Retamal wrote:
>
> > Dear gromacs users,
> > I’m trying to replicate the following paper:
> http://www.nature.com/ncomms/2014/140708/ncomms5377/full/ncomms5377.html
> >
> > On that way i:
> > - Create a CG (two different ones, with and without elastic-network
> restraints) representation of my K2P protein by using martinize.py
> > - I embedded it in a POPC bilayer membrane using insane.py
> > After some energy minimization and equilibration i run a 500ns MD of
> production.
> > The problem was that during both simulation the protein starts to move
> across the box to a different box.
> > By using tryconv as follows:
> > > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol
> -o LastFrame.gro
> >
> >
> > i was able to ‘fix’ the protein (fix the pbc issue of the protein), but
> its remains out of the box.
> > I even used -center keyword without luck.
> > And since i need a structure where the protein remains in the middle of
> the POPC membrane in order to perform the ‘backward’ step to obtain an AA
> representation of my system and perform a new MD simulation i’m kind of
> stuck.
> > I don’t know what to do :/
> > Hope someone can help me.
> > Have a nice week,
> > Carlos
> >
> >
> > --
> > Carlos Navarro Retamal
> > Bioinformatic engineer
> > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > Center of Bioinformatics and Molecular Simulations (CBSM)
> > Universidad de Talca
> > 2 Norte 685, Casilla 721, Talca - Chile
> > Teléfono: 56-71-201 798,
> > Fax: 56-71-201 561
> > Email: carlos.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com)
> or cnava...@utalca.cl (mailto:cnava...@utalca.cl)
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org (mailto:
> gmx-users-requ...@gromacs.org).
> >
> >
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
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
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Problem - How to center a protein in a CG simulation

[Erik Marklund]

Dear Carlos,

I guess it's just not obvious to most of us why this is a problem at all. If 
the protein diffuses (as proteins do) you can just translate/rotate it back to 
where it was. Strictly speaking , there is no 'middle' in a periodic system. Or 
are we missing something?

In any case, adding restraints can affect the dynamics and you can often use 
trjconv -nojump followed by trjconv -fit to get your protein sit steadily in 
the middle of your box, assuming the protein was where you wanted it to be in 
the first place.

Kind regards,
Erik


Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 10 Nov 2014, at 15:01, Carlos Navarro Retamal 
mailto:cnava...@utalca.cl>> wrote:

nobody?
if there is not a way to do this at this moment (after the simulation) is there 
a way to apply a restraint to maintain fix the protein in the middle of the 
POPC bilayer (other than elastic network) during the MD simulation in order to 
avoid this problem?
Best regards,
Carlos

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


On Monday, November 10, 2014 at 2:11 AM, Carlos Navarro Retamal wrote:

Dear gromacs users,
I’m trying to replicate the following paper: 
http://www.nature.com/ncomms/2014/140708/ncomms5377/full/ncomms5377.html

On that way i:
- Create a CG (two different ones, with and without elastic-network restraints) 
representation of my K2P protein by using martinize.py
- I embedded it in a POPC bilayer membrane using insane.py
After some energy minimization and equilibration i run a 500ns MD of production.
The problem was that during both simulation the protein starts to move across 
the box to a different box.
By using tryconv as follows:
trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol -o 
LastFrame.gro


i was able to ‘fix’ the protein (fix the pbc issue of the protein), but its 
remains out of the box.
I even used -center keyword without luck.
And since i need a structure where the protein remains in the middle of the 
POPC membrane in order to perform the ‘backward’ step to obtain an AA 
representation of my system and perform a new MD simulation i’m kind of stuck.
I don’t know what to do :/
Hope someone can help me.
Have a nice week,
Carlos


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

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Re: [gmx-users] Problem - How to center a protein in a CG simulation

[Carlos Navarro Retamal]

nobody?  
if there is not a way to do this at this moment (after the simulation) is there 
a way to apply a restraint to maintain fix the protein in the middle of the 
POPC bilayer (other than elastic network) during the MD simulation in order to 
avoid this problem?
Best regards,
Carlos

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


On Monday, November 10, 2014 at 2:11 AM, Carlos Navarro Retamal wrote:

> Dear gromacs users,  
> I’m trying to replicate the following paper: 
> http://www.nature.com/ncomms/2014/140708/ncomms5377/full/ncomms5377.html
>  
> On that way i:
> - Create a CG (two different ones, with and without elastic-network 
> restraints) representation of my K2P protein by using martinize.py
> - I embedded it in a POPC bilayer membrane using insane.py
> After some energy minimization and equilibration i run a 500ns MD of 
> production.
> The problem was that during both simulation the protein starts to move across 
> the box to a different box.  
> By using tryconv as follows:
> > trjconv -f dynamic-NO-Elastic.gro -s dynamic-NO-Elastic.tpr -pbc mol -o 
> > LastFrame.gro
>  
>  
> i was able to ‘fix’ the protein (fix the pbc issue of the protein), but its 
> remains out of the box.
> I even used -center keyword without luck.
> And since i need a structure where the protein remains in the middle of the 
> POPC membrane in order to perform the ‘backward’ step to obtain an AA 
> representation of my system and perform a new MD simulation i’m kind of stuck.
> I don’t know what to do :/
> Hope someone can help me.
> Have a nice week,
> Carlos
>  
>  
> --  
> Carlos Navarro Retamal
> Bioinformatic engineer
> Ph.D(c) in Applied Science, Universidad de Talca, Chile
> Center of Bioinformatics and Molecular Simulations (CBSM)
> Universidad de Talca
> 2 Norte 685, Casilla 721, Talca - Chile  
> Teléfono: 56-71-201 798,  
> Fax: 56-71-201 561
> Email: carlos.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com) or 
> cnava...@utalca.cl (mailto:cnava...@utalca.cl)
>  
> --  
> Gromacs Users mailing list
>  
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>  
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>  
>  


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Re: [gmx-users] SASA with rhombic dodecahedron

[rajat desikan]

Hi Tsjerk,

Is this the resolved g_sas issue that you were alluding to?
http://redmine.gromacs.org/issues/1445

I don't know if it is the solution to using a non-rectangular box. SASA
calculations form an integral part of my conclusions, and I would like to
be sure about their calculation. Thanks.

Regards,

On Mon, Nov 10, 2014 at 6:36 PM, rajat desikan 
wrote:

> Thank you, Tsjerk. I will take a look. Are there any compatibility issues
> with a 4.6.4 trajectory and GMX 5 analysis tools?
>
> On Mon, Nov 10, 2014 at 4:04 PM, Tsjerk Wassenaar 
> wrote:
>
>> Hi Rajat,
>>
>> Maybe try GMX 5. It appears this was fixed.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Mon, Nov 10, 2014 at 9:49 AM, rajat desikan 
>> wrote:
>>
>> > Dear All,
>> >
>> > SASA calculations of a solvated protein in a rhombic dodecahedron gives
>> the
>> > following warning:
>> >
>> > WARNING: non-rectangular boxes may give erroneous results or crashes.
>> > Analysis based on vacuum simulations (with the possibility of
>> evaporation)
>> > will certainly crash the analysis.
>> >
>> > Is there any way to go about this? Repeating the simulation is
>> > unfortunately not an option. Thanks.
>> >
>> > Regards,
>> >
>> > --
>> > Rajat Desikan (Ph.D Scholar)
>> > Prof. K. Ganapathy Ayappa's Lab (no 13),
>> > Dept. of Chemical Engineering,
>> > Indian Institute of Science, Bangalore
>> > --
>> > 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.
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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>>
>
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] SASA with rhombic dodecahedron

[rajat desikan]

Thank you, Tsjerk. I will take a look. Are there any compatibility issues
with a 4.6.4 trajectory and GMX 5 analysis tools?

On Mon, Nov 10, 2014 at 4:04 PM, Tsjerk Wassenaar  wrote:

> Hi Rajat,
>
> Maybe try GMX 5. It appears this was fixed.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Nov 10, 2014 at 9:49 AM, rajat desikan 
> wrote:
>
> > Dear All,
> >
> > SASA calculations of a solvated protein in a rhombic dodecahedron gives
> the
> > following warning:
> >
> > WARNING: non-rectangular boxes may give erroneous results or crashes.
> > Analysis based on vacuum simulations (with the possibility of
> evaporation)
> > will certainly crash the analysis.
> >
> > Is there any way to go about this? Repeating the simulation is
> > unfortunately not an option. Thanks.
> >
> > Regards,
> >
> > --
> > Rajat Desikan (Ph.D Scholar)
> > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
> > --
> > 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.
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
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>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions

[Justin Lemkul]

On 11/10/14 7:58 AM, Kester Wong wrote:

Dear Justin,



Thank you for the feedback. I have also tried the following:

i) separating OH- and Na+ ions

ii) placing the ions much closer to water droplet

iii) increase the spacing between each ions, i.e. using a larger box


Perhaps I should try having the ions in a larger box,  then fill the box with
water molecules and then redo the energy minimisation and NVT?



Well, like Erik said, there really isn't a smoking gun and what I'm observing 
might be either causative or symptomatic, there's just no way to know at this 
point.  I don't know what good any of those three options will do, because I 
don't understand what you're trying to accomplish.  What was the logic of 
putting a lattice of OH- and random Na+ in vacuo above a water droplet?  What is 
the goal of your simulations?


-Justin




Regards,

Kester

On 11/10/14 5:04 AM, Erik Marklund wrote:
> Dear Kester,
>
> Hm. No obvious smoking gun as far as I can see. You could try a two-step 
minimisation where you first do one minimisation with soft-core potentials and 
then one without.
>

What's strange to me is the lattice of OH- at the top of the box and the 
sodium
ions that are floating out in the middle of nowhere.  I don't understand the
construction of this system, but having highly charged stuff in close 
contact
and floating around in vacuum certainly looks like it could be trouble.

-Justin

> Kind regards,
> Erik
>
> On 7 Nov 2014, at 05:36, Kester Wong> wrote:
>
>
> Dear Erik,
>
> The starting structure consists of water on graphene that has already 
been energy minimised, and subsequently equilibrated (NVT) for 20ns.
> Using that (water droplet on graphene), I added the ions for energy 
minimisation.
> I followed a two-step minimisation:
> i) Minimisation with no constraints (-DFLEXIBLE)
> ii) Minimisation with constraints (SETTLES for TIPS3P water, and 
(-DCONSTRAINTS) for hydroxide)
>
> With the ions:
> I have tried placing the ions box lower toward water droplet, but the Max 
Force remains large upon energy minimisation.
>
> The input files can be accessed here:
> 
https://drive.google.com/folderview?id=0B7ym8d6G9-e2dG5pOFQ4SWVyZG8&usp=sharing
>
> The hydroxide parameter is taken from Gerrit Groenhof, based on the 
supplementary material in this paper:
> http://dx.doi.org/10.1016/j.bpj.2014.04.062
>
> In short, this model was developed very similarly to the polarisable 
version of hydroxide in the SWM4-NDP force field.
> As for sodium and graphene, the topology parameters were taken from 
CHARMM27; TIPS3P was used for the water model.
>
> Visualisation after the energy minimisation showed a distorted virtual 
site of the hydroxide ions, where one of the four virtual sites no longer conform 
to the constraint. So, I am guessing whether the extremely large Max Force 
originates from the force constants in the hydroxide topology?
>
> Thank you for your time and assistance!
> -Kester
> - 원본 메일 -
> 보낸사람 : Erik Marklund>
> 받는사람 : ">">
> 받은날짜 : 2014년 11월 6일(목) 20:35:59
> 제목 : Re: [gmx-users] Very large Max Force [Energy minimisation] in water 
with ions
>
> Dear Kester,
>
> The potential energy is highly positive in the first case and the force 
is enormous in the second case, so no wonder that they blow up. How did you 
prepare these systems?
>
> Kind regards,
> Erik
>
> Erik Marklund, PhD
> Postdoctoral Research Fellow, Fulford JRF
>
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
>
> On 6 Nov 2014, at 04:31, Kester Wong > wrote:
>
>
> Dear all,
>
> I have been trying to energy minimise ~1980 water (tips3p) molecules with 
20 OH- anions (with virtual sites and dummy atoms) and 20 Na+ cations, however, I 
always ended up getting a very large Max Force.
>
> Using emtol = 1000 and emstep = 0.0001, I get:
>
> Potential Energy  =  3.79607808453231e+09
> Maximum force =  9.86741557582003e+02 on atom 42394
> Norm of force =  2.38846729392462e+01
>
> Using emtol = 700 and emstep = 0.0001, I get:
>
> Potential Energy  = -6.43566327273198e+13
> Maximum force =  9.24568347101016e+25 on atom 42262
> Norm of force =  5.74744822148669e+23
>
> As expected, both structures blew up during NVT equilibration.
>
> Could this be due to the arrangement of the ions? I tried separating the 
anions and cations in two boxes (placed on top of the water droplet), but that 
also yield a very large Max Force.
>
> FYI, the water droplet on graphene was equilibrated for 20ns.
> Any input is greatly appreciated. Thanks.
>
> - Kester
>
> --
> G

Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions

[Kester Wong]

<<< text/html; charset=UTF-8: Unrecognized >>>
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Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions

[Justin Lemkul]

On 11/10/14 5:04 AM, Erik Marklund wrote:

Dear Kester,

Hm. No obvious smoking gun as far as I can see. You could try a two-step 
minimisation where you first do one minimisation with soft-core potentials and 
then one without.



What's strange to me is the lattice of OH- at the top of the box and the sodium 
ions that are floating out in the middle of nowhere.  I don't understand the 
construction of this system, but having highly charged stuff in close contact 
and floating around in vacuum certainly looks like it could be trouble.


-Justin


Kind regards,
Erik

On 7 Nov 2014, at 05:36, Kester Wong 
mailto:kester2...@ibs.re.kr>> wrote:


Dear Erik,

The starting structure consists of water on graphene that has already been 
energy minimised, and subsequently equilibrated (NVT) for 20ns.
Using that (water droplet on graphene), I added the ions for energy 
minimisation.
I followed a two-step minimisation:
i) Minimisation with no constraints (-DFLEXIBLE)
ii) Minimisation with constraints (SETTLES for TIPS3P water, and 
(-DCONSTRAINTS) for hydroxide)

With the ions:
I have tried placing the ions box lower toward water droplet, but the Max Force 
remains large upon energy minimisation.

The input files can be accessed here:
https://drive.google.com/folderview?id=0B7ym8d6G9-e2dG5pOFQ4SWVyZG8&usp=sharing

The hydroxide parameter is taken from Gerrit Groenhof, based on the 
supplementary material in this paper:
http://dx.doi.org/10.1016/j.bpj.2014.04.062

In short, this model was developed very similarly to the polarisable version of 
hydroxide in the SWM4-NDP force field.
As for sodium and graphene, the topology parameters were taken from CHARMM27; 
TIPS3P was used for the water model.

Visualisation after the energy minimisation showed a distorted virtual site of 
the hydroxide ions, where one of the four virtual sites no longer conform to 
the constraint. So, I am guessing whether the extremely large Max Force 
originates from the force constants in the hydroxide topology?

Thank you for your time and assistance!
-Kester
- 원본 메일 -
보낸사람 : Erik Marklund 
mailto:erik.markl...@chem.ox.ac.uk>>
받는사람 : "mailto:gmx-us...@gromacs.org>>" 
mailto:gmx-us...@gromacs.org>>
받은날짜 : 2014년 11월 6일(목) 20:35:59
제목 : Re: [gmx-users] Very large Max Force [Energy minimisation] in water with 
ions

Dear Kester,

The potential energy is highly positive in the first case and the force is 
enormous in the second case, so no wonder that they blow up. How did you 
prepare these systems?

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 6 Nov 2014, at 04:31, Kester Wong > wrote:


Dear all,

I have been trying to energy minimise ~1980 water (tips3p) molecules with 20 
OH- anions (with virtual sites and dummy atoms) and 20 Na+ cations, however, I 
always ended up getting a very large Max Force.

Using emtol = 1000 and emstep = 0.0001, I get:

Potential Energy  =  3.79607808453231e+09
Maximum force =  9.86741557582003e+02 on atom 42394
Norm of force =  2.38846729392462e+01

Using emtol = 700 and emstep = 0.0001, I get:

Potential Energy  = -6.43566327273198e+13
Maximum force =  9.24568347101016e+25 on atom 42262
Norm of force =  5.74744822148669e+23

As expected, both structures blew up during NVT equilibration.

Could this be due to the arrangement of the ions? I tried separating the anions 
and cations in two boxes (placed on top of the water droplet), but that also 
yield a very large Max Force.

FYI, the water droplet on graphene was equilibrated for 20ns.
Any input is greatly appreciated. Thanks.

- Kester

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--
==

Justin A. Lem

Re: [gmx-users] Simulating Multiple Solute Particles

[Justin Lemkul]

On 11/10/14 3:07 AM, Nathan K Houtz wrote:

Thank you again, Dr. Lemkul! I went with the first option because my advisor 
wants me to use tip3p water. Unfortunately, I immediately got myself stuck on 
the next step, but this time I think the solution may not be as trivial. The 
command to output em.tpr seems to work without any errors. The command,



Well, strictly speaking, either option works because the parameters of TIP3P are 
not force field-dependent, just translated between different conventions for 
nonbonded parameters, but that's just a pedantic issue.



gmx mdrun -deffnm em


gives me a lot of errors. (It stops after 1000). Here's a small sample:


Steepest Descents:
   Tolerance (Fmax)   =  1.0e+03
   Number of steps=5

Step 1, time 0.001 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.373893, max 0.619462 (between atoms 1747 and 1748)
bonds that rotated more than 30 degrees:
atom 1 atom 2  angle  previous, current, constraint length
  4  5   74.80.1130   0.0501  0.1204
 11 12   75.00.1132   0.0510  0.1204
 18 19   74.90.1129   0.0497  0.1204
 25 26   75.60.1126   0.0488  0.1204
 32 33   74.90.1132   0.0513  0.1204
 39 40   75.70.1129   0.0503  0.1204


etc. There are 7 atoms (the methyl group is a united atom, otherwise there 
would be 10) in each TTA molecule, so you'll notice that it's complaining about 
the bond between the 4th and 5th atoms on every one of them. My best guess is 
that my topology file has insufficient or incorrect constraints, allowing this 
particular bond to rotate. The entire molecule is supposed to be rigid. I did 
constrain all the distances, but not the angles or dihedrals. One of the 
example topology files I used did the same: constrained distances but not 
angles or dihedrals. I was skeptical because it seems to allow some degrees of 
freedom but I assumed gromacs somehow took care of it. Even in this instance, 
it doesn't make sense to me that only one of the bonds is problematic if none 
of them are constrained. So, I'm unsure of what exactly is being left out. The 
bond in question is between the double bonded C=O. My molecule looks like this:

H  O
   \  //
H - C ≡ C - C
   /  \
H O-H

My topology file is available from a previous message in this thread (minus the 
last force field correction), linked here from the archive: 
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg07776.html

If anyone knows directly how to fix the error, I would greatly appreciate it, but helping 
me understand the error would also be very useful: Does "relative constraint 
deviation" mean that a constraint has been broken, or that there is no constraint 
where there should be one? Also, when it's saying the bonds are rotating more than 30 
degrees, is that the bond angle changing or does it mean that a dihedral is changing by 
that much?



Your system is http://www.gromacs.org/Documentation/Terminology/Blowing_Up 
because the topology is probably unstable.  Triple bonds need to be handled 
using virtual sites.  See previous discussions about linear construction 
(examples are acetonitrile and others) and my tutorial on doing just this.


-Justin


Thanks again in advance - I really appreciate the help!
N.H.

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Tuesday, November 4, 2014 7:45:39 AM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles



On 11/4/14 12:45 AM, Nathan K Houtz wrote:

Thanks for your reply. However, I'm still confused. I thought that the command:

#include "oplsaa.ff/tip3p.itp"

is a call to the opls-aa force field. If this is not the correct way to include 
the force field parameters, how should I do that?



That line does not call a force field, it calls a topology for TIP3P, which
makes use of OPLS-AA parameters (well, more correctly TIP3P parameters as
translated into OPLS-AA atom types and functional form).  Your options are
either (1) #include "oplsaa.ff/forcefield.itp" at the start of the topology and
remove the [defaults] directive in your TETR topology or (2) translate TIP3P
into atom types that are self-contained in your topology.

-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

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Re: [gmx-users] energy minimization of protein taken from PDB

[Justin Lemkul]

On 11/10/14 2:36 AM, md kashif wrote:

Dear all
I have downloaded a protein from RCSB, having two chains. In order to go
for energy minimization should I delete one chain as both are similar and
other molecules like SO4, water etc? Is the protein having chain A only can
be used for energy minimization  using tutorial

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/index.html
I have gromacs 4.6.5 installed on my  i7 processor laptop.



Whether or not you remove the second chain depends on whether or not it has any 
functional significance or if it simply crystallizes as a dimer.  For that, you 
need to read the paper associated with the structure and make your decision.


-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

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Re: [gmx-users] change in energy minimization

[Justin Lemkul]

On 11/10/14 1:17 AM, Indu Kumari wrote:

Gd morning,

Check the dt of em.mdp file and vary it accordingly.



dt has no effect in energy minimization, only in dynamics.

-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
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Re: [gmx-users] change in energy minimization

[Justin Lemkul]

On 11/10/14 12:16 AM, md kashif wrote:

Dear all
I am new user and stuck with the energy minimization conflict.
I am following the gromacs tutorial (
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
  ,lysozyme
in water) for my protein and getting the energy minimized protein with
Epot= -1.5248922e+06  is this value correct? I have used mdp files same as
given in the sample tutorial.


There is no way to know what the "correct" value is for any given system.  If 
the potential is negative and Fmax has converged below emtol, then minimization 
did its job.


-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

==
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Re: [gmx-users] crazy bonds in xtc file

[Justin Lemkul]

On 11/10/14 12:33 AM, RINU KHATTRI wrote:

hello everyone
i am working on protein ligand with popc membrane i have loaded the
xtc file with gro file in vmd  gro is ok but xtc is showing crazy
bonds i searched the mailing list i got trajconv command to use but
where i am at 50ns
i have to go back and  correct the file or i can continue where i have
to use this trajconv
kindly help
http://s48.photobucket.com/user/mittukhattri/media/Screenshot_zpse0fea8a0.png.html



This is just a periodicity effect, as you have found from the previous mailing 
list posts.  There is nothing wrong with the run, and you only need to invoke 
trjconv for visualization purposes after everything is done.


-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

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Re: [gmx-users] SASA with rhombic dodecahedron

[Tsjerk Wassenaar]

Hi Rajat,

Maybe try GMX 5. It appears this was fixed.

Cheers,

Tsjerk

On Mon, Nov 10, 2014 at 9:49 AM, rajat desikan 
wrote:

> Dear All,
>
> SASA calculations of a solvated protein in a rhombic dodecahedron gives the
> following warning:
>
> WARNING: non-rectangular boxes may give erroneous results or crashes.
> Analysis based on vacuum simulations (with the possibility of evaporation)
> will certainly crash the analysis.
>
> Is there any way to go about this? Repeating the simulation is
> unfortunately not an option. Thanks.
>
> Regards,
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] Very large Max Force [Energy minimisation] in water with ions

[Erik Marklund]

Dear Kester,

Hm. No obvious smoking gun as far as I can see. You could try a two-step 
minimisation where you first do one minimisation with soft-core potentials and 
then one without.

Kind regards,
Erik

On 7 Nov 2014, at 05:36, Kester Wong 
mailto:kester2...@ibs.re.kr>> wrote:


Dear Erik,

The starting structure consists of water on graphene that has already been 
energy minimised, and subsequently equilibrated (NVT) for 20ns.
Using that (water droplet on graphene), I added the ions for energy 
minimisation.
I followed a two-step minimisation:
i) Minimisation with no constraints (-DFLEXIBLE)
ii) Minimisation with constraints (SETTLES for TIPS3P water, and 
(-DCONSTRAINTS) for hydroxide)

With the ions:
I have tried placing the ions box lower toward water droplet, but the Max Force 
remains large upon energy minimisation.

The input files can be accessed here:
https://drive.google.com/folderview?id=0B7ym8d6G9-e2dG5pOFQ4SWVyZG8&usp=sharing

The hydroxide parameter is taken from Gerrit Groenhof, based on the 
supplementary material in this paper:
http://dx.doi.org/10.1016/j.bpj.2014.04.062

In short, this model was developed very similarly to the polarisable version of 
hydroxide in the SWM4-NDP force field.
As for sodium and graphene, the topology parameters were taken from CHARMM27; 
TIPS3P was used for the water model.

Visualisation after the energy minimisation showed a distorted virtual site of 
the hydroxide ions, where one of the four virtual sites no longer conform to 
the constraint. So, I am guessing whether the extremely large Max Force 
originates from the force constants in the hydroxide topology?

Thank you for your time and assistance!
-Kester
- 원본 메일 -
보낸사람 : Erik Marklund 
mailto:erik.markl...@chem.ox.ac.uk>>
받는사람 : "mailto:gmx-us...@gromacs.org>>" 
mailto:gmx-us...@gromacs.org>>
받은날짜 : 2014년 11월 6일(목) 20:35:59
제목 : Re: [gmx-users] Very large Max Force [Energy minimisation] in water with 
ions

Dear Kester,

The potential energy is highly positive in the first case and the force is 
enormous in the second case, so no wonder that they blow up. How did you 
prepare these systems?

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Fellow, Fulford JRF

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 6 Nov 2014, at 04:31, Kester Wong > wrote:


Dear all,

I have been trying to energy minimise ~1980 water (tips3p) molecules with 20 
OH- anions (with virtual sites and dummy atoms) and 20 Na+ cations, however, I 
always ended up getting a very large Max Force.

Using emtol = 1000 and emstep = 0.0001, I get:

Potential Energy  =  3.79607808453231e+09
Maximum force =  9.86741557582003e+02 on atom 42394
Norm of force =  2.38846729392462e+01

Using emtol = 700 and emstep = 0.0001, I get:

Potential Energy  = -6.43566327273198e+13
Maximum force =  9.24568347101016e+25 on atom 42262
Norm of force =  5.74744822148669e+23

As expected, both structures blew up during NVT equilibration.

Could this be due to the arrangement of the ions? I tried separating the anions 
and cations in two boxes (placed on top of the water droplet), but that also 
yield a very large Max Force.

FYI, the water droplet on graphene was equilibrated for 20ns.
Any input is greatly appreciated. Thanks.

- Kester

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[gmx-users] SASA with rhombic dodecahedron

[rajat desikan]

Dear All,

SASA calculations of a solvated protein in a rhombic dodecahedron gives the
following warning:

WARNING: non-rectangular boxes may give erroneous results or crashes.
Analysis based on vacuum simulations (with the possibility of evaporation)
will certainly crash the analysis.

Is there any way to go about this? Repeating the simulation is
unfortunately not an option. Thanks.

Regards,

-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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Re: [gmx-users] Freezing groups and energy conservation

[Francesco Mambretti]

I am running in single precision, my time-step is 1 fs (0.001 ps, usually
works fine). However, I achieved very good energy conservation when I
changed integrator from "md" to "md-vv". It sounds quite strange to me, but
it works, so...
Thanks, however!

Francesco

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Re: [gmx-users] Simulating Multiple Solute Particles

[Nathan K Houtz]

Thank you again, Dr. Lemkul! I went with the first option because my advisor 
wants me to use tip3p water. Unfortunately, I immediately got myself stuck on 
the next step, but this time I think the solution may not be as trivial. The 
command to output em.tpr seems to work without any errors. The command,

> gmx mdrun -deffnm em

gives me a lot of errors. (It stops after 1000). Here's a small sample:

>Steepest Descents:
>   Tolerance (Fmax)   =  1.0e+03
>   Number of steps=5
>
>Step 1, time 0.001 (ps)  LINCS WARNING
>relative constraint deviation after LINCS:
>rms 0.373893, max 0.619462 (between atoms 1747 and 1748)
>bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>  4  5   74.80.1130   0.0501  0.1204
> 11 12   75.00.1132   0.0510  0.1204
> 18 19   74.90.1129   0.0497  0.1204
> 25 26   75.60.1126   0.0488  0.1204
> 32 33   74.90.1132   0.0513  0.1204
> 39 40   75.70.1129   0.0503  0.1204

etc. There are 7 atoms (the methyl group is a united atom, otherwise there 
would be 10) in each TTA molecule, so you'll notice that it's complaining about 
the bond between the 4th and 5th atoms on every one of them. My best guess is 
that my topology file has insufficient or incorrect constraints, allowing this 
particular bond to rotate. The entire molecule is supposed to be rigid. I did 
constrain all the distances, but not the angles or dihedrals. One of the 
example topology files I used did the same: constrained distances but not 
angles or dihedrals. I was skeptical because it seems to allow some degrees of 
freedom but I assumed gromacs somehow took care of it. Even in this instance, 
it doesn't make sense to me that only one of the bonds is problematic if none 
of them are constrained. So, I'm unsure of what exactly is being left out. The 
bond in question is between the double bonded C=O. My molecule looks like this:

H  O
  \  //
H - C ≡ C - C
  /  \
H O-H

My topology file is available from a previous message in this thread (minus the 
last force field correction), linked here from the archive: 
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg07776.html

If anyone knows directly how to fix the error, I would greatly appreciate it, 
but helping me understand the error would also be very useful: Does "relative 
constraint deviation" mean that a constraint has been broken, or that there is 
no constraint where there should be one? Also, when it's saying the bonds are 
rotating more than 30 degrees, is that the bond angle changing or does it mean 
that a dihedral is changing by that much? 

Thanks again in advance - I really appreciate the help!
N.H.

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Tuesday, November 4, 2014 7:45:39 AM
Subject: Re: [gmx-users] Simulating Multiple Solute Particles



On 11/4/14 12:45 AM, Nathan K Houtz wrote:
> Thanks for your reply. However, I'm still confused. I thought that the 
> command:
>
> #include "oplsaa.ff/tip3p.itp"
>
> is a call to the opls-aa force field. If this is not the correct way to 
> include the force field parameters, how should I do that?
>

That line does not call a force field, it calls a topology for TIP3P, which 
makes use of OPLS-AA parameters (well, more correctly TIP3P parameters as 
translated into OPLS-AA atom types and functional form).  Your options are 
either (1) #include "oplsaa.ff/forcefield.itp" at the start of the topology and 
remove the [defaults] directive in your TETR topology or (2) translate TIP3P 
into atom types that are self-contained in your topology.

-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

==
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