[gmx-users] Regarding the forcefield, topology..

[Dilip H N]

Hello,
1] I want to simulate molecules as Methylamine(CH3NH2),Dimethylamine((CH3)2NH),
Trimethylamine((CH3)3N), TrimethylamineN-oxide((CH3)3NO-).
Can anybody suggest me the right forcefield in gromacs for these
moleculesin which forcefield is this available along with its residues..
2] Are the forcefields for all these molecules available in the same
forcefield..?
3] and thn i want to simulate an aminoacid with the above molecules...how
can i simulate if the aminoacid and the above said molecules are in
different forcefields..??

Thank you

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



   Sent with Mailtrack

-- 
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] Lennard Jones and Buckingham potential together in one simulation

[Mark Abraham]

Hi,

That pdf twice specifies the correct value for nbfunc. For example, the
last sentence of section 1. I don't understand where the confusion lies.

Mark

On Thu, 8 Jun 2017 10:46 Narjes Khosravian 
wrote:

> Is there any guideline for that?
>
>
> My exact question is about topology file for  using tabulated potential.  What
> should be the statement
> mentioning nbfunc ( and combination-rule) in .top file when I wanted to
> have both potential (LJ and BKS)?
>
> Best,
> Narjes
>
>
>  Narjes Khosravian
>  Postdoc Researcher
>  Department of Physics, Materials and Surface Theory
>  Chalmers University of Technology
>  SE-412 96 Göteborg, Sweden
>
>
> *From:* gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> *Sent:* Thursday, June 8, 2017 10:38:01 AM
>
> *To:* gmx-us...@gromacs.org
> *Subject:* Re: [gmx-users] Lennard Jones and Buckingham potential
> together in one simulation
> Hi,
>
> Isn't this covered in those PDFs?
>
> Mark
>
> On Thu, Jun 8, 2017 at 10:34 AM Narjes Khosravian <
> narjes.khosrav...@chalmers.se> wrote:
>
> > Hi Mark,
> >
> > Thanks for your reply!
> >
> > Actually I am using tabulated-potential based on the bellow manual by
> > Gareth Tribello.
> > 
> >
> > 
> > http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
> >
> > My problem is that:
> >
> > Since I have LJ and buckingham both, what should be the statement
> > mentioning nbfunc ( and combination-rule) in .top file? e.g. nbfunc=1
> > followed by LJ parameters  C and A for the concerned pairs and
> >
> > then nbfunc=2 (and whatever combination rule) , followed by buckingham
> > parameters C, A , B for concerned pairs in the .top file?
> >
> > I greatly appreciate for any help in this matter.
> > Best,
> > Narjes
> >
> >
> >
> > 
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> > Abraham 
> > Sent: Thursday, May 4, 2017 3:49:26 PM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Lennard Jones and Buckingham potential together
> > in one simulation
> >
> > Hi,
> >
> > This procedure is usually motivated by trying to mix force fields that
> were
> > never intended to be used together, and thus need to be shown work well
> > together. In that case, you may as well parameterize a consistent model.
> >
> > Technically, you might be able to get this to work, but each atom in
> > GROMACS can have only one set of VDW parameters, so you need to make the
> > same parameters work with both functional forms, and this either
> impossible
> > or tricky. The best bet is using tabulated interactions. Don't try to set
> > up your intended target simulation in your first attempt - make something
> > simple that lets you prove to yourself you have the interactions working
> > the way that you think they should, then add complexity.
> >
> > Mark
> >
> > On Wed, May 3, 2017 at 8:41 PM Narjes Khosravian <
> > narjes.khosrav...@chalmers.se> wrote:
> >
> > > Dear gromacs users,
> > >
> > >
> > > I am trying to  use Lennard Jones and Buckingham potential  together in
> > > one simulation as part of my system is treated by LJ and rest by Buck
> > > potential.
> > >
> > >
> > > My question is that how I can include Lennard Jones parameters in
> > topology
> > > file while my [defaults ] was chosen 2  1 to consider Buckingham
> > parameter?
> > >
> > > I have created table for buck and LJ.
> > >
> > >
> > > I greatly appreciate for any guide in this matter.
> > >
> > > Narjes
> > >
> > >
> > >  Narjes Khosravian
> > >  Postdoc Researcher
> > >  Department of Physics, Materials and Surface Theory
> > >  Chalmers University of Technology
> > >  SE-412 96 Göteborg, Sweden
> > >
> > > --
> > > 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
> > 

[gmx-users] How to mix Amber FF with Slipid FF

[Quyen V. Vu]

Dear GMX user,
I want to simulate membrane protein using Amber forcefield for protein,
Slipid for membrane POPC.
I use MemBuilder v2 to build POPC membrane and downloaded Slipid/Amber.ff.
How can I mix amber forcefield with Slipid just the same with Gromos force
field on Justin's tutorial?
Thanks,
Quyen
-- 
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] Using PME with Slab Boundaries

[Sanim Rahman]

Hello,

I was attempting to run an equilibration on my system that has slab
boundaries. I am using 3dc Ewald Geometry and PME. I am also using PBC in
the x,y,z dimensions.

During grompp, I received the following warning:

*WARNING: With PME and ewald_geometry = 3dc you should use pbc = xy*

I have seen simulations using PBC in all three dimensions with slab
boundaries with PME. What are the consequences of running a simulation with
slab geometry and pbc in all three dimensions with PME?

Regards,
Sanim Rahman
-- 
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] Doubt about Free Energy Calculations using g_bar

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

I was interested in the process *prior* to the free energy change is carried 
out, before we carry out simulations pertaining to couple-lambda0 = vdw and 
couple-lambda1 = none. Hence, I am curious as to *how* the charges are set to 
zero in the topology for the ligand and if is it necessary in Gromacs 5.0 
version.

For the Protein-ligand system, the tutorial suggests: (for version 5.0)
couple-lambda0  = none
couple-lambda1  = vdw-q
vdw_lambdas = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00
coul_lambdas= 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00

So, if this is done, is it necessary to set the charges zero in topology for 
the ligand? If yes, can you please suggest me as to how can we do that using 
the index file and topology file?

-Bhagyesh

- Original Message -
From: "Justin Lemkul" 
To: gmx-us...@gromacs.org
Sent: Friday, June 9, 2017 2:40:38 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar

On 6/8/17 11:46 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear all,
> 
> I am attempting to find Binding affinity of a Protein-ligand system by 
> following the Free Energy tutorials 
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html).
> It says : "The procedure in this tutorial essentially assumes that charges 
> have been properly been turned off prior to this point". How do we turn off 
> the charges of a group specified in an index file (the ligand in my case) ?
> 

Either set them to zero in the topology or define couple-lambda0 = vdw and 
couple-lambda1 = none.

-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] Remove all but N closest water molecules from protein

[Jose Borreguero]

Hi Mark,

The following lines select solvent molecules within some cutoff distance of
the protein:

close_solvent_atoms = group "SOL" and within 0.5 of group "Protein";
close_solvent_molecules = same resindex as close_solvent_atoms;
"strippedSystem" group "Protein" or close_solvent_molecules;

It's not exactly what I wanted, butI can select N closest water molecules
by tuning the cutoff distance.

.Jose

On Thu, Jun 8, 2017 at 4:34 AM, Mark Abraham 
wrote:

> Hi,
>
> Or gmx select to make an index group for the nearest waters, and gmx
> trjconv to make the subset with the index group.
>
> Mark
>
> On Thu, Jun 8, 2017 at 9:05 AM João Henriques <
> joao.m.a.henriq...@gmail.com>
> wrote:
>
> > Hi,
> >
> > trjorder can reorder the water molecules in each frame according to their
> > distance to the protein. Then you either manually prune the gro file(s)
> or
> > use an index file to get rid of the extra stuff. I don't know of any
> native
> > tool that does all of this in one step but I may be outdated regarding
> new
> > stuff on gmx 2016.
> >
> > Cheers,
> > João
> >
> > On Jun 8, 2017 2:49 AM, "Jose Borreguero"  wrote:
> >
> > Dear Gromacs users,
> >
> > I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow
> > me to create a new *.gro file containing the protein and the N closest
> > water molecules to the protein
> > ​, starting from a system of a solvated protein​
> > ?
> >
> > Best,
> > Jose Borreguero
> > --
> > 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] Output center of mass of each molecules in a system.

[Justin Lemkul]

On 6/8/17 12:19 PM, Christopher Neale wrote:

make an index file with gmx make_ndx and then script it to create an index for 
each water molecule, e.g.:


gmx make_ndx -f my.gro -o index.ndx << EOF

$(for((i=1;i<=100;i++)); do echo r${i}; done)

q

EOF




Even easier:

splitres (number of desired group)

-Justin


then you can likewise script the input to gmx traj


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Li, Shi 

Sent: 08 June 2017 11:26:46
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Output center of mass of each molecules in a system.

Dear GMX users,

I want to output the center of mass of each molecule in my simulation box.
I think I should use gmx traj, with -com option. But this only gave me the
center of mass for the whole system. If my system only contains 100 same
solvent molecules, is there a method to output the center of mass for each
individual molecule in the system?

Thank you for any help!
Shi
--
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.
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] Doubt about Free Energy Calculations using g_bar

[Justin Lemkul]

On 6/8/17 11:46 AM, Varvdekar Bhagyesh Rajendra wrote:

Dear all,

I am attempting to find Binding affinity of a Protein-ligand system by 
following the Free Energy tutorials 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html).
It says : "The procedure in this tutorial essentially assumes that charges have been 
properly been turned off prior to this point". How do we turn off the charges of a 
group specified in an index file (the ligand in my case) ?



Either set them to zero in the topology or define couple-lambda0 = vdw and 
couple-lambda1 = none.


-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] Error in deuterium order parameters, index, nr

[Justin Lemkul]

On 6/8/17 10:47 AM, Poncho Arvayo Zatarain wrote:



Hello gromacs users: i´m trying to graph my xvg of deuterium order parameters with the 
command: gmx order -s file.tpr -f fiile.xtc -n sn1.ndx -d z -od deuter_sn1.xvg but the 
following error appears: Error in user input: Invalid input lines in option nr. Required 
option was not provided and the default file "index" does not exist or is not 
accessible. The following extensions were tried to complete the file name: .ndx.
Before that, to generate .ndx file i use the command: gmx make_ndx -f file.tpr 
-o sn1.ndx. What can i do to solve this? What is option nr? is necessary to use 
it?



The error is saying that the -nr option is looking for a file called index.ndx 
but that doesn't exist.


-nr should only be used in the case of radial calculations; it seems older 
versions incorrectly listed it as a mandatory argument rather than an optional 
one.  Upgrade to the latest GROMACS and try again.


-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] Output center of mass of each molecules in a system.

[Christopher Neale]

make an index file with gmx make_ndx and then script it to create an index for 
each water molecule, e.g.:


gmx make_ndx -f my.gro -o index.ndx << EOF

$(for((i=1;i<=100;i++)); do echo r${i}; done)

q

EOF


then you can likewise script the input to gmx traj


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Li, Shi 

Sent: 08 June 2017 11:26:46
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Output center of mass of each molecules in a system.

Dear GMX users,

I want to output the center of mass of each molecule in my simulation box.
I think I should use gmx traj, with -com option. But this only gave me the
center of mass for the whole system. If my system only contains 100 same
solvent molecules, is there a method to output the center of mass for each
individual molecule in the system?

Thank you for any help!
Shi
--
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] Doubt about Free Energy Calculations using g_bar

[Varvdekar Bhagyesh Rajendra]

Dear all,

I am attempting to find Binding affinity of a Protein-ligand system by 
following the Free Energy tutorials 
(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html).
 
It says : "The procedure in this tutorial essentially assumes that charges have 
been properly been turned off prior to this point". How do we turn off the 
charges of a group specified in an index file (the ligand in my case) ?


Thanking in anticipation,

Best Regards,

Bhagyesh 
-- 
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] Output center of mass of each molecules in a system.

[Li, Shi]

Dear GMX users,

I want to output the center of mass of each molecule in my simulation box.
I think I should use gmx traj, with -com option. But this only gave me the
center of mass for the whole system. If my system only contains 100 same
solvent molecules, is there a method to output the center of mass for each
individual molecule in the system?

Thank you for any help!
Shi
-- 
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] Error in deuterium order parameters, index, nr

[Poncho Arvayo Zatarain]

Hello gromacs users: i´m trying to graph my xvg of deuterium order parameters 
with the command: gmx order -s file.tpr -f fiile.xtc -n sn1.ndx -d z -od 
deuter_sn1.xvg but the following error appears: Error in user input: Invalid 
input lines in option nr. Required option was not provided and the default file 
"index" does not exist or is not accessible. The following extensions were 
tried to complete the file name: .ndx.
Before that, to generate .ndx file i use the command: gmx make_ndx -f file.tpr 
-o sn1.ndx. What can i do to solve this? What is option nr? is necessary to use 
it?

Thanks
-- 
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] gmx insert-molecules

[Justin Lemkul]

On 6/8/17 9:15 AM, Shi Li wrote:


Again, please don't reply to the entire digest.


Sorry about the inconvenience, I am not very familiar with the process. Hope 
this is right now.


Neither approach avoids having re-equilibrate the system.  Your approach of
inserting B into an existing box of A perturbs the system and requires a new
equilibration.  This is especially true if you play tricks like messing with vdW
radii to force B into small voids in A.  You need to minimize and equilibrate,
because these are new systems.

My approach is less prone to failure and ultimately I would expect it to take
less time overall because you will not have instances in which the insertion of
B into A fails and requires you to revisit those systems, change seeds, hack vdW
radii, and potentially deal with problematic minimizations.



I would like to solvate the box too, it is indeed less effort. In our approach, 
we want to have a box with a fixed number of A+B, that?s why we want to 
manually replace certain number of A with B, so that we still maintain the same 
total number of molecules but create different concentration. If I solvate the 
box with A, then the number of molecule A goes into the box will not be the 
number we want it to be. Is there ways to define the number of solvent when we 
do the gmx solvate?



Yes, that is exactly what -maxsol does.


Thank you!

But that’s the maximum number of solvent to add into the box, right? Can I 
solvate the box with a fixed number of solvent molecule? If the size of the box 
is a little small, will it automatically adjust the box size to insure the 
right number of solvent can go in?



No, you have to make sure the box is large enough.  Box adjustment is a dynamics 
process, not anything that the preparation tools do.  So either gmx 
insert-moleucles for both A and B, or gmx solvate for A with -maxsol.  Either 
way, you need to know the per-molecule volume to create a reasonably sized box.


-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] gmx insert-molecules

[Shi Li]

>>> 
>>> Again, please don't reply to the entire digest.
>> 
>> Sorry about the inconvenience, I am not very familiar with the process. Hope 
>> this is right now.
>>> 
>>> Neither approach avoids having re-equilibrate the system.  Your approach of
>>> inserting B into an existing box of A perturbs the system and requires a new
>>> equilibration.  This is especially true if you play tricks like messing 
>>> with vdW
>>> radii to force B into small voids in A.  You need to minimize and 
>>> equilibrate,
>>> because these are new systems.
>>> 
>>> My approach is less prone to failure and ultimately I would expect it to 
>>> take
>>> less time overall because you will not have instances in which the 
>>> insertion of
>>> B into A fails and requires you to revisit those systems, change seeds, 
>>> hack vdW
>>> radii, and potentially deal with problematic minimizations.
>>> 
>> 
>> I would like to solvate the box too, it is indeed less effort. In our 
>> approach, we want to have a box with a fixed number of A+B, that?s why we 
>> want to manually replace certain number of A with B, so that we still 
>> maintain the same total number of molecules but create different 
>> concentration. If I solvate the box with A, then the number of molecule A 
>> goes into the box will not be the number we want it to be. Is there ways to 
>> define the number of solvent when we do the gmx solvate?
>> 
> 
> Yes, that is exactly what -maxsol does.

Thank you!

But that’s the maximum number of solvent to add into the box, right? Can I 
solvate the box with a fixed number of solvent molecule? If the size of the box 
is a little small, will it automatically adjust the box size to insure the 
right number of solvent can go in?

Shi
> 
> -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.
> 
> End of gromacs.org_gmx-users Digest, Vol 158, Issue 54
> **

-- 
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] gmx insert-molecules

[Justin Lemkul]

On 6/8/17 9:09 AM, Shi Li wrote:





I am trying to avoid the long step of equilibrium as I have many systems 
corresponding to different concentrations. I was thinking if I replace a small 
number of molecule A with molecule B (the system A is very large and 
pre-equilibriumed) then I only need to apply a short time-step of NPT in order 
to let the system expand or shrink. Then I can use the new system to continue 
replacing A with B to generate a new concentration. Is this practical?

The problem is when B is slightly larger than A, I can?t insert the same number 
of B into the system. Is there way to avoid the overlapping or force the 
molecule in?

You can reduce the vdW radius of atoms to *try* to force the molecules to fit,
but then all you've done is introduce bad clashes that have to be subjected to
minimization and re-equilibration.  So at that point, all you've done is build
your system in the most inefficient way possible.  By trying to avoid
equilibration, you've necessitated it :)

Build the system the robust way - solute first, then solvent.  It's ultimately
less work and less prone to failure.

-Justin

--



Thank you Justin.

In the way solute first then solvent, I will still need to fully re-equilbrium 
the system, is that right? My problem is that I have about a hundred of 
systems, each of them will have about half a million atoms. The full 
equilibrium will be too time consuming. Since each systems are only slightly 
different in concentration (by replacing molecule A with molecule B), I am 
wondering if there will be a easier way to do a quick/roughly equilibrium.


Again, please don't reply to the entire digest.


Sorry about the inconvenience, I am not very familiar with the process. Hope 
this is right now.


Neither approach avoids having re-equilibrate the system.  Your approach of
inserting B into an existing box of A perturbs the system and requires a new
equilibration.  This is especially true if you play tricks like messing with vdW
radii to force B into small voids in A.  You need to minimize and equilibrate,
because these are new systems.

My approach is less prone to failure and ultimately I would expect it to take
less time overall because you will not have instances in which the insertion of
B into A fails and requires you to revisit those systems, change seeds, hack vdW
radii, and potentially deal with problematic minimizations.



I would like to solvate the box too, it is indeed less effort. In our approach, 
we want to have a box with a fixed number of A+B, that’s why we want to 
manually replace certain number of A with B, so that we still maintain the same 
total number of molecules but create different concentration. If I solvate the 
box with A, then the number of molecule A goes into the box will not be the 
number we want it to be. Is there ways to define the number of solvent when we 
do the gmx solvate?



Yes, that is exactly what -maxsol does.

-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] gmx insert-molecules

[Shi Li]

> 
 I am trying to avoid the long step of equilibrium as I have many systems 
 corresponding to different concentrations. I was thinking if I replace a 
 small number of molecule A with molecule B (the system A is very large and 
 pre-equilibriumed) then I only need to apply a short time-step of NPT in 
 order to let the system expand or shrink. Then I can use the new system to 
 continue replacing A with B to generate a new concentration. Is this 
 practical?
 
 The problem is when B is slightly larger than A, I can?t insert the same 
 number of B into the system. Is there way to avoid the overlapping or 
 force the molecule in?
>>> You can reduce the vdW radius of atoms to *try* to force the molecules to 
>>> fit,
>>> but then all you've done is introduce bad clashes that have to be subjected 
>>> to
>>> minimization and re-equilibration.  So at that point, all you've done is 
>>> build
>>> your system in the most inefficient way possible.  By trying to avoid
>>> equilibration, you've necessitated it :)
>>> 
>>> Build the system the robust way - solute first, then solvent.  It's 
>>> ultimately
>>> less work and less prone to failure.
>>> 
>>> -Justin
>>> 
>>> -- 
>> 
>> 
>> Thank you Justin.
>> 
>> In the way solute first then solvent, I will still need to fully 
>> re-equilbrium the system, is that right? My problem is that I have about a 
>> hundred of systems, each of them will have about half a million atoms. The 
>> full equilibrium will be too time consuming. Since each systems are only 
>> slightly different in concentration (by replacing molecule A with molecule 
>> B), I am wondering if there will be a easier way to do a quick/roughly 
>> equilibrium.
> 
> Again, please don't reply to the entire digest. 

Sorry about the inconvenience, I am not very familiar with the process. Hope 
this is right now.
> 
> Neither approach avoids having re-equilibrate the system.  Your approach of 
> inserting B into an existing box of A perturbs the system and requires a new 
> equilibration.  This is especially true if you play tricks like messing with 
> vdW 
> radii to force B into small voids in A.  You need to minimize and 
> equilibrate, 
> because these are new systems.
> 
> My approach is less prone to failure and ultimately I would expect it to take 
> less time overall because you will not have instances in which the insertion 
> of 
> B into A fails and requires you to revisit those systems, change seeds, hack 
> vdW 
> radii, and potentially deal with problematic minimizations.
> 

I would like to solvate the box too, it is indeed less effort. In our approach, 
we want to have a box with a fixed number of A+B, that’s why we want to 
manually replace certain number of A with B, so that we still maintain the same 
total number of molecules but create different concentration. If I solvate the 
box with A, then the number of molecule A goes into the box will not be the 
number we want it to be. Is there ways to define the number of solvent when we 
do the gmx solvate? 

Thank you!
Shi



-- 
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] Doubt regarding enthalpy calculation

[Tushar Ranjan Moharana]

Hi all,
I want to calculate enthalpy between 2 energy group (I wanted to calculate
interaction energy, however I understood that it is challenging. I will
appreciate if someone proves me wrong). I achieved it by performing MD
simulation (energy minimization, NVT, NPT production run). I made different
energy group and rerun the production run and extract LJ  and coulombic
(both short and 14) interaction between them. I got enthalpy by adding the
above terms. Now my doubts are:

1) Am I doing anything wrong or in appropriate?
2) Production run is as mentioned in tutorial by Justine A Lemkule. I want
to know which ensemble it is (NVT, NPT or NVE) and what is the optimum
ensemble to calculate enthalpy (or energy ).
3) Is the enthalpy between one molecule and rest of the system calculated
by above method, if correct, is enthalpy difference between the molecule in
isolation and in the given environment?


Kindly help me understand the above.
Thanks a lot


"A society with free knowledge is better than a society with free food"
-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
-- 
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] LJ-Buckham potential

[Narjes Khosravian]

Hi Mark,


I have read the PFD file prepared by Gareth Tribello, is there any other PDF 
you mean?


Anyways, in the manual by Gareth Tribello it was not defined that when we have 
both potential (LJ and BLS) in one simulation what should be the default of non 
bound function? Should it be 1, which is related to LJ or 2 that is related to 
BKS?



Thanks for your answer,

Narjes

 Narjes Khosravian
 Postdoc Researcher
 Department of Physics, Materials and Surface Theory
 Chalmers University of Technology
 SE-412 96 Göteborg, Sweden



From: Mark Abraham 
Sent: Thursday, June 8, 2017 11:59:39 AM
To: Narjes Khosravian
Subject: Re: LJ-Buckham potential

Hi,

Please keep the discussion on the list. The first PDF discusses nbfunc. Why is 
the problem unsolved?

Mark

On Thu, Jun 8, 2017 at 10:58 AM Narjes Khosravian 
> wrote:

Is there any guideline for that?

My exact question is about topology file for  using tabulated potential.  What 
should be the statement
mentioning nbfunc ( and combination-rule) in .top file when I wanted to have 
both potential (LJ and BKS)?
Best,
Narjes



 Narjes Khosravian
 Postdoc Researcher
 Department of Physics, Materials and Surface Theory
 Chalmers University of Technology
 SE-412 96 Göteborg, Sweden

-- 
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] Remove all but N closest water molecules from protein

[João Henriques]

Thanks for the clarification.

João

On Thu, Jun 8, 2017 at 11:58 AM, Mark Abraham 
wrote:

> Hi,
>
> No. gmx select will write index groups that could implement a dynamic
> selection, but trjconv can't do anything sensible with it. You'd have to
> split the trajectory into a file per frame and match the index group to the
> file to get the selection into a new file. Even if trjconv was smart
> enough, you'd also need to use a trajectory format and downstream tools
> that were about to be flexible about the number of atoms (which is
> typically not the case)... In principle, our TNG format is able to be
> flexible, but there's a lot of infrastructure work if people would actually
> write such files and expect to read them and have everything work well.
> Better to work on tools that can use the dynamic selection without needing
> to serialize and de-serialize files (and the new GROMACS analysis framework
> has such support, but we don't have much funding for implementing / porting
> tools to it).
>
> Mark
>
> On Thu, Jun 8, 2017 at 10:48 AM João Henriques <
> joao.m.a.henriq...@gmail.com>
> wrote:
>
> > Hi Mark,
> >
> > Does your solution output variable numbers of water molecules per frame?
> > That is exactly what I've been wanting to do for a while, but with my
> > solution it becomes very difficult to do so and I usually end up using a
> > fixed number of closest waters for all frames.
> >
> > João
> >
> >
> >
> > On Thu, Jun 8, 2017 at 10:34 AM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Or gmx select to make an index group for the nearest waters, and gmx
> > > trjconv to make the subset with the index group.
> > >
> > > Mark
> > >
> > > On Thu, Jun 8, 2017 at 9:05 AM João Henriques <
> > > joao.m.a.henriq...@gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > trjorder can reorder the water molecules in each frame according to
> > their
> > > > distance to the protein. Then you either manually prune the gro
> file(s)
> > > or
> > > > use an index file to get rid of the extra stuff. I don't know of any
> > > native
> > > > tool that does all of this in one step but I may be outdated
> regarding
> > > new
> > > > stuff on gmx 2016.
> > > >
> > > > Cheers,
> > > > João
> > > >
> > > > On Jun 8, 2017 2:49 AM, "Jose Borreguero" 
> > wrote:
> > > >
> > > > Dear Gromacs users,
> > > >
> > > > I'm a newbie with Gromacs. Is there a Gromacs native tool that will
> > allow
> > > > me to create a new *.gro file containing the protein and the N
> closest
> > > > water molecules to the protein
> > > > ​, starting from a system of a solvated protein​
> > > > ?
> > > >
> > > > Best,
> > > > Jose Borreguero
> > > > --
> > > > 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.
> --
> 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 

Re: [gmx-users] Gromacs

[Justin Lemkul]

On 6/8/17 3:10 AM, saranya wrote:

I have simulated the protein in water and protein with ligand for 100ns by
using GPU and the edr file was generated using -rerun command on
another system.I have just checked the pressure of my system by using
gmx energy
command, then i have selected pressure (group), but the calculated pressure
is quite altered (20,000 pressure bar). Moreover, when I calculated the
temperature of my system, the result was zero.


If you're recalculating energies from an .xtc, this is what you should expect. 
There are no velocities in an .xtc file so all properties related to kinetic 
energy (temperature and virial, hence pressure) are all garbage.


The original .edr file has these quantities.  You just can't use energygrps to 
decompose short-range nonbonded interaction energies on a GPU.  The other 
quantities are valid.


-Justin


I have used below mdp file for the calculation
title   = Protein-ligand complex NPT equilibration
define  = -DPOSRES_LIG  ; position restrain the protein and ligand
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 100 ps
nstvout = 100   ; save velocities every 100 ps
nstenergy   = 100   ; save energies every 100 ps
nstlog  = 100   ; update log file every 100 ps
energygrps  = Protein
; Bond parameters
continuation= yes   ; 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 ; 10 fs
rlist   = 0.9   ; short-range neighborlist 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_EPI 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  = Parrinello-Rahman ; pressure coupling is on for
NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; 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
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; velocity generation off after NVT

*With Regards,*

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*
*Coimbatore-46*



--
==

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] summary_distances.dat file not complete

[Justin Lemkul]

On 6/7/17 10:56 PM, Norfarisha Mohd Fadil wrote:

Dear users,

I ran the Perl script for Umbrella Sampling Tutorial 3, and it generated an 
incomplete summary_distances.dat :



This means the gmx distance command failed for some windows.  Ditch the script 
and run the command yourself on those windows to see why.


-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] number of coordinates does not match after POSRES

[Justin Lemkul]

On 6/8/17 12:23 AM, Simon Kit Sang Chu wrote:

Hi Justin,

Thanks for your advice. Since we are using a forcefield which could only
incorporate with gromacs 3.3.1, we have no choice but to prepare the system
in the old version, then run it with the latest version of gromacs.



The only change in force fields between 3.3.x and now is a reorganization into 
directories.  It's a trivial adjustment to make.  You'll get much faster 
performance and thousands of bug fixes if you update to something modern.



Yes, indeed the option should be with -DPOSRES instead. And the topology
file should #include chainA-pace.top, then chainA_posres.itp in this
alternative manner. It seems that writing all chainA chainB.top first and
all pores.itp later would not do it. Please tell me if I am wrong.



Right, position restraints are on a per-moleculetype basis.  Any 
[position_restraints] directive applies to the [moleculetype] that immediately 
precedes it in the 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

==
--
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] Cylinder pulling through bilayer

[Gmx QA]

Anyone?

Thanks again
/PK

2017-06-07 21:22 GMT+02:00 Gmx QA :

> Dear list
>
> I am attempting to pull a small molecule though a bilayer using the pull
> geometry cylinder with gromacs v 2016.
>
> This is the relevant portion of my mdp-file:
>
> pull  = yes
> pull-ngroups = 2
> pull-ncoords = 1
> pull-coord1-groups   = 1 2
> pull-group1-name = LIG
> pull-group2-name = MEM
> pull-coord1-type = umbrella
> pull-coord1-geometry = cylinder
> pull-coord1-rate = 0.1
> pull-coord1-vec  = 0 0 1
> pull-coord1-k= 1000
> pull-coord1-start= yes
> pull-coord1-init = 0
> pull-cylinder-r  = 1.5
>
> The pull-rate is very fast because I'm only doing preliminary test. At the
> start, the drug molecule is in -z position compared to the membrane.
>
> When doing grompp:
>
> $ gmx grompp -f umbrella_md_test.mdp -c npt.gro -p topol.top -o
> pull_test.tpr
>
> The output makes no sense:
> Using a fourier grid of 72x72x192, spacing 0.113 0.113 0.111
> Pull group  natoms  pbc atom  distance at start  reference at t=0
>13618
>2 32500 64286-nan nm   -nan nm
> Estimate for the relative computational load of the PME mesh part: 0.44
> This run will generate roughly 14 Mb of data
>
>
> I.e. nan's for distance. If I however switch in the mdp file so that
> pull-group1-name = MEM and pull-group2-name = LIG, the distance gets
> correctly calculated. But this does not seem to be what is prescribed in
> the manual for cylinder pulling, where is says that the cylinder is formed
> from the first group (should be the drug molecule) and through the com of
> the reference group (the membrane in my case),
>
> I think there is something I am missing?
>
> Thanks!
> /PK
>
-- 
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] gmx insert-molecules

[Justin Lemkul]

On 6/7/17 7:33 PM, Shi Li wrote:


I am trying to avoid the long step of equilibrium as I have many systems 
corresponding to different concentrations. I was thinking if I replace a small 
number of molecule A with molecule B (the system A is very large and 
pre-equilibriumed) then I only need to apply a short time-step of NPT in order 
to let the system expand or shrink. Then I can use the new system to continue 
replacing A with B to generate a new concentration. Is this practical?

The problem is when B is slightly larger than A, I can?t insert the same number 
of B into the system. Is there way to avoid the overlapping or force the 
molecule in?

You can reduce the vdW radius of atoms to *try* to force the molecules to fit,
but then all you've done is introduce bad clashes that have to be subjected to
minimization and re-equilibration.  So at that point, all you've done is build
your system in the most inefficient way possible.  By trying to avoid
equilibration, you've necessitated it :)

Build the system the robust way - solute first, then solvent.  It's ultimately
less work and less prone to failure.

-Justin

--



Thank you Justin.

In the way solute first then solvent, I will still need to fully re-equilbrium 
the system, is that right? My problem is that I have about a hundred of 
systems, each of them will have about half a million atoms. The full 
equilibrium will be too time consuming. Since each systems are only slightly 
different in concentration (by replacing molecule A with molecule B), I am 
wondering if there will be a easier way to do a quick/roughly equilibrium.


Again, please don't reply to the entire digest.

Neither approach avoids having re-equilibrate the system.  Your approach of 
inserting B into an existing box of A perturbs the system and requires a new 
equilibration.  This is especially true if you play tricks like messing with vdW 
radii to force B into small voids in A.  You need to minimize and equilibrate, 
because these are new systems.


My approach is less prone to failure and ultimately I would expect it to take 
less time overall because you will not have instances in which the insertion of 
B into A fails and requires you to revisit those systems, change seeds, hack vdW 
radii, and potentially deal with problematic minimizations.


-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] Remove all but N closest water molecules from protein

[Mark Abraham]

Hi,

No. gmx select will write index groups that could implement a dynamic
selection, but trjconv can't do anything sensible with it. You'd have to
split the trajectory into a file per frame and match the index group to the
file to get the selection into a new file. Even if trjconv was smart
enough, you'd also need to use a trajectory format and downstream tools
that were about to be flexible about the number of atoms (which is
typically not the case)... In principle, our TNG format is able to be
flexible, but there's a lot of infrastructure work if people would actually
write such files and expect to read them and have everything work well.
Better to work on tools that can use the dynamic selection without needing
to serialize and de-serialize files (and the new GROMACS analysis framework
has such support, but we don't have much funding for implementing / porting
tools to it).

Mark

On Thu, Jun 8, 2017 at 10:48 AM João Henriques 
wrote:

> Hi Mark,
>
> Does your solution output variable numbers of water molecules per frame?
> That is exactly what I've been wanting to do for a while, but with my
> solution it becomes very difficult to do so and I usually end up using a
> fixed number of closest waters for all frames.
>
> João
>
>
>
> On Thu, Jun 8, 2017 at 10:34 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Or gmx select to make an index group for the nearest waters, and gmx
> > trjconv to make the subset with the index group.
> >
> > Mark
> >
> > On Thu, Jun 8, 2017 at 9:05 AM João Henriques <
> > joao.m.a.henriq...@gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > trjorder can reorder the water molecules in each frame according to
> their
> > > distance to the protein. Then you either manually prune the gro file(s)
> > or
> > > use an index file to get rid of the extra stuff. I don't know of any
> > native
> > > tool that does all of this in one step but I may be outdated regarding
> > new
> > > stuff on gmx 2016.
> > >
> > > Cheers,
> > > João
> > >
> > > On Jun 8, 2017 2:49 AM, "Jose Borreguero" 
> wrote:
> > >
> > > Dear Gromacs users,
> > >
> > > I'm a newbie with Gromacs. Is there a Gromacs native tool that will
> allow
> > > me to create a new *.gro file containing the protein and the N closest
> > > water molecules to the protein
> > > ​, starting from a system of a solvated protein​
> > > ?
> > >
> > > Best,
> > > Jose Borreguero
> > > --
> > > 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.
-- 
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] Reference point of position restraint

[Mark Abraham]

Hi,

Yes, the tpr position, but see grompp -h about the -r option.

Mark

On Thu, Jun 8, 2017 at 11:45 AM Simon Kit Sang Chu 
wrote:

> Hi,
>
> Just a short question. When I check GROMACS manual, it is stated that
> position restraint is applying a strong harmonic potential to the atom in
> reference to a reference point. However, should I assume the reference
> point is the position of the atom in the first frame?
>
> Thanks,
> Simon
> --
> 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] Reference point of position restraint

[Simon Kit Sang Chu]

Hi,

Just a short question. When I check GROMACS manual, it is stated that
position restraint is applying a strong harmonic potential to the atom in
reference to a reference point. However, should I assume the reference
point is the position of the atom in the first frame?

Thanks,
Simon
-- 
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] gromacs.org_gmx-users Digest, Vol 158, Issue 49

[ABEL Stephane]

Hello Xujun

>>Could someone give me some suggestion on choosing one typical type of bile 
>>salts for the study? Which force field is better?
You will to read first some biological/physiological textbooks. Moreover, bile 
salts are complex molecules and probably difficult to model. so I would suggest 
to read also literature and see what types of bile salt were already 
simulated/studied and thus choose the the force field accordingly. 

HTH

Stéphane from Paris ;)

--

Message: 1
Date: Thu, 8 Jun 2017 14:26:26 +0800
From: "=?ISO-8859-1?B?bHhqMjU4Ng==?=" 
To: "=?ISO-8859-1?B?Z3JvbWFjcy5vcmdfZ214LXVzZXJz?="

Subject: [gmx-users] Enquiry about simulating the aggregation behavior
of  bile salts in GROMACS
Message-ID: 
Content-Type: text/plain;   charset="ISO-8859-1"

Dear users,


I am planing to simulate how small organic molecules (i.e. pyrene and 
phenanthrene) bind to bile salts in the gut using GROMACS. However, there are 
diverse groups of bile salts in the intestinal systems. Could someone give me 
some suggestion on choosing one typical type of bile salts for the study? Which 
force field is better?


Many thanks for your time and help!


Sincerely yours,


Xujun Liang


--
Xujun LIANG, PhD
 School of Environment and Energy
South China University of Technology
Guangzhou, 510006
Guangdong Province
China


 Best wishes to you!!
-- 
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] Remove all but N closest water molecules from protein

[João Henriques]

Hi Mark,

Does your solution output variable numbers of water molecules per frame?
That is exactly what I've been wanting to do for a while, but with my
solution it becomes very difficult to do so and I usually end up using a
fixed number of closest waters for all frames.

João



On Thu, Jun 8, 2017 at 10:34 AM, Mark Abraham 
wrote:

> Hi,
>
> Or gmx select to make an index group for the nearest waters, and gmx
> trjconv to make the subset with the index group.
>
> Mark
>
> On Thu, Jun 8, 2017 at 9:05 AM João Henriques <
> joao.m.a.henriq...@gmail.com>
> wrote:
>
> > Hi,
> >
> > trjorder can reorder the water molecules in each frame according to their
> > distance to the protein. Then you either manually prune the gro file(s)
> or
> > use an index file to get rid of the extra stuff. I don't know of any
> native
> > tool that does all of this in one step but I may be outdated regarding
> new
> > stuff on gmx 2016.
> >
> > Cheers,
> > João
> >
> > On Jun 8, 2017 2:49 AM, "Jose Borreguero"  wrote:
> >
> > Dear Gromacs users,
> >
> > I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow
> > me to create a new *.gro file containing the protein and the N closest
> > water molecules to the protein
> > ​, starting from a system of a solvated protein​
> > ?
> >
> > Best,
> > Jose Borreguero
> > --
> > 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] Lennard Jones and Buckingham potential together in one simulation

[Narjes Khosravian]

Is there any guideline for that?


My exact question is about topology file for  using tabulated potential.  What 
should be the statement
mentioning nbfunc ( and combination-rule) in .top file when I wanted to have 
both potential (LJ and BKS)?

Best,

Narjes


 Narjes Khosravian
 Postdoc Researcher
 Department of Physics, Materials and Surface Theory
 Chalmers University of Technology
 SE-412 96 Göteborg, Sweden



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

Sent: Thursday, June 8, 2017 10:38:01 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Lennard Jones and Buckingham potential together in one 
simulation

Hi,

Isn't this covered in those PDFs?

Mark

On Thu, Jun 8, 2017 at 10:34 AM Narjes Khosravian <
narjes.khosrav...@chalmers.se> wrote:

> Hi Mark,
>
> Thanks for your reply!
>
> Actually I am using tabulated-potential based on the bellow manual by
> Gareth Tribello.
> 
>
> 
> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
>
> My problem is that:
>
> Since I have LJ and buckingham both, what should be the statement
> mentioning nbfunc ( and combination-rule) in .top file? e.g. nbfunc=1
> followed by LJ parameters  C and A for the concerned pairs and
>
> then nbfunc=2 (and whatever combination rule) , followed by buckingham
> parameters C, A , B for concerned pairs in the .top file?
>
> I greatly appreciate for any help in this matter.
> Best,
> Narjes
>
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Thursday, May 4, 2017 3:49:26 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Lennard Jones and Buckingham potential together
> in one simulation
>
> Hi,
>
> This procedure is usually motivated by trying to mix force fields that were
> never intended to be used together, and thus need to be shown work well
> together. In that case, you may as well parameterize a consistent model.
>
> Technically, you might be able to get this to work, but each atom in
> GROMACS can have only one set of VDW parameters, so you need to make the
> same parameters work with both functional forms, and this either impossible
> or tricky. The best bet is using tabulated interactions. Don't try to set
> up your intended target simulation in your first attempt - make something
> simple that lets you prove to yourself you have the interactions working
> the way that you think they should, then add complexity.
>
> Mark
>
> On Wed, May 3, 2017 at 8:41 PM Narjes Khosravian <
> narjes.khosrav...@chalmers.se> wrote:
>
> > Dear gromacs users,
> >
> >
> > I am trying to  use Lennard Jones and Buckingham potential  together in
> > one simulation as part of my system is treated by LJ and rest by Buck
> > potential.
> >
> >
> > My question is that how I can include Lennard Jones parameters in
> topology
> > file while my [defaults ] was chosen 2  1 to consider Buckingham
> parameter?
> >
> > I have created table for buck and LJ.
> >
> >
> > I greatly appreciate for any guide in this matter.
> >
> > Narjes
> >
> >
> >  Narjes Khosravian
> >  Postdoc Researcher
> >  Department of Physics, Materials and Surface Theory
> >  Chalmers University of Technology
> >  SE-412 96 Göteborg, Sweden
> >
> > --
> > 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

Re: [gmx-users] Lennard Jones and Buckingham potential together in one simulation

[Mark Abraham]

Hi,

Isn't this covered in those PDFs?

Mark

On Thu, Jun 8, 2017 at 10:34 AM Narjes Khosravian <
narjes.khosrav...@chalmers.se> wrote:

> Hi Mark,
>
> Thanks for your reply!
>
> Actually I am using tabulated-potential based on the bellow manual by
> Gareth Tribello.
> 
>
> 
> http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf
>
> My problem is that:
>
> Since I have LJ and buckingham both, what should be the statement
> mentioning nbfunc ( and combination-rule) in .top file? e.g. nbfunc=1
> followed by LJ parameters  C and A for the concerned pairs and
>
> then nbfunc=2 (and whatever combination rule) , followed by buckingham
> parameters C, A , B for concerned pairs in the .top file?
>
> I greatly appreciate for any help in this matter.
> Best,
> Narjes
>
>
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: Thursday, May 4, 2017 3:49:26 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Lennard Jones and Buckingham potential together
> in one simulation
>
> Hi,
>
> This procedure is usually motivated by trying to mix force fields that were
> never intended to be used together, and thus need to be shown work well
> together. In that case, you may as well parameterize a consistent model.
>
> Technically, you might be able to get this to work, but each atom in
> GROMACS can have only one set of VDW parameters, so you need to make the
> same parameters work with both functional forms, and this either impossible
> or tricky. The best bet is using tabulated interactions. Don't try to set
> up your intended target simulation in your first attempt - make something
> simple that lets you prove to yourself you have the interactions working
> the way that you think they should, then add complexity.
>
> Mark
>
> On Wed, May 3, 2017 at 8:41 PM Narjes Khosravian <
> narjes.khosrav...@chalmers.se> wrote:
>
> > Dear gromacs users,
> >
> >
> > I am trying to  use Lennard Jones and Buckingham potential  together in
> > one simulation as part of my system is treated by LJ and rest by Buck
> > potential.
> >
> >
> > My question is that how I can include Lennard Jones parameters in
> topology
> > file while my [defaults ] was chosen 2  1 to consider Buckingham
> parameter?
> >
> > I have created table for buck and LJ.
> >
> >
> > I greatly appreciate for any guide in this matter.
> >
> > Narjes
> >
> >
> >  Narjes Khosravian
> >  Postdoc Researcher
> >  Department of Physics, Materials and Surface Theory
> >  Chalmers University of Technology
> >  SE-412 96 Göteborg, Sweden
> >
> > --
> > 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] Remove all but N closest water molecules from protein

[Mark Abraham]

Hi,

Or gmx select to make an index group for the nearest waters, and gmx
trjconv to make the subset with the index group.

Mark

On Thu, Jun 8, 2017 at 9:05 AM João Henriques 
wrote:

> Hi,
>
> trjorder can reorder the water molecules in each frame according to their
> distance to the protein. Then you either manually prune the gro file(s) or
> use an index file to get rid of the extra stuff. I don't know of any native
> tool that does all of this in one step but I may be outdated regarding new
> stuff on gmx 2016.
>
> Cheers,
> João
>
> On Jun 8, 2017 2:49 AM, "Jose Borreguero"  wrote:
>
> Dear Gromacs users,
>
> I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow
> me to create a new *.gro file containing the protein and the N closest
> water molecules to the protein
> ​, starting from a system of a solvated protein​
> ?
>
> Best,
> Jose Borreguero
> --
> 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] GMX GPU Rest Time

[Mark Abraham]

Hi,

On Thu, Jun 8, 2017 at 8:55 AM Daniel Kozuch  wrote:

> Hello,
>
> I recently changed the number of cpus I was pairing with each gpu and I
> noticed a significant slowdown, more than I would have expected simply due
> to a reduction in the number of cpus.
>
> From the log file it appears that the GPU is resting for a large amount of
> time. Is there something I can do about this?
>

That's not just the GPUs resting, clearly many are stalled waiting for
exchange attempt synchronization.

I have attached parts of the log file. For reference this is a REMD
> simulation with 60 replicas on 360 cpus and 60 gpus.


The run reports 15 nodes and 24 GPUs and 28 cores per node, so mapping your
simulation system to your hardware is the first thing to focus on. All the
replicas progress only at the rate of the slowest replica, so at least some
of them are sharing GPUs, so the ones that finish first sit waiting for the
other ones

If e.g. this cluster has 4 GPUs and 28 cores per node, then you want to
place 4 replicas per node, e.g. 1 MPI rank per replica with 7 OpenMP
threads per core. See https://arxiv.org/abs/1507.00898 for further clues.

GROMACS 2016 does slightly improve the implementation of coupling of the
simulations in replica exchange, but you need to address all the above
issues first.

Mark

I have set the local
> variable OMP_NUM_THREADS to six in order to assign 6 cpus to each replica
> and avoid domain decomposition for my small system (as recommend in an
> earlier correspondence).
>
> Any help is appreciated,
> Dan
>
>
> -
>
> GROMACS:  gmx mdrun, VERSION 5.1.4
> Executable:   /home/dkozuch/programs/gromacs_514_gpu/bin/gmx_514_gpu
> Data prefix:  /home/dkozuch/programs/gromacs_514_gpu
> Command line:
>   gmx_514_gpu mdrun -v -deffnm 1msi_eq -multidir 1 2 3 4 5 6 7 8 9 10 11 12
> 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37
> 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 -pin
> on
>
> GROMACS version:VERSION 5.1.4
> Precision:  single
> Memory model:   64 bit
> MPI library:MPI
> OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
> GPU support:enabled
> OpenCL support: disabled
> invsqrt routine:gmx_software_invsqrt(x)
> SIMD instructions:  AVX2_256
> FFT library:fftw-3.3.4-sse2-avx
> RDTSCP usage:   enabled
> C++11 compilation:  disabled
> TNG support:enabled
> Tracing support:disabled
> Built on:   Mon May 22 18:29:21 EDT 2017
> Built by:   dkoz...@tigergpu.princeton.edu [CMAKE]
> Build OS/arch:  Linux 3.10.0-514.16.1.el7.x86_64 x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
> Build CPU family:   6   Model: 79   Stepping: 1
> Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
> lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
> rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> C compiler: /usr/bin/cc GNU 4.8.5
> C compiler flags:-march=core-avx2-Wextra
> -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall
> -Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG
> -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
> C++ compiler:   /usr/bin/c++ GNU 4.8.5
> C++ compiler flags:  -march=core-avx2-Wextra
> -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function
>  -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
> Boost version:  1.53.0 (external)
> CUDA compiler:  /usr/local/cuda-8.0/bin/nvcc nvcc: NVIDIA (R) Cuda
> compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on
> Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44
> CUDA compiler
>
> flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;;
>
> ;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
> CUDA driver:8.0
> CUDA runtime:   8.0
>
>
> Number of logical cores detected (28) does not match the number reported by
> OpenMP (6).
> Consider setting the launch configuration manually!
>
> Running on 15 nodes with total 420 cores, 420 logical cores, 24 compatible
> GPUs
>   Cores per node:   28
>   Logical cores per node:   28
>   Compatible GPUs per node:  0 -  4
>   Different nodes have different type(s) and/or order of GPUs
> Hardware 

Re: [gmx-users] Gromacs

[saranya]

I have simulated the protein in water and protein with ligand for 100ns by
using GPU and the edr file was generated using -rerun command on
another system.I have just checked the pressure of my system by using
gmx energy
command, then i have selected pressure (group), but the calculated pressure
is quite altered (20,000 pressure bar). Moreover, when I calculated the
temperature of my system, the result was zero.
I have used below mdp file for the calculation
title   = Protein-ligand complex NPT equilibration
define  = -DPOSRES_LIG  ; position restrain the protein and ligand
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 5 ; 2 * 5 = 100 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 100 ps
nstvout = 100   ; save velocities every 100 ps
nstenergy   = 100   ; save energies every 100 ps
nstlog  = 100   ; update log file every 100 ps
energygrps  = Protein
; Bond parameters
continuation= yes   ; 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 ; 10 fs
rlist   = 0.9   ; short-range neighborlist 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_EPI 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  = Parrinello-Rahman ; pressure coupling is on for
NPT
pcoupltype  = isotropic ; uniform scaling of box vectors
tau_p   = 2.0   ; 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
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no; velocity generation off after NVT

*With Regards,*

*Saranya Vasudevan,*

*Research Scholar,*

*Molecular Quantum Mechanics Laboratory,*

*Department of Physics,*

*Bharathiar University,*
*Coimbatore-46*
-- 
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] Remove all but N closest water molecules from protein

[João Henriques]

Hi,

trjorder can reorder the water molecules in each frame according to their
distance to the protein. Then you either manually prune the gro file(s) or
use an index file to get rid of the extra stuff. I don't know of any native
tool that does all of this in one step but I may be outdated regarding new
stuff on gmx 2016.

Cheers,
João

On Jun 8, 2017 2:49 AM, "Jose Borreguero"  wrote:

Dear Gromacs users,

I'm a newbie with Gromacs. Is there a Gromacs native tool that will allow
me to create a new *.gro file containing the protein and the N closest
water molecules to the protein
​, starting from a system of a solvated protein​
?

Best,
Jose Borreguero
--
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] Calculating the radius of gyration of clusters

[GAYATHRI S]

Dear all,

I ran MD simulations of a small molecule and clustered structurally
similar frames together. I wanted to find the radius of gyration of all
the members of each cluster.

To do the same, I used the command:

$ g_gyrate -f cluster.xtc -s full.tpr -o cluster_rg.xvg

Here, the file "cluster.xtc" was obtained as output from the g_cluster
command.

When I ran the above command, I got the following error multiple times:

There were 10 inconsistent shifts. Check your topology.

Is there a better way of finding the radius of gyration of all the cluster
members in a given cluster? Please suggest how I should go about.

Thank you

Regards,
Gayathri



-- 
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] GMX GPU Rest Time

[Daniel Kozuch]

Hello,

I recently changed the number of cpus I was pairing with each gpu and I
noticed a significant slowdown, more than I would have expected simply due
to a reduction in the number of cpus.

>From the log file it appears that the GPU is resting for a large amount of
time. Is there something I can do about this?

I have attached parts of the log file. For reference this is a REMD
simulation with 60 replicas on 360 cpus and 60 gpus. I have set the local
variable OMP_NUM_THREADS to six in order to assign 6 cpus to each replica
and avoid domain decomposition for my small system (as recommend in an
earlier correspondence).

Any help is appreciated,
Dan

-

GROMACS:  gmx mdrun, VERSION 5.1.4
Executable:   /home/dkozuch/programs/gromacs_514_gpu/bin/gmx_514_gpu
Data prefix:  /home/dkozuch/programs/gromacs_514_gpu
Command line:
  gmx_514_gpu mdrun -v -deffnm 1msi_eq -multidir 1 2 3 4 5 6 7 8 9 10 11 12
13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37
38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 -pin on

GROMACS version:VERSION 5.1.4
Precision:  single
Memory model:   64 bit
MPI library:MPI
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support:enabled
OpenCL support: disabled
invsqrt routine:gmx_software_invsqrt(x)
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.4-sse2-avx
RDTSCP usage:   enabled
C++11 compilation:  disabled
TNG support:enabled
Tracing support:disabled
Built on:   Mon May 22 18:29:21 EDT 2017
Built by:   dkoz...@tigergpu.princeton.edu [CMAKE]
Build OS/arch:  Linux 3.10.0-514.16.1.el7.x86_64 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
Build CPU family:   6   Model: 79   Stepping: 1
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 4.8.5
C compiler flags:-march=core-avx2-Wextra
-Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall
-Wno-unused -Wunused-value -Wunused-parameter  -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
C++ compiler:   /usr/bin/c++ GNU 4.8.5
C++ compiler flags:  -march=core-avx2-Wextra
-Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function
 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast  -Wno-array-bounds
Boost version:  1.53.0 (external)
CUDA compiler:  /usr/local/cuda-8.0/bin/nvcc nvcc: NVIDIA (R) Cuda
compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on
Sun_Sep__4_22:14:01_CDT_2016;Cuda compilation tools, release 8.0, V8.0.44
CUDA compiler
flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;;
;-march=core-avx2;-Wextra;-Wno-missing-field-initializers;-Wpointer-arith;-Wall;-Wno-unused-function;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast;-Wno-array-bounds;
CUDA driver:8.0
CUDA runtime:   8.0


Number of logical cores detected (28) does not match the number reported by
OpenMP (6).
Consider setting the launch configuration manually!

Running on 15 nodes with total 420 cores, 420 logical cores, 24 compatible
GPUs
  Cores per node:   28
  Logical cores per node:   28
  Compatible GPUs per node:  0 -  4
  Different nodes have different type(s) and/or order of GPUs
Hardware detected on host tiger-i20g2 (the node of MPI rank 4):
  CPU info:
Vendor: GenuineIntel
Brand:  Intel(R) Xeon(R) CPU E5-2680 v4 @ 2.40GHz
Family:  6  model: 79  stepping:  1
CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt
lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX2_256
  GPU info:
Number of GPUs detected: 4
#0: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat:
compatible
#1: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat:
compatible
#2: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat:
compatible
#3: NVIDIA Tesla P100-PCIE-16GB, compute cap.: 6.0, ECC: yes, stat:
compatible

This is simulation 4 out of 60 running as a composite GROMACS
multi-simulation job. Setup for this simulation:

Using 1 MPI process
Using 6 OpenMP threads

4 compatible 

[gmx-users] Enquiry about simulating the aggregation behavior of bile salts in GROMACS

[lxj2586]

Dear users,


I am planing to simulate how small organic molecules (i.e. pyrene and 
phenanthrene) bind to bile salts in the gut using GROMACS. However, there are 
diverse groups of bile salts in the intestinal systems. Could someone give me 
some suggestion on choosing one typical type of bile salts for the study? Which 
force field is better?


Many thanks for your time and help!


Sincerely yours,


Xujun Liang


--
Xujun LIANG, PhD
 School of Environment and Energy
South China University of Technology
Guangzhou, 510006
Guangdong Province
China
 

 Best wishes to you!!
-- 
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.