Re: [gmx-users] gmx insert-molecules question

[Mala L Radhakrishnan]

Thanks!  (and sorry about all the typos in my original email -- just
re-read it and saw it was barely intelligible!)

M

On Thu, Jul 25, 2019 at 4:25 PM Justin Lemkul  wrote:

>
>
> On 7/25/19 4:11 PM, Mala L Radhakrishnan wrote:
> > Hi,
> >
> > I am trying to crod snapshots with multiple copies of a molecule.  When I
> > run gmx insert-molecules and I have a box of a certain size, does it make
> > sure that there is no overlap of molecules even considering pbc?  What I
> > mean by this is if I do a trjconv on the resulting  crowded snapshot,
> using
> > -pbc atom, will any of the atoms/molecules overlap?  Or maybe another way
> > of saying it is, if a molecule, when places, falls partially outside the
> > box does it ensure that another molecule wouldn't overlap with the
> periodic
> > image of that first molecule?
>
> Yes, the insert-molecules code uses PBC in its neighbor searching.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==
>
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-- 
Mala L. Radhakrishnan
Associate Professor of Chemistry
Director, Biochemistry Program
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981
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Re: [gmx-users] gmx insert-molecules question

[Justin Lemkul]

On 7/25/19 4:11 PM, Mala L Radhakrishnan wrote:

Hi,

I am trying to crod snapshots with multiple copies of a molecule.  When I
run gmx insert-molecules and I have a box of a certain size, does it make
sure that there is no overlap of molecules even considering pbc?  What I
mean by this is if I do a trjconv on the resulting  crowded snapshot, using
-pbc atom, will any of the atoms/molecules overlap?  Or maybe another way
of saying it is, if a molecule, when places, falls partially outside the
box does it ensure that another molecule wouldn't overlap with the periodic
image of that first molecule?


Yes, the insert-molecules code uses PBC in its neighbor searching.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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[gmx-users] gmx insert-molecules question

[Mala L Radhakrishnan]

Hi,

I am trying to crod snapshots with multiple copies of a molecule.  When I
run gmx insert-molecules and I have a box of a certain size, does it make
sure that there is no overlap of molecules even considering pbc?  What I
mean by this is if I do a trjconv on the resulting  crowded snapshot, using
-pbc atom, will any of the atoms/molecules overlap?  Or maybe another way
of saying it is, if a molecule, when places, falls partially outside the
box does it ensure that another molecule wouldn't overlap with the periodic
image of that first molecule?

Hope this question makes sense -- thanks!

Mala

-- 
Mala L. Radhakrishnan
Associate Professor of Chemistry
Director, Biochemistry Program
Wellesley College
106 Central Street
Wellesley, MA 02481
(781)283-2981
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Re: [gmx-users] gmx insert-molecules not inserting molecules

[Justin Lemkul]

On 9/13/17 5:54 AM, Souparno Adhikary wrote:

We tried to simulate a small molecule using GROMACS. We generated the
topology file and the GROMACS coordinate file using the PRODRG server. We
optimized the molecule prior to generating topology using GAUSSIAN 09.


Don't use PRODRG unless you reparametrize the charges and charge 
groups.  It is well known that the topologies from PRODRG are well below 
the necessary accuracy for an MD simulation.



However, we tried to study the interaction between multiple copies of the
same molecule in a water box. We generated the PBC and water box
successfully and then we went on to using gmx insert-molecules to insert
multiple copies of the molecule in the waterbox. It yielded the following
output:

Reading solute configuration
PRODRG COORDS
Containing 33766 atoms in 11201 residues


You appear to be trying to insert molecules into an already solvated 
system.  There will not be sufficient void space in such a system to add 
anything, so you get zero insertions.  Add your small molecules before 
adding water.


-Justin


Reading molecule configuration
PRODRG COORDS
Containing 166 atoms in 1 residues
Initialising inter-atomic distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
  based on residue and atom names, since they could not be
  definitively assigned from the information in your input
  files. These guessed numbers might deviate from the mass
  and radius of the atom type. Please check the output
  files if necessary.

NOTE: From version 5.0 gmx uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
  --- Thank You ---  

Try 40
Added 0 molecules (out of 4 requested)
Writing generated configuration to g1new.gro

Output configuration contains 33766 atoms in 11201 residues


What could be the possible problem??? We used the gmx insert-molecules as:

gmx insert-molecules -f mol1wt.gro -ci mol1_op.gro -o mol1new.gro -nmol 4

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.


--
==

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

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

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

==

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[gmx-users] gmx insert-molecules not inserting molecules

[Souparno Adhikary]

We tried to simulate a small molecule using GROMACS. We generated the
topology file and the GROMACS coordinate file using the PRODRG server. We
optimized the molecule prior to generating topology using GAUSSIAN 09.

However, we tried to study the interaction between multiple copies of the
same molecule in a water box. We generated the PBC and water box
successfully and then we went on to using gmx insert-molecules to insert
multiple copies of the molecule in the waterbox. It yielded the following
output:

Reading solute configuration
PRODRG COORDS
Containing 33766 atoms in 11201 residues
Reading molecule configuration
PRODRG COORDS
Containing 166 atoms in 1 residues
Initialising inter-atomic distances...

WARNING: Masses and atomic (Van der Waals) radii will be guessed
 based on residue and atom names, since they could not be
 definitively assigned from the information in your input
 files. These guessed numbers might deviate from the mass
 and radius of the atom type. Please check the output
 files if necessary.

NOTE: From version 5.0 gmx uses the Van der Waals radii
from the source below. This means the results may be different
compared to previous GROMACS versions.

 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
A. Bondi
van der Waals Volumes and Radii
J. Phys. Chem. 68 (1964) pp. 441-451
  --- Thank You ---  

Try 40
Added 0 molecules (out of 4 requested)
Writing generated configuration to g1new.gro

Output configuration contains 33766 atoms in 11201 residues


What could be the possible problem??? We used the gmx insert-molecules as:

gmx insert-molecules -f mol1wt.gro -ci mol1_op.gro -o mol1new.gro -nmol 4

Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
University of Calcutta.
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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

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

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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

==
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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



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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

==
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Re: [gmx-users] gmx insert-molecules

[Shi Li]

> 在 2017年6月7日，16:26，gromacs.org_gmx-users-requ...@maillist.sys.kth.se 写道：
> 
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>   1. Cylinder pulling through bilayer (Gmx QA)
>   2. Re: gmx insert-molecules (Justin Lemkul)
>   3. deltaG shifts in g_wham (Alex)
>   4. Re: deltaG shifts in g_wham (Justin Lemkul)
>   5. problem with "gmx rdf": It cannot find the center of mass of
>  a reference group (Sajjad Kavyani)
>   6. problem with "gmx rdf": It cannot find the center of mass of
>  a reference group (Sajjad Kavyani)
> 
> 
> --
> 
> Message: 1
> Date: Wed, 7 Jun 2017 21:22:04 +0200
> From: Gmx QA <gmxquesti...@gmail.com>
> To: Discussion list for GROMACS users <gmx-us...@gromacs.org>
> Subject: [gmx-users] Cylinder pulling through bilayer
> Message-ID:
>   <canftednr4vnomgpbytdbpvu3bzwreyb6_glcpa3jodg_kag...@mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
> 
> 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
> 
> 
> --
> 
> Message: 2
> Date: Wed, 7 Jun 2017 16:07:54 -0400
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] gmx insert-molecules
> Message-ID: <72ae4ffd-7c78-05ec-fb7f-5784e8e6b...@vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> 
> Please do not reply to the whole digest.
> 
> On 6/7/17 2:46 PM, Shi Li wrote:
>>> 
>>> On 6/7/17 1:20 PM, Li, Shi wrote:
>>>> Dear GMX users,
>>>> 
>>>> I have a pure solvent system A with 100 molecules. Then I randomly removed
>>>> 10 molecules out of the box, but keep the box size. Now I want to do a gmx
>>>> insert-molecule to insert 10 molecule B into the system box. The problem is
>>>> molecule B is slightly larger than molecule A. So in some cases, I couldn't
>>>> insert the exact 10 molecules of B into the system. Is there a way to
>>>> automatically adjust the size of the box according to the radius of
>>>> molecule B, so that they can fit in? Or, is there a better solution to do
>>>> this?
>>>> 
>>> 
>>> Insert 10 of molecule B into an empty box, t

Re: [gmx-users] gmx insert-molecules

[Justin Lemkul]

Please do not reply to the whole digest.

On 6/7/17 2:46 PM, Shi Li wrote:


On 6/7/17 1:20 PM, Li, Shi wrote:

Dear GMX users,

I have a pure solvent system A with 100 molecules. Then I randomly removed
10 molecules out of the box, but keep the box size. Now I want to do a gmx
insert-molecule to insert 10 molecule B into the system box. The problem is
molecule B is slightly larger than molecule A. So in some cases, I couldn't
insert the exact 10 molecules of B into the system. Is there a way to
automatically adjust the size of the box according to the radius of
molecule B, so that they can fit in? Or, is there a better solution to do
this?



Insert 10 of molecule B into an empty box, then solvate with a pre-equilibrated
box of molecule A.  Works every time.

-Justin


Thank you Justin,

In this case, I will need to apply a full equilibrium process (em, nvt, npt) to 
the new system, is that right?

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

--
==

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

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

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

==
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Re: [gmx-users] gmx insert-molecules

[Shi Li]

> 在 2017年6月7日，13:31，gromacs.org_gmx-users-requ...@maillist.sys.kth.se 写道：
> 
> Send gromacs.org_gmx-users mailing list submissions to
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> or, via email, send a message with subject or body 'help' to
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
> 
> 
> Today's Topics:
> 
>   1. Re: Simulate protein at subzero condition in aqueous buffer
>  (=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=)
>   2. Re: Simulate protein at subzero condition in aqueous buffer
>  (Jo?o Henriques)
>   3. gmx insert-molecules (Li, Shi)
>   4. Re: gmx insert-molecules (Justin Lemkul)
>   5. Re: Simulate protein at subzero condition in aqueous buffer
>  (Jo?o Henriques)
> 
> 
> --
> 
> Message: 1
> Date: Thu, 8 Jun 2017 01:07:40 +0800
> From: "=?ISO-8859-1?B?WkhBTkcgQ2hlbmc=?=" <272699...@qq.com>
> To: "=?ISO-8859-1?B?Z3JvbWFjcy5vcmdfZ214LXVzZXJz?="
>   
> Subject: Re: [gmx-users] Simulate protein at subzero condition in
>   aqueous buffer
> Message-ID: 
> Content-Type: text/plain; charset="ISO-8859-1"
> 
> Dear Justin,
> Thank you very much. I will try the possible water models.
> 
> 
> Do you know if there are water models to resemble frozen state?
> 
> 
> Yours sincerely
> Cheng
> 
> 
> 
> 
> -- Original --
> From:  "ZHANG Cheng";<272699...@qq.com>;
> Date:  Thu, Jun 8, 2017 00:50 AM
> To:  "ZHANG Cheng"<272699...@qq.com>; 
> "gromacs.org_gmx-users"; 
> 
> Subject:  Re: Simulate protein at subzero condition in aqueous buffer
> 
> 
> 
> Dear Joao,
> Thank you for your help and the paper link.
> 
> 
> I was following Justin's tutorial
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html
> On that page, it says "spc216.gro as the solvent configuration for SPC, 
> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) 
> after the solvation step. So I assume "spc216.gro" refer to all the 
> three-point water models?
> 
> 
> I am trying to see if my protein will be denatured in cold condition. 
> 
> 
> Yours sincerely
> Cheng
> 
> 
> -- Original --
> From:  "ZHANG Cheng";<272699...@qq.com>;
> Date:  Wed, Jun 7, 2017 10:01 PM
> To:  "gromacs.org_gmx-users"; 
> Cc:  "ZHANG Cheng"<272699...@qq.com>; 
> Subject:  Simulate protein at subzero condition in aqueous buffer
> 
> 
> 
> Dear Gromacs,
> I would like to simulate the protein at subzero condition in aqueous buffer, 
> to see if it becomes more stable than the elevated temperature (e.g. 65 C). 
> Can I ask what is the valid temperature range for water "spc216.gro" ? If I 
> run the simulation at -40 C, does it still assume the system as liquid state 
> instead of frozen state? Thank you.
> 
> 
> Yours sincerely
> Cheng
> 
> --
> 
> Message: 2
> Date: Wed, 7 Jun 2017 19:15:58 +0200
> From: Jo?o Henriques 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Simulate protein at subzero condition in
>   aqueous buffer
> Message-ID:
>   

Re: [gmx-users] gmx insert-molecules

[Justin Lemkul]

On 6/7/17 1:20 PM, Li, Shi wrote:

Dear GMX users,

I have a pure solvent system A with 100 molecules. Then I randomly removed
10 molecules out of the box, but keep the box size. Now I want to do a gmx
insert-molecule to insert 10 molecule B into the system box. The problem is
molecule B is slightly larger than molecule A. So in some cases, I couldn't
insert the exact 10 molecules of B into the system. Is there a way to
automatically adjust the size of the box according to the radius of
molecule B, so that they can fit in? Or, is there a better solution to do
this?



Insert 10 of molecule B into an empty box, then solvate with a pre-equilibrated 
box of molecule A.  Works every time.


-Justin

--
==

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

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

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

==
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[gmx-users] gmx insert-molecules

[Li, Shi]

Dear GMX users,

I have a pure solvent system A with 100 molecules. Then I randomly removed
10 molecules out of the box, but keep the box size. Now I want to do a gmx
insert-molecule to insert 10 molecule B into the system box. The problem is
molecule B is slightly larger than molecule A. So in some cases, I couldn't
insert the exact 10 molecules of B into the system. Is there a way to
automatically adjust the size of the box according to the radius of
molecule B, so that they can fit in? Or, is there a better solution to do
this?

Or, is there a way to ignore the overlapping of molecules? In that case,
even the inserted molecule is overlapping with surrounding molecules, it
can still be inserted in?

Many thanks,
Shi
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Re: [gmx-users] gmx insert-molecules - molecules "sticking out of the box"

[Mark Abraham]

Hi,

On Tue, Apr 4, 2017 at 10:02 AM Jernej Zidar  wrote:

> Hi,
>
> I am using 'gmx insert-molecules' to insert ten rather large polymer
> molecules into a 16x16x16 nm box. The problem is that the utility inserts
> the molecules randomly (which is good) in way that leaves the polymer
> molecules sticking outside the defined box and leaving lots of space empty.
>

As Magnus says, so long as the result honours the periodicity, which
representation is chosen is not of great importance (and readily changed
with trjconv).


> The manual lists a number of potential useful options under the switch
> "-selrpos" but the manual says nothing about what do the options do.
>

Ah, that could be improved. It likely relates to
http://manual.gromacs.org/documentation/2016/user-guide/cmdline.html#gmx-insert-molecules,
and because it is common to several tools, is documented at
http://manual.gromacs.org/documentation/2016/onlinehelp/selections.html#specifying-selections-from-command-line
.


> How to instruct 'gmx insert-molecules' to keep the inserted molecules
> whole?
>

It did that already, right? :-)

Mark


> Thanks,
> Jernej
> --
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Re: [gmx-users] gmx insert-molecules - molecules "sticking out of the box"

[Magnus Lundborg]

Hi,

Assuming that you are using a periodic box it shouldn't matter that the
molecules are placed crossing the edges - that just means the rest will be
on the opposing side of the box when you simulate. If you wish to visualize
the system you could experiment with the -pbc options of the trjconv tool.

Cheers,

Magnus

Den 4 apr. 2017 10:03 skrev "Jernej Zidar" :

> Hi,
>
> I am using 'gmx insert-molecules' to insert ten rather large polymer
> molecules into a 16x16x16 nm box. The problem is that the utility inserts
> the molecules randomly (which is good) in way that leaves the polymer
> molecules sticking outside the defined box and leaving lots of space empty.
>
> The manual lists a number of potential useful options under the switch
> "-selrpos" but the manual says nothing about what do the options do.
>
> How to instruct 'gmx insert-molecules' to keep the inserted molecules
> whole?
>
> Thanks,
> Jernej
> --
> Gromacs Users mailing list
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[gmx-users] gmx insert-molecules - molecules "sticking out of the box"

[Jernej Zidar]

Hi,

I am using 'gmx insert-molecules' to insert ten rather large polymer
molecules into a 16x16x16 nm box. The problem is that the utility inserts
the molecules randomly (which is good) in way that leaves the polymer
molecules sticking outside the defined box and leaving lots of space empty.

The manual lists a number of potential useful options under the switch
"-selrpos" but the manual says nothing about what do the options do.

How to instruct 'gmx insert-molecules' to keep the inserted molecules whole?

Thanks,
Jernej
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Re: [gmx-users] gmx insert-molecules not adding the required number of molecules

[Mark Abraham]

Hi,

Adding a big thing, then lots of small things randomly and then lots of
medium sized things randomly isn't going to work very well to give you
something approximately close-packed at the end. You're just not likely to
end up with exactly enough holes suitable for things of medium size. So
work from biggest to smallest. You may find you want to play with the radii
of urea atoms to get the right number to insert (into holes nominally too
small for them), and then very gentle equilibration to start off with.

Mark

On Wed, Nov 30, 2016 at 1:56 PM soumadwip ghosh 
wrote:

> Hi all,
>  I have recently been looking at the dynamics of protein in
> presence of urea+osmolyte. The protein I have taken is a chicken villin
> headpiece subdomain (HP-36). It is inside a cubic box of 141 nm3 volume. 8M
> urea corresponding to this box volume = 680 number of urea molecules and I
> want the osmolyte to be in half of its molarity. Thus, the required number
> of osmolyte is 340. Previously, I have worked with 1:5 molar ratio of
> urea:osmolyte and it proceeds without any difficulty. This time what I
> encounter is:
>
> 1. 680 number of urea molecules goes inside the protein box using gmx
> insert-molecules command without any difficulty.
>
> 2. When I call the same command for inserting my osmolyte (340 in number)
> it can only insert 220 molecules even with the -nmol x, -try x option.
>
> 3. If I try to insert a random number of osmolytes (say 500) it takes a
> long time for gmx insert-molecules before printing the execution has been
> 'killed' and it does not generate any output file.
>
> 4. If I try a bigger box, then the required number of species increases and
> I face the same problem with my osmolyte even though urea addition is
> successful.
>
> What is happening here? Is there a way to play around with the gmx
> insert-molecules/genbox command to obtain the desired number of molecules
> inside a box of known dimensions in which something already resides (in my
> case protein+8M urea). I shall be obliged if someone helps me out with this
>
> P.S: I am using GROMACS 5.0.4 in combination with OPLS-AA force field.
>
> Thnaks and regards,
> Soumadwip Ghosh
> Research Associate
> Indian Institute of Technology Bombay
> India
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[gmx-users] gmx insert-molecules not adding the required number of molecules

[soumadwip ghosh]

Hi all,
 I have recently been looking at the dynamics of protein in
presence of urea+osmolyte. The protein I have taken is a chicken villin
headpiece subdomain (HP-36). It is inside a cubic box of 141 nm3 volume. 8M
urea corresponding to this box volume = 680 number of urea molecules and I
want the osmolyte to be in half of its molarity. Thus, the required number
of osmolyte is 340. Previously, I have worked with 1:5 molar ratio of
urea:osmolyte and it proceeds without any difficulty. This time what I
encounter is:

1. 680 number of urea molecules goes inside the protein box using gmx
insert-molecules command without any difficulty.

2. When I call the same command for inserting my osmolyte (340 in number)
it can only insert 220 molecules even with the -nmol x, -try x option.

3. If I try to insert a random number of osmolytes (say 500) it takes a
long time for gmx insert-molecules before printing the execution has been
'killed' and it does not generate any output file.

4. If I try a bigger box, then the required number of species increases and
I face the same problem with my osmolyte even though urea addition is
successful.

What is happening here? Is there a way to play around with the gmx
insert-molecules/genbox command to obtain the desired number of molecules
inside a box of known dimensions in which something already resides (in my
case protein+8M urea). I shall be obliged if someone helps me out with this

P.S: I am using GROMACS 5.0.4 in combination with OPLS-AA force field.

Thnaks and regards,
Soumadwip Ghosh
Research Associate
Indian Institute of Technology Bombay
India
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Re: [gmx-users] gmx insert-molecules

[Dave Michael]

Thanks, Justin.
I followed "Energy minimization" in
http://md.chem.rug.nl/%7Emdcourse/md.html (pre-running with
http://md.chem.rug.nl/%7Emdcourse/minim.mdp) and it worked just fine.

Dave


On Mon, Jul 11, 2016 at 3:41 PM, Justin Lemkul  wrote:

>
>
> On 7/11/16 8:38 AM, Dave Michael wrote:
>
>> As I said, I've got limited experience in the chemical/physical aspects of
>> system/topology etc. and I just want some performance indexes
>>
>> Did I make a mistake in the insert-molecules?
>> The online documentation (
>> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>> )
>> suggests the energy minimization is the next step but I don't know how to
>> do it, can you guide me in the right direction?
>>
>>
> There are lots of GROMACS tutorials available (
> http://www.gromacs.org/Documentation/Tutorials) though CG systems tend to
> work a bit differently.  Since you're starting with MARTINI water systems,
> look into their tutorials (http://md.chem.rug.nl/index.php/tutorials)
> which should provide all the inputs and things you need.
>
> -Justin
>
> Dave
>>
>> On Mon, Jul 11, 2016 at 3:25 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 7/11/16 8:15 AM, Dave Michael wrote:
>>>
>>> Hi guys,

 I've got a system of 400 water molecules (
 http://md.chem.rug.nl/index.php/example-applications2/solvent-systems)
 and
 I want to make and simulate a system with 1k, 10k, 100k and 1M
 particles.

 So far, I've done:
 gmx insert-molecules -ci water.gro -o water.gro -box 4.59151 -nmol 400
 -radius 0.05
 (what I've tried doing is double the box volume and double the number of
 particles and it didn't work without -radius 0.05 / default radius
 doesn't
 add new molecules to the system)


>>> Probably because insert-molecules doesn't understand whatever the
>>> particle
>>> type is that it's being provided unless you tell it.  CG types are often
>>> not anything like normal atoms.
>>>
>>> And I got a file with 800 particles, some of them have negative
>>> coordinates
>>>
 (I presume those are initial coordinates) and no initial velocities.


 There are no velocities because insert-molecules doesn't serve that
>>> function, nor would any velocities be meaningful or useful in any way at
>>> this stage.
>>>
>>> Running (GROMACS 5.1.2) md on that file doesn't work as the simulation
>>>
 hangs @ step 0. Using gmx energy I can see that the total energy and
 temperature are off the scales but the density is fine (990 kg/m^3)


 This suggests something is topologically incorrect.  Have you done
>>> energy
>>> minimization?
>>>
>>> -Justin
>>>
>>> I don't have much experience in the chemical / physical aspects, can you
>>>
 please tell me (step by step if possible) what I missed and what should
 I
 do next?

 Dave


 --
>>> ==
>>>
>>> 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!
>>>
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>>>
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>>> 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
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> posting!
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Re: [gmx-users] gmx insert-molecules

[Justin Lemkul]

On 7/11/16 8:38 AM, Dave Michael wrote:

As I said, I've got limited experience in the chemical/physical aspects of
system/topology etc. and I just want some performance indexes

Did I make a mistake in the insert-molecules?
The online documentation (
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation)
suggests the energy minimization is the next step but I don't know how to
do it, can you guide me in the right direction?



There are lots of GROMACS tutorials available 
(http://www.gromacs.org/Documentation/Tutorials) though CG systems tend to work 
a bit differently.  Since you're starting with MARTINI water systems, look into 
their tutorials (http://md.chem.rug.nl/index.php/tutorials) which should provide 
all the inputs and things you need.


-Justin


Dave

On Mon, Jul 11, 2016 at 3:25 PM, Justin Lemkul  wrote:




On 7/11/16 8:15 AM, Dave Michael wrote:


Hi guys,

I've got a system of 400 water molecules (
http://md.chem.rug.nl/index.php/example-applications2/solvent-systems)
and
I want to make and simulate a system with 1k, 10k, 100k and 1M particles.

So far, I've done:
gmx insert-molecules -ci water.gro -o water.gro -box 4.59151 -nmol 400
-radius 0.05
(what I've tried doing is double the box volume and double the number of
particles and it didn't work without -radius 0.05 / default radius doesn't
add new molecules to the system)



Probably because insert-molecules doesn't understand whatever the particle
type is that it's being provided unless you tell it.  CG types are often
not anything like normal atoms.

And I got a file with 800 particles, some of them have negative coordinates

(I presume those are initial coordinates) and no initial velocities.



There are no velocities because insert-molecules doesn't serve that
function, nor would any velocities be meaningful or useful in any way at
this stage.

Running (GROMACS 5.1.2) md on that file doesn't work as the simulation

hangs @ step 0. Using gmx energy I can see that the total energy and
temperature are off the scales but the density is fine (990 kg/m^3)



This suggests something is topologically incorrect.  Have you done energy
minimization?

-Justin

I don't have much experience in the chemical / physical aspects, can you

please tell me (step by step if possible) what I missed and what should I
do next?

Dave



--
==

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

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

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

==
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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

==
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Re: [gmx-users] gmx insert-molecules

[Justin Lemkul]

On 7/11/16 8:15 AM, Dave Michael wrote:

Hi guys,

I've got a system of 400 water molecules (
http://md.chem.rug.nl/index.php/example-applications2/solvent-systems) and
I want to make and simulate a system with 1k, 10k, 100k and 1M particles.

So far, I've done:
gmx insert-molecules -ci water.gro -o water.gro -box 4.59151 -nmol 400
-radius 0.05
(what I've tried doing is double the box volume and double the number of
particles and it didn't work without -radius 0.05 / default radius doesn't
add new molecules to the system)


Probably because insert-molecules doesn't understand whatever the particle type 
is that it's being provided unless you tell it.  CG types are often not anything 
like normal atoms.



And I got a file with 800 particles, some of them have negative coordinates
(I presume those are initial coordinates) and no initial velocities.



There are no velocities because insert-molecules doesn't serve that function, 
nor would any velocities be meaningful or useful in any way at this stage.



Running (GROMACS 5.1.2) md on that file doesn't work as the simulation
hangs @ step 0. Using gmx energy I can see that the total energy and
temperature are off the scales but the density is fine (990 kg/m^3)



This suggests something is topologically incorrect.  Have you done energy 
minimization?


-Justin


I don't have much experience in the chemical / physical aspects, can you
please tell me (step by step if possible) what I missed and what should I
do next?

Dave



--
==

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

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

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

==
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Gromacs Users mailing list

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[gmx-users] gmx insert-molecules

[Dave Michael]

Hi guys,

I've got a system of 400 water molecules (
http://md.chem.rug.nl/index.php/example-applications2/solvent-systems) and
I want to make and simulate a system with 1k, 10k, 100k and 1M particles.

So far, I've done:
gmx insert-molecules -ci water.gro -o water.gro -box 4.59151 -nmol 400
-radius 0.05
(what I've tried doing is double the box volume and double the number of
particles and it didn't work without -radius 0.05 / default radius doesn't
add new molecules to the system)
And I got a file with 800 particles, some of them have negative coordinates
(I presume those are initial coordinates) and no initial velocities.

Running (GROMACS 5.1.2) md on that file doesn't work as the simulation
hangs @ step 0. Using gmx energy I can see that the total energy and
temperature are off the scales but the density is fine (990 kg/m^3)

I don't have much experience in the chemical / physical aspects, can you
please tell me (step by step if possible) what I missed and what should I
do next?

Dave
-- 
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