[gmx-users] gmx insert-molecules
Shi Li
sli259 at g.uky.edu
Thu Jun 8 01:33:16 CEST 2017
> 在 2017年6月7日，16:26，gromacs.org_gmx-users-request at maillist.sys.kth.se 写道：
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> Today's Topics:
>
> 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 <gmxquestions at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] Cylinder pulling through bilayer
> Message-ID:
> <CANftEdNR4vnOMGpbytDbpVU3BzwrEyb6_GLCpa3jOdg_KAGMrg at 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
> 1 36 18
> 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 <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gmx insert-molecules
> Message-ID: <72ae4ffd-7c78-05ec-fb7f-5784e8e6b6e6 at 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, 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
>
> --
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.
Shi
> ==================================================
>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 7 Jun 2017 14:18:37 -0600
> From: Alex <nedomacho at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] deltaG shifts in g_wham
> Message-ID:
> <CAMJZ6qHUAH_XorTN-1AMFEfyMQKGGs9gO3jG5DyGYJ--PANQiA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi all,
>
> I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane
> with a narrow pore and an ion. The configurations correspond to various
> heights "above" the membrane (0 to 1.5 nm).
>
> In one case, the ion is K+, in another Na+. In both cases the results are
> fairly reasonable, but there is a bit of a numerical caveat.
>
> For sodium, the free energy away from the pore is close to zero and
> considerably negative inside the pore, as one might expect. For potassium
> (the input files are nearly identical), the free energy far away from the
> pore is a considerable _positive_ value and zero inside the pore. I do
> realize that absolute values are meaningless and I can always "shift" the
> results to correspond to near-zero far away from the reactive site (and
> when I do, I even have reasonable agreement with experiment). However, I
> want to understand what is happening with the utility. My simulation times
> are quite moderate (1 ns for each config).
>
> Can someone help?
>
> Thanks,
>
> Alex
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 7 Jun 2017 16:26:03 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] deltaG shifts in g_wham
> Message-ID: <010e24d2-4f74-a59d-a92c-0e754435f62e at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 6/7/17 4:18 PM, Alex wrote:
>> Hi all,
>>
>> I am using 'gmx wham' (GMX 5.0.4) on a system that consists of a membrane
>> with a narrow pore and an ion. The configurations correspond to various
>> heights "above" the membrane (0 to 1.5 nm).
>>
>> In one case, the ion is K+, in another Na+. In both cases the results are
>> fairly reasonable, but there is a bit of a numerical caveat.
>>
>> For sodium, the free energy away from the pore is close to zero and
>> considerably negative inside the pore, as one might expect. For potassium
>> (the input files are nearly identical), the free energy far away from the
>> pore is a considerable _positive_ value and zero inside the pore. I do
>> realize that absolute values are meaningless and I can always "shift" the
>> results to correspond to near-zero far away from the reactive site (and
>> when I do, I even have reasonable agreement with experiment). However, I
>> want to understand what is happening with the utility. My simulation times
>> are quite moderate (1 ns for each config).
>>
>> Can someone help?
>>
>
> WHAM sets the "left-most" window (i.e. smallest value of zeta) to zero and
> calculates all free energy values relative to that. This is why you can offset
> at any given point.
>
> -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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 8 Jun 2017 00:56:29 +0430
> From: Sajjad Kavyani <kavyani.sajjad at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se, gmx-users at gromacs.org
> Subject: [gmx-users] problem with "gmx rdf": It cannot find the center
> of mass of a reference group
> Message-ID:
> <CAMns7=5awO=LWCmxDmV=v-CfZtCorBAC01buRUMsK99qsAZ6vA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear experts,
> Recently I ask a question entitled "RDF of a group around CNT axis" in the
> mailing list in order to find proper command-line for it it turns out that
> the "-xy" option can help
> But I encounter an unusual problem therefore I decided to ask another
> question
>
> It turns out that the gmx rdf cannot find the com coordinate of the CNT (as
> reference) because as I choose different command-lines with various
> "-selrpos" arguments, all of the results gave me EXACTLY the SAME result
> which all of them are wrong! Commands like:
> gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg
> gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos res_com
> gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos res_cog
> gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos mol_com
> gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos mol_cog
> (CNT group has been chosen for both groups is gmx rdf)
>
> But when I manually placed a single particle in the COM of the cnt (in the
> cgs.gro) and then select this single particle as reference group, the gmx
> rdf resulted the desired value!
>
>
> Could you please help me to manage the problem?
> How to tell the gmx rdf in order to find com of cnt without manually
> placing a single particle in the input file?
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 8 Jun 2017 00:56:29 +0430
> From: Sajjad Kavyani <kavyani.sajjad at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se, gmx-users at gromacs.org
> Subject: [gmx-users] problem with "gmx rdf": It cannot find the center
> of mass of a reference group
> Message-ID:
> <CAMns7=5awO=LWCmxDmV=v-CfZtCorBAC01buRUMsK99qsAZ6vA at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear experts,
> Recently I ask a question entitled "RDF of a group around CNT axis" in the
> mailing list in order to find proper command-line for it it turns out that
> the "-xy" option can help
> But I encounter an unusual problem therefore I decided to ask another
> question
>
> It turns out that the gmx rdf cannot find the com coordinate of the CNT (as
> reference) because as I choose different command-lines with various
> "-selrpos" arguments, all of the results gave me EXACTLY the SAME result
> which all of them are wrong! Commands like:
> gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg
> gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos res_com
> gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos res_cog
> gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos mol_com
> gmx rdf -f cgs.gro -s md.tpr -xy -o rdf.xvg -selrpos mol_cog
> (CNT group has been chosen for both groups is gmx rdf)
>
> But when I manually placed a single particle in the COM of the cnt (in the
> cgs.gro) and then select this single particle as reference group, the gmx
> rdf resulted the desired value!
>
>
> Could you please help me to manage the problem?
> How to tell the gmx rdf in order to find com of cnt without manually
> placing a single particle in the input file?
>
>
> ------------------------------
>
> --
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