[gmx-users] gromacs.org_gmx-users Digest, Vol 160, Issue 2

王珍 348363213 at qq.com
Tue Aug 1 04:57:07 CEST 2017 

------------------ Original ------------------
From:  "gromacs.org_gmx-users-request";<gromacs.org_gmx-users-request at maillist.sys.kth.se>;
Date:  Tue, Aug 1, 2017 07:16 AM
To:  "gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se>; 

Subject:  gromacs.org_gmx-users Digest, Vol 160, Issue 2



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Today's Topics:

   1. Re: gromacs rerun calculate the energy (Justin Lemkul)
   2. Re: How can I implement a radial potential field in GROMACS?
      (Justin Lemkul)
   3. Re: ligand topology (Justin Lemkul)
   4. Re: Question on Umbrella Sampling with varied ionic strength.
      (Justin Lemkul)
   5. Question on Umbrella Sampling with varied ionic	strength.
      (Yuanchao Liu (MSU))


----------------------------------------------------------------------

Message: 1
Date: Mon, 31 Jul 2017 18:50:54 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gromacs rerun calculate the energy
Message-ID: <6cbf4380-f268-b0e8-df8f-716bf3d60094 at vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed



On 7/31/17 8:03 AM, ?? wrote:
> Hi all,
>        I used Gromacs run the biological system,  which contains water, ions(Na+,Cl-), and nucleic. I used gromacs run the system, and the coulombtype was PME and the cutoff was 10 angstrom,  then I want to use the commond rerun to calculate the interaction of resid 1 and resid 2, I add the energygrps in my mdp, and the coulombtype was PME, the .edr file can be obtained. Then I use g_energy to calculate the coulomb interaction. I have three question.
> first, when the rcoulomb=10 angstrom, and coulombtype=PME, within 10 angstrom, is PME algorithm using ?
> 

Yes, because there are both real-space (within rcoulomb) and Fourier space 
(long-range) terms.

> 


Thank you for your reply,  for the short range, is the Gromacs using the error function? 





> 
> second, The PME algorithm dived into long range interaction and short range interaction, whereas we only calculate the short range of the coulomb energy using Gromacs, can we obtain the long range of the coulomb energy?
> 

Perhaps by clever use of convert-tpr to zero out charges of certain groups 
(there is a post in the archive from some time ago about this) but I am 
skeptical about the value of such a number.

> 
> 
> Third, when I use rerun to calculate the coulomb energy, the rcoulomb from 1.0 nanometre change to half of the water box I built, and the coulombtype from PME to cut-off, is it reasonable to calculate the coulomb energy?
> 

This is probably the more straightforward way to determine a reasonable estimate 
of the longer-range energy contributions.

-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: 2
Date: Mon, 31 Jul 2017 18:52:35 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] How can I implement a radial potential field
	in GROMACS?
Message-ID: <d46210fe-8293-9db7-a2ca-95fd0db82fac at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 7/31/17 1:07 PM, Wes Michaels wrote:
> Hello,
> 
> (Cross-post from my original post here: https://www.researchgate.net/post/How_can_I_implement_a_radial_potential_field_in_a_MD_simulation_GROMACS)
> 
> Is there a way to apply a potential field to all atoms in a simulation box in GROMACS? I'd like to implement some radial potential energy function, such as U(r)=k*r^2 or similar, that applies a force to each atom as a function of its position. In my case, I?d like to draw atoms towards the center of the box.
> 
> I looked into implementing this with the pull code with a dummy atom, but I gathered that the pull code acts on the center of mass of the specified index group, not on each atom in the group. So, if all the atoms in my simulation in a given index group are distributed radially around the center of my box, no force will be applied. Scaling behavior of Coulomb and LJ potentials on the dummy atom seems to rule them out as possible sources of a potential, too.
> 
> Is there a way I can modify the reference positions of position restraints of atoms to be centered at the middle of the box, instead of the atom's initial position? Or, can I implement a solution using force switching that acts only on the dummy atom? Or, is there another way to tackle this problem?
> 
> Thanks! Any and all suggestions are appreciated. If clarification is needed on my desired goal, just let me know.
> 

It seems to me that you can do this with a simple use of position restraints on 
all atoms, with a reference position set for each at the middle of the box via 
grompp -r.

-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: 3
Date: Mon, 31 Jul 2017 18:53:22 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] ligand topology
Message-ID: <66468c31-83ad-20ee-0f32-0851e07fcbd7 at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 7/31/17 2:42 PM, Mohammad Zahidul Hossain Khan wrote:
> Dear Sir
> 
> I am new for protein-ligand complex. I want amber force field (ff03) for my
> protein, tip3p for water model and gaff (General Amber force field) for
> ligand. I do not know how to produce gaff force field from pdb and then
> convert for gromacs topology.
> 
> I have tried ff03 with gromos ligand topology and tip3p water model
> 
> it gives me the error:
> atomtype OM not found
> 
> and when I have tried ff03 with gromos topology and spc water model it
> gives me the error like:
> atomtype HW not found.
> 
> Can anyone help me about it?
> 

You can't mix and match force fields; it's fundamentally wrong.  You need to 
develop ligand parameters that are consistent with the parent protein force 
field.  Various tools exist for different force fields, with varying degrees of 
reliability.

-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: 4
Date: Mon, 31 Jul 2017 18:55:45 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Question on Umbrella Sampling with varied
	ionic strength.
Message-ID: <af52fa11-0b8a-d61d-03e3-624fa8a85f9c at vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 7/31/17 5:19 PM, Yuanchao Liu (MSU) wrote:
> Hi all
> 
> I have a question on umbrella sampling results under varied ionic strength.
> I have just done some regular umbrella sampling on the system of glucose
> 6-phosphate (small ligand molecule) on oligopeptide with LYS side chains. I
> mostly follow the tutorial by Justin
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bevanlab.biochem.vt.edu_Pages_Personal_justin_gmx-2Dtutorials_umbrella_index.html&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV&m=wjjoIomb4xozoyp9lqY4_wEzyhxGWILHcyUjAvXhess&s=--TZVWbKNWMqlgnHsfsMQUCzOJsx1PMTs4thX-y0jhM&e= >.
> I use explicit ions to represent the ionic strength level.
> 
> There is hardly any difference between my calculated adsorption energy (by
> PMF) under different ionic strengths (0, 20, 40, 70, 120 mM). However, we
> did observe apparent difference on surface retention time in regular MD
> simulations, which indicated a weaker surface interaction. During my
> simulation, the sampling time is 10 ns for each window, and I am wondering
> if the effect of explicit ions need longer simulation time to be reflected
> on results.
> 
> Here is some detail of my simulation:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.evernote.com_l_AAMCVXRkp3tPYrhq-5F4oRHdtfnRb1VJo71U0_&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=gCy395jfSTIKIGBjdJ8SwSg8yN7wywRqF0ilx8ZoefpMNPZKIUY0jXzHKcFUwcQV&m=wjjoIomb4xozoyp9lqY4_wEzyhxGWILHcyUjAvXhess&s=B67nP5cwU6r5g_KBORUyrzAardEsfEzcojVKVZFomfU&e=
> 
> I will appreciate it if anybody with relevant experience can give me some
> suggestion on this. Thank you.
> 

It will be difficult to determine any real, meaningful difference with such 
small changes in ionic strength.  Your histogram overlap looks good, so I doubt 
that more sampling will improve the result.  Is the observed difference in 
retention time reproducible?  How did you determine it, and over what time 
scale?  Is it possible that those simulations simply got stuck in a local 
minimum (common in MD simulations) rather than actually reflecting a real 
physical difference?  Additionally, if the retention times are not substantially 
different, then the energy differences may not be large enough to resolve via 
umbrella sampling.

-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: Mon, 31 Jul 2017 17:02:40 -0400
From: "Yuanchao Liu (MSU)" <liuyuan6 at msu.edu>
To: gmx-users at gromacs.org
Subject: [gmx-users] Question on Umbrella Sampling with varied ionic
	strength.
Message-ID:
	<CAADN9k4_j1zDYkSccAZ3yLeYSBNEMt+HbDryXk278TcfBtLPVw at mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi all

I have a question on umbrella sampling results under varied ionic strength.
I have just done some regular umbrella sampling on the system of glucose
6-phosphate (small ligand molecule) on oligopeptide with LYS side chains. I
mostly follow the tutorial by Justin
<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bevanlab.biochem.vt.edu_Pages_Personal_justin_gmx-2Dtutorials_umbrella_index.html&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=NpiNrs4JMs7x7VUghg3wpVUJ_O9DzzTJ8Mf9sATZN4E&m=BARutmaSsjnyhUuJ1NkYpSuBLCDEspqRUVRAXBYSUjQ&s=9L52pxEuFcjHHeCYHv5KvrMyWeV3meWk9qJVA1CenQo&e= >.
I use explicit ions to represent the ionic strength level.

There is hardly any difference between my calculated adsorption energy (by
PMF) under different ionic strengths (0, 20, 40, 70, 120 mM). However, we
did observe apparent difference on surface retention time in regular MD
simulations, which indicated a weaker surface interaction. During my
simulation, the sampling time is 10 ns for each window, and I am wondering
if the effect of explicit ions need longer simulation time to be reflected
on results.

Here is some detail of my simulation:
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.evernote.com_l_AAMCVXRkp3tPYrhq-5F4oRHdtfnRb1VJo71U0_&d=DwIFaQ&c=nE__W8dFE-shTxStwXtp0A&r=NpiNrs4JMs7x7VUghg3wpVUJ_O9DzzTJ8Mf9sATZN4E&m=BARutmaSsjnyhUuJ1NkYpSuBLCDEspqRUVRAXBYSUjQ&s=KihiO_75Ay2xIRdGttNqM_4P72Pq4rWLizplUq9mr3Q&e= 

I will appreciate it if anybody with relevant experience can give me some
suggestion on this. Thank you.


Yuanchao Liu (???)
Ph.D. Candidate
Department of Chemical Engineering and Materials Science
428 South Shaw Lane, Room 3263
Michigan State University
East Lansing, Michigan 48824-4437

Email: ycLiu1987 at gmail.com; liuyuan6 at msu.edu; liuyuan6 at egr.msu.edu
Cell:+1 (517)-763-1806


------------------------------

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