Re: [gmx-users] PBC issues with membrane-peptide simulation
Dear users, Well, I have found another solution for avoiding the diffusion through the periodic boundary in such simulations. Hope this is helpful to others doing similar work. Basically, the idea is to apply a biasing potential to the COM of the peptides to pull them towards the membrane so as to ensure interaction with the lipid bilayer. Thereafter, normal production simulations can be performed on the peptide membrane complex. See the following paper: Li, J., Liu, S., Lakshminarayanan, R., Bai, Y., Pervushin, K., Verma, C., and Beuerman, R.W. (2013). Molecular simulations suggest how a branched antimicrobial peptide perturbs a bacterial membrane and enhances permeability. Biochim. Biophys. Acta *1828*, 1112–1121. Best Regards, Abhishek Acharya On Thu, Nov 10, 2016 at 12:48 PM, Abhi Acharya <abhi117acha...@gmail.com> wrote: > Sorry for that Mark. > > Basically, our experimental studies show that our designed peptides (2-3 > different peptides) are involved in membrane destabilization but their > activity (in terms of MIC values) varies. We want to understand the > molecular underpinnings of the membrane destabilization process and > possibly explain the variation in activities of the peptides. Therefore, we > wanted to perform some simulations starting from the point where some > amount of peptides are randomly added to the simulation box on one side of > the membrane (about 5 nm away from the upper leaflet) and see how the > system evolves. > > The problem is that some of the peptides diffuse along the z-direction > such that they exit the simulation box and appear on the other side near to > the lower leaflet. > > Hope this is helpful. > > Thanks and Regards, > Abhishek Acharya > > > > > > On Thu, Nov 10, 2016 at 9:57 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > >> Hi, >> >> You haven't said what you're trying to model, so it's going to be hard for >> someone to help out :-) >> >> Mark >> >> On Thu, 10 Nov 2016 05:21 Abhi Acharya <abhi117acha...@gmail.com> wrote: >> >> > Thank you Stephane for your suggestion. Though this seems like a nice >> > solution to circumvent the problem, but do you think this is the normal >> way >> > to go about it? I have never found anyone reporting such a methodology >> for >> > membrane peptide simulation. Also, I can anticipate significant >> increase in >> > computational costs for a double bilayer system. I have a 800 lipid >> > molecules in a single bilayer, so this is significant factor for me. >> > >> > Thanks and Regards, >> > Abhishek >> > >> > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 < >> stephane.a...@cea.fr >> > > >> > wrote: >> > >> > > Hi, >> > > >> > > it is not an issue !! To resolve your problem you could simulate two >> > > bilayer in box and insert the peptides between them. >> > > >> > > HTH >> > > >> > > -- >> > > >> > > Message: 6 >> > > Date: Wed, 9 Nov 2016 16:07:26 +0530 >> > > From: Abhi Acharya <abhi117acha...@gmail.com> >> > > To: gromacs.org_gmx-users@maillist.sys.kth.se >> > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation >> > > Message-ID: >> > > <CAB1aw3zkCH7wmR6Za9H4OHm1PLG95cAeO0HJksxyxZi8yXC9Cg@mail. >> > > gmail.com> >> > > Content-Type: text/plain; charset=UTF-8 >> > > >> > > Dear Gromacs users, >> > > >> > > I am trying to simulate a system consisting of a lipid bilayer and few >> > > peptides. The peptides have been added randomly to the simulation box >> > only >> > > on one side of the membrane. I ran a 100 ns simulation of the system >> > using >> > > CHARMM36 forcefeild. However, I find that within the first few ns, >> some >> > of >> > > the peptides appear on the other side of the membrane. I think that >> this >> > is >> > > because of the diffusion of the peptides though the periodic boundary. >> > > Kindly suggest how to tackle this problem. I have used COM motion >> > removal >> > > on the whole system for the said simulation. >> > > >> > > Regards, >> > > Abhishek Acharya >> > > >> > > >> > > -- >> > > >> > > -- >> > > Gromacs Users mailing list >> > > >> >
Re: [gmx-users] PBC issues with membrane-peptide simulation
Sorry for that Mark. Basically, our experimental studies show that our designed peptides (2-3 different peptides) are involved in membrane destabilization but their activity (in terms of MIC values) varies. We want to understand the molecular underpinnings of the membrane destabilization process and possibly explain the variation in activities of the peptides. Therefore, we wanted to perform some simulations starting from the point where some amount of peptides are randomly added to the simulation box on one side of the membrane (about 5 nm away from the upper leaflet) and see how the system evolves. The problem is that some of the peptides diffuse along the z-direction such that they exit the simulation box and appear on the other side near to the lower leaflet. Hope this is helpful. Thanks and Regards, Abhishek Acharya On Thu, Nov 10, 2016 at 9:57 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > You haven't said what you're trying to model, so it's going to be hard for > someone to help out :-) > > Mark > > On Thu, 10 Nov 2016 05:21 Abhi Acharya <abhi117acha...@gmail.com> wrote: > > > Thank you Stephane for your suggestion. Though this seems like a nice > > solution to circumvent the problem, but do you think this is the normal > way > > to go about it? I have never found anyone reporting such a methodology > for > > membrane peptide simulation. Also, I can anticipate significant increase > in > > computational costs for a double bilayer system. I have a 800 lipid > > molecules in a single bilayer, so this is significant factor for me. > > > > Thanks and Regards, > > Abhishek > > > > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 < > stephane.a...@cea.fr > > > > > wrote: > > > > > Hi, > > > > > > it is not an issue !! To resolve your problem you could simulate two > > > bilayer in box and insert the peptides between them. > > > > > > HTH > > > > > > -------------- > > > > > > Message: 6 > > > Date: Wed, 9 Nov 2016 16:07:26 +0530 > > > From: Abhi Acharya <abhi117acha...@gmail.com> > > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation > > > Message-ID: > > > <CAB1aw3zkCH7wmR6Za9H4OHm1PLG95cAeO0HJksxyxZi8yXC9Cg@mail. > > > gmail.com> > > > Content-Type: text/plain; charset=UTF-8 > > > > > > Dear Gromacs users, > > > > > > I am trying to simulate a system consisting of a lipid bilayer and few > > > peptides. The peptides have been added randomly to the simulation box > > only > > > on one side of the membrane. I ran a 100 ns simulation of the system > > using > > > CHARMM36 forcefeild. However, I find that within the first few ns, some > > of > > > the peptides appear on the other side of the membrane. I think that > this > > is > > > because of the diffusion of the peptides though the periodic boundary. > > > Kindly suggest how to tackle this problem. I have used COM motion > > removal > > > on the whole system for the said simulation. > > > > > > Regards, > > > Abhishek Acharya > > > > > > > > > -- > > > > > > -- > > > 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 151, Issue 32 > > > ** > > > -- > > > 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_L
Re: [gmx-users] PBC issues with membrane-peptide simulation
Hi, You haven't said what you're trying to model, so it's going to be hard for someone to help out :-) Mark On Thu, 10 Nov 2016 05:21 Abhi Acharya <abhi117acha...@gmail.com> wrote: > Thank you Stephane for your suggestion. Though this seems like a nice > solution to circumvent the problem, but do you think this is the normal way > to go about it? I have never found anyone reporting such a methodology for > membrane peptide simulation. Also, I can anticipate significant increase in > computational costs for a double bilayer system. I have a 800 lipid > molecules in a single bilayer, so this is significant factor for me. > > Thanks and Regards, > Abhishek > > On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 <stephane.a...@cea.fr > > > wrote: > > > Hi, > > > > it is not an issue !! To resolve your problem you could simulate two > > bilayer in box and insert the peptides between them. > > > > HTH > > > > -- > > > > Message: 6 > > Date: Wed, 9 Nov 2016 16:07:26 +0530 > > From: Abhi Acharya <abhi117acha...@gmail.com> > > To: gromacs.org_gmx-users@maillist.sys.kth.se > > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation > > Message-ID: > > <CAB1aw3zkCH7wmR6Za9H4OHm1PLG95cAeO0HJksxyxZi8yXC9Cg@mail. > > gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Dear Gromacs users, > > > > I am trying to simulate a system consisting of a lipid bilayer and few > > peptides. The peptides have been added randomly to the simulation box > only > > on one side of the membrane. I ran a 100 ns simulation of the system > using > > CHARMM36 forcefeild. However, I find that within the first few ns, some > of > > the peptides appear on the other side of the membrane. I think that this > is > > because of the diffusion of the peptides though the periodic boundary. > > Kindly suggest how to tackle this problem. I have used COM motion > removal > > on the whole system for the said simulation. > > > > Regards, > > Abhishek Acharya > > > > > > -- > > > > -- > > 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 151, Issue 32 > > ** > > -- > > 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] PBC issues with membrane-peptide simulation
Thank you Stephane for your suggestion. Though this seems like a nice solution to circumvent the problem, but do you think this is the normal way to go about it? I have never found anyone reporting such a methodology for membrane peptide simulation. Also, I can anticipate significant increase in computational costs for a double bilayer system. I have a 800 lipid molecules in a single bilayer, so this is significant factor for me. Thanks and Regards, Abhishek On Wed, Nov 9, 2016 at 4:53 PM, ABEL Stephane 175950 <stephane.a...@cea.fr> wrote: > Hi, > > it is not an issue !! To resolve your problem you could simulate two > bilayer in box and insert the peptides between them. > > HTH > > -- > > Message: 6 > Date: Wed, 9 Nov 2016 16:07:26 +0530 > From: Abhi Acharya <abhi117acha...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation > Message-ID: > <CAB1aw3zkCH7wmR6Za9H4OHm1PLG95cAeO0HJksxyxZi8yXC9Cg@mail. > gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Dear Gromacs users, > > I am trying to simulate a system consisting of a lipid bilayer and few > peptides. The peptides have been added randomly to the simulation box only > on one side of the membrane. I ran a 100 ns simulation of the system using > CHARMM36 forcefeild. However, I find that within the first few ns, some of > the peptides appear on the other side of the membrane. I think that this is > because of the diffusion of the peptides though the periodic boundary. > Kindly suggest how to tackle this problem. I have used COM motion removal > on the whole system for the said simulation. > > Regards, > Abhishek Acharya > > > -- > > -- > 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 151, Issue 32 > ** > -- > 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] PBC issues with membrane-peptide simulation
Hi, it is not an issue !! To resolve your problem you could simulate two bilayer in box and insert the peptides between them. HTH -- Message: 6 Date: Wed, 9 Nov 2016 16:07:26 +0530 From: Abhi Acharya <abhi117acha...@gmail.com> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Fwd: PBC issues with membrane-peptide simulation Message-ID: <cab1aw3zkch7wmr6za9h4ohm1plg95caeo0hjksxyxzi8yxc...@mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Dear Gromacs users, I am trying to simulate a system consisting of a lipid bilayer and few peptides. The peptides have been added randomly to the simulation box only on one side of the membrane. I ran a 100 ns simulation of the system using CHARMM36 forcefeild. However, I find that within the first few ns, some of the peptides appear on the other side of the membrane. I think that this is because of the diffusion of the peptides though the periodic boundary. Kindly suggest how to tackle this problem. I have used COM motion removal on the whole system for the said simulation. Regards, Abhishek Acharya -- -- 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 151, Issue 32 ** -- 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.
