Re: [gmx-users] membrane-protein system by using charmm36 ff
What happened after 10 ns? In any case, reasonable equilibration is quite important in these simulations to ensure lipid integrity and also avoid protein distortions in production. Whether the structure you got after 10 ns is any good, i guess noone would know, so i'd just try to follow the protocol for membrane equilibration. Alex On Jun 18, 2018 3:33 AM, "Olga Press" wrote: Alex thank you for your advice. I have a problem with the pre-equilibration of the membrane before embedding the protein into it. I've used charm-gui membrane builder website and followed the README file at it is, including the length of the MD production and continued the protocol as you mentioned. The problem is that at the time I've started the simulation I produced only 10ns equilibration of the membrane. When I've checked the pressure it didn't reach the 1bar, and I continued the protocol by performing log NPT equilibration (200ns) of the entire system (protein+membrane). So, my question is should I start from the beginning or should I continue? Thank you, Olga 2018-06-18 12:02 GMT+03:00 Alex : > in point #1, 'it' refers to the protein. ;) > > > > On 6/18/2018 3:00 AM, Alex wrote: > >> I haven't done lipid+protein simulations in a while, but your NVT >> equilibration appears to be a bit strange, because equilibration under >> pressure is very important for the lipid. >> >> Here is my general suggestion -- it may be too careful, but this is from >> some experience with very poorly behaving porins: >> >> 1. Embed protein into a pre-equilibrated (semiisotropic NPT) membrane and >> restrain it. >> >> 2. Run NPT equilibration of the system in multiple steps (say, a few ns >> each), gradually reducing protein restraint. >> >> 3. NPT or NVT production. >> >> The choices for thermostats/barostats for all equilibration and >> production runs should be appropriate. >> >> Alex >> >> >> On 6/18/2018 2:50 AM, Olga Press wrote: >> >>> Thank you for your help! >>> How important is it to make a good pre-equilibration before embedding a >>> protein into the membrane if I'm going to perform long (200-300ns) >>> equilibration of the whole system (mempare+protein) using NVT followed by >>> NPT ensemble before production of MD simulation? >>> Thank you all for your help. >>> >>> >>> Olga >>> >>> >>> >>> >>> 2018-06-17 15:34 GMT+03:00 Shreyas Kaptan : >>> >>> Hi. Maybe you already know this but you can also build the whole embedded system with charmm-gui. Also, your parameters appear reasonable to me at first glance. As for the equilibration, that is a system specific question. If you have a "simple" uniform lipid content in the bilayer I would say from my experience, that the equilibration depends on the lipid heads and tails. Large heads and long tails generally imply a longer equilibration. Mixed lipids can require up to "microseconds" worth of equilibratio. I would take the saturation to a nearly fixed value of the Area per lipid and the bilayer thickness as an indication that it is safe to consider the "equilibration" enough. Do not use the 0.495 ns as some timescale. It is in fact quite short. On Sun, Jun 17, 2018 at 1:25 PM Olga Press wrote: Dear Gromacs users, > I'm new in the field of Molecular Dynamics especially in using Gromacs. > I have several questions regarding mdp file and I'll be very grateful > if > you can help me with them. > I'm using a membrane-protein system with Charmm36 ff. After I have > constructed bilayer membrane by using CHARMM-GUI membrane builder I > have > run the README file as it, without changing the equilibration time > (total > equilibration time of 0.475ns). Followed by embedded protein into the > membrane by using g_membed and performed solvation and minimization of > the > entire system as was described in the KALP15-DPPC tutorial by Dr. > Justin > A.Lemkul. > > those are my questions: > 1. Does the pre-equilibration of 0.475ns is enough before embedding > protein > into the membrane and followed by long equilibration of the whole > system > for 200ns by using NVT followed by NPT equilibration? > > 2. I've read that when using CHARMM36 ff in gromacs is better to switch > the > following parameters > constraints = h-bonds > cutoff-scheme = Verlet > vdwtype = cutoff > vdw-modifier = force-switch > rlist = 1.2 > rvdw = 1.2 > rvdw-switch = 1.0 > coulombtype = PME > rcoulomb = 1.2 > DispCorr = no > > I'm using the original mdout.mdp files produces by gromacs.Are those > parameters optimal for a membrane-protein system or just for the > lipids? > > Thank you all for your help. > Olga > -- > Gromacs Users mailing list > > * Please search the archive at >
Re: [gmx-users] membrane-protein system by using charmm36 ff
Hi. it is quite important that you do a pre-equilibration generally. This is assuming that you are starting with membranes built from scratch. If you have a patch that you obtained from charmm-gui website or other sources that someone has previously equilibrated, then, of course, you can forgo the pre-equilibration. The reason pre-equilibration is so important is that membranes generated by insertion methods tend to have a lot of clashes. NVT simulations (even short ones, approx. 1ns) ensure that given a box size you can accommodate the lipids and relax them before you attach the pressure coupling. An equlibration of 200-300 ns *might* be an overkill if your protein does not have a too large hydrophobic mismatch. but of course, more equilibration only helps. Once again, use parameters appropriate for the system to determine if the equilibration is enough instead of using some default timescale. Shreyas On Mon, Jun 18, 2018 at 10:51 AM Olga Press wrote: > Thank you for your help! > How important is it to make a good pre-equilibration before embedding a > protein into the membrane if I'm going to perform long (200-300ns) > equilibration of the whole system (mempare+protein) using NVT followed by > NPT ensemble before production of MD simulation? > Thank you all for your help. > > > Olga > > > > > 2018-06-17 15:34 GMT+03:00 Shreyas Kaptan : > > > Hi. > > > > Maybe you already know this but you can also build the whole embedded > > system with charmm-gui. Also, your parameters appear reasonable to me at > > first glance. > > > > As for the equilibration, that is a system specific question. If you > have a > > "simple" uniform lipid content in the bilayer I would say from my > > experience, that the equilibration depends on the lipid heads and tails. > > Large heads and long tails generally imply a longer equilibration. Mixed > > lipids can require up to "microseconds" worth of equilibratio. I would > take > > the saturation to a nearly fixed value of the Area per lipid and the > > bilayer thickness as an indication that it is safe to consider the > > "equilibration" enough. > > > > Do not use the 0.495 ns as some timescale. It is in fact quite short. > > > > > > > > On Sun, Jun 17, 2018 at 1:25 PM Olga Press > wrote: > > > > > Dear Gromacs users, > > > I'm new in the field of Molecular Dynamics especially in using Gromacs. > > > I have several questions regarding mdp file and I'll be very grateful > if > > > you can help me with them. > > > I'm using a membrane-protein system with Charmm36 ff. After I have > > > constructed bilayer membrane by using CHARMM-GUI membrane builder I > have > > > run the README file as it, without changing the equilibration time > (total > > > equilibration time of 0.475ns). Followed by embedded protein into the > > > membrane by using g_membed and performed solvation and minimization of > > the > > > entire system as was described in the KALP15-DPPC tutorial by Dr. > Justin > > > A.Lemkul. > > > > > > those are my questions: > > > 1. Does the pre-equilibration of 0.475ns is enough before embedding > > protein > > > into the membrane and followed by long equilibration of the whole > system > > > for 200ns by using NVT followed by NPT equilibration? > > > > > > 2. I've read that when using CHARMM36 ff in gromacs is better to switch > > the > > > following parameters > > > constraints = h-bonds > > > cutoff-scheme = Verlet > > > vdwtype = cutoff > > > vdw-modifier = force-switch > > > rlist = 1.2 > > > rvdw = 1.2 > > > rvdw-switch = 1.0 > > > coulombtype = PME > > > rcoulomb = 1.2 > > > DispCorr = no > > > > > > I'm using the original mdout.mdp files produces by gromacs.Are those > > > parameters optimal for a membrane-protein system or just for the > lipids? > > > > > > Thank you all for your help. > > > Olga > > > -- > > > 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. > > > > > > > > > -- > > Shreyas Sanjay Kaptan > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit >
Re: [gmx-users] membrane-protein system by using charmm36 ff
Alex thank you for your advice. I have a problem with the pre-equilibration of the membrane before embedding the protein into it. I've used charm-gui membrane builder website and followed the README file at it is, including the length of the MD production and continued the protocol as you mentioned. The problem is that at the time I've started the simulation I produced only 10ns equilibration of the membrane. When I've checked the pressure it didn't reach the 1bar, and I continued the protocol by performing log NPT equilibration (200ns) of the entire system (protein+membrane). So, my question is should I start from the beginning or should I continue? Thank you, Olga 2018-06-18 12:02 GMT+03:00 Alex : > in point #1, 'it' refers to the protein. ;) > > > > On 6/18/2018 3:00 AM, Alex wrote: > >> I haven't done lipid+protein simulations in a while, but your NVT >> equilibration appears to be a bit strange, because equilibration under >> pressure is very important for the lipid. >> >> Here is my general suggestion -- it may be too careful, but this is from >> some experience with very poorly behaving porins: >> >> 1. Embed protein into a pre-equilibrated (semiisotropic NPT) membrane and >> restrain it. >> >> 2. Run NPT equilibration of the system in multiple steps (say, a few ns >> each), gradually reducing protein restraint. >> >> 3. NPT or NVT production. >> >> The choices for thermostats/barostats for all equilibration and >> production runs should be appropriate. >> >> Alex >> >> >> On 6/18/2018 2:50 AM, Olga Press wrote: >> >>> Thank you for your help! >>> How important is it to make a good pre-equilibration before embedding a >>> protein into the membrane if I'm going to perform long (200-300ns) >>> equilibration of the whole system (mempare+protein) using NVT followed by >>> NPT ensemble before production of MD simulation? >>> Thank you all for your help. >>> >>> >>> Olga >>> >>> >>> >>> >>> 2018-06-17 15:34 GMT+03:00 Shreyas Kaptan : >>> >>> Hi. Maybe you already know this but you can also build the whole embedded system with charmm-gui. Also, your parameters appear reasonable to me at first glance. As for the equilibration, that is a system specific question. If you have a "simple" uniform lipid content in the bilayer I would say from my experience, that the equilibration depends on the lipid heads and tails. Large heads and long tails generally imply a longer equilibration. Mixed lipids can require up to "microseconds" worth of equilibratio. I would take the saturation to a nearly fixed value of the Area per lipid and the bilayer thickness as an indication that it is safe to consider the "equilibration" enough. Do not use the 0.495 ns as some timescale. It is in fact quite short. On Sun, Jun 17, 2018 at 1:25 PM Olga Press wrote: Dear Gromacs users, > I'm new in the field of Molecular Dynamics especially in using Gromacs. > I have several questions regarding mdp file and I'll be very grateful > if > you can help me with them. > I'm using a membrane-protein system with Charmm36 ff. After I have > constructed bilayer membrane by using CHARMM-GUI membrane builder I > have > run the README file as it, without changing the equilibration time > (total > equilibration time of 0.475ns). Followed by embedded protein into the > membrane by using g_membed and performed solvation and minimization of > the > entire system as was described in the KALP15-DPPC tutorial by Dr. > Justin > A.Lemkul. > > those are my questions: > 1. Does the pre-equilibration of 0.475ns is enough before embedding > protein > into the membrane and followed by long equilibration of the whole > system > for 200ns by using NVT followed by NPT equilibration? > > 2. I've read that when using CHARMM36 ff in gromacs is better to switch > the > following parameters > constraints = h-bonds > cutoff-scheme = Verlet > vdwtype = cutoff > vdw-modifier = force-switch > rlist = 1.2 > rvdw = 1.2 > rvdw-switch = 1.0 > coulombtype = PME > rcoulomb = 1.2 > DispCorr = no > > I'm using the original mdout.mdp files produces by gromacs.Are those > parameters optimal for a membrane-protein system or just for the > lipids? > > Thank you all for your help. > Olga > -- > 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. > > -- Shreyas Sanjay Kaptan --
Re: [gmx-users] membrane-protein system by using charmm36 ff
in point #1, 'it' refers to the protein. ;) On 6/18/2018 3:00 AM, Alex wrote: I haven't done lipid+protein simulations in a while, but your NVT equilibration appears to be a bit strange, because equilibration under pressure is very important for the lipid. Here is my general suggestion -- it may be too careful, but this is from some experience with very poorly behaving porins: 1. Embed protein into a pre-equilibrated (semiisotropic NPT) membrane and restrain it. 2. Run NPT equilibration of the system in multiple steps (say, a few ns each), gradually reducing protein restraint. 3. NPT or NVT production. The choices for thermostats/barostats for all equilibration and production runs should be appropriate. Alex On 6/18/2018 2:50 AM, Olga Press wrote: Thank you for your help! How important is it to make a good pre-equilibration before embedding a protein into the membrane if I'm going to perform long (200-300ns) equilibration of the whole system (mempare+protein) using NVT followed by NPT ensemble before production of MD simulation? Thank you all for your help. Olga 2018-06-17 15:34 GMT+03:00 Shreyas Kaptan : Hi. Maybe you already know this but you can also build the whole embedded system with charmm-gui. Also, your parameters appear reasonable to me at first glance. As for the equilibration, that is a system specific question. If you have a "simple" uniform lipid content in the bilayer I would say from my experience, that the equilibration depends on the lipid heads and tails. Large heads and long tails generally imply a longer equilibration. Mixed lipids can require up to "microseconds" worth of equilibratio. I would take the saturation to a nearly fixed value of the Area per lipid and the bilayer thickness as an indication that it is safe to consider the "equilibration" enough. Do not use the 0.495 ns as some timescale. It is in fact quite short. On Sun, Jun 17, 2018 at 1:25 PM Olga Press wrote: Dear Gromacs users, I'm new in the field of Molecular Dynamics especially in using Gromacs. I have several questions regarding mdp file and I'll be very grateful if you can help me with them. I'm using a membrane-protein system with Charmm36 ff. After I have constructed bilayer membrane by using CHARMM-GUI membrane builder I have run the README file as it, without changing the equilibration time (total equilibration time of 0.475ns). Followed by embedded protein into the membrane by using g_membed and performed solvation and minimization of the entire system as was described in the KALP15-DPPC tutorial by Dr. Justin A.Lemkul. those are my questions: 1. Does the pre-equilibration of 0.475ns is enough before embedding protein into the membrane and followed by long equilibration of the whole system for 200ns by using NVT followed by NPT equilibration? 2. I've read that when using CHARMM36 ff in gromacs is better to switch the following parameters constraints = h-bonds cutoff-scheme = Verlet vdwtype = cutoff vdw-modifier = force-switch rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 coulombtype = PME rcoulomb = 1.2 DispCorr = no I'm using the original mdout.mdp files produces by gromacs.Are those parameters optimal for a membrane-protein system or just for the lipids? Thank you all for your help. Olga -- 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. -- Shreyas Sanjay Kaptan -- 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] membrane-protein system by using charmm36 ff
I haven't done lipid+protein simulations in a while, but your NVT equilibration appears to be a bit strange, because equilibration under pressure is very important for the lipid. Here is my general suggestion -- it may be too careful, but this is from some experience with very poorly behaving porins: 1. Embed protein into a pre-equilibrated (semiisotropic NPT) membrane and restrain it. 2. Run NPT equilibration of the system in multiple steps (say, a few ns each), gradually reducing protein restraint. 3. NPT or NVT production. The choices for thermostats/barostats for all equilibration and production runs should be appropriate. Alex On 6/18/2018 2:50 AM, Olga Press wrote: Thank you for your help! How important is it to make a good pre-equilibration before embedding a protein into the membrane if I'm going to perform long (200-300ns) equilibration of the whole system (mempare+protein) using NVT followed by NPT ensemble before production of MD simulation? Thank you all for your help. Olga 2018-06-17 15:34 GMT+03:00 Shreyas Kaptan : Hi. Maybe you already know this but you can also build the whole embedded system with charmm-gui. Also, your parameters appear reasonable to me at first glance. As for the equilibration, that is a system specific question. If you have a "simple" uniform lipid content in the bilayer I would say from my experience, that the equilibration depends on the lipid heads and tails. Large heads and long tails generally imply a longer equilibration. Mixed lipids can require up to "microseconds" worth of equilibratio. I would take the saturation to a nearly fixed value of the Area per lipid and the bilayer thickness as an indication that it is safe to consider the "equilibration" enough. Do not use the 0.495 ns as some timescale. It is in fact quite short. On Sun, Jun 17, 2018 at 1:25 PM Olga Press wrote: Dear Gromacs users, I'm new in the field of Molecular Dynamics especially in using Gromacs. I have several questions regarding mdp file and I'll be very grateful if you can help me with them. I'm using a membrane-protein system with Charmm36 ff. After I have constructed bilayer membrane by using CHARMM-GUI membrane builder I have run the README file as it, without changing the equilibration time (total equilibration time of 0.475ns). Followed by embedded protein into the membrane by using g_membed and performed solvation and minimization of the entire system as was described in the KALP15-DPPC tutorial by Dr. Justin A.Lemkul. those are my questions: 1. Does the pre-equilibration of 0.475ns is enough before embedding protein into the membrane and followed by long equilibration of the whole system for 200ns by using NVT followed by NPT equilibration? 2. I've read that when using CHARMM36 ff in gromacs is better to switch the following parameters constraints = h-bonds cutoff-scheme = Verlet vdwtype = cutoff vdw-modifier = force-switch rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 coulombtype = PME rcoulomb = 1.2 DispCorr = no I'm using the original mdout.mdp files produces by gromacs.Are those parameters optimal for a membrane-protein system or just for the lipids? Thank you all for your help. Olga -- 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. -- Shreyas Sanjay Kaptan -- 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] membrane-protein system by using charmm36 ff
Thank you for your help! How important is it to make a good pre-equilibration before embedding a protein into the membrane if I'm going to perform long (200-300ns) equilibration of the whole system (mempare+protein) using NVT followed by NPT ensemble before production of MD simulation? Thank you all for your help. Olga 2018-06-17 15:34 GMT+03:00 Shreyas Kaptan : > Hi. > > Maybe you already know this but you can also build the whole embedded > system with charmm-gui. Also, your parameters appear reasonable to me at > first glance. > > As for the equilibration, that is a system specific question. If you have a > "simple" uniform lipid content in the bilayer I would say from my > experience, that the equilibration depends on the lipid heads and tails. > Large heads and long tails generally imply a longer equilibration. Mixed > lipids can require up to "microseconds" worth of equilibratio. I would take > the saturation to a nearly fixed value of the Area per lipid and the > bilayer thickness as an indication that it is safe to consider the > "equilibration" enough. > > Do not use the 0.495 ns as some timescale. It is in fact quite short. > > > > On Sun, Jun 17, 2018 at 1:25 PM Olga Press wrote: > > > Dear Gromacs users, > > I'm new in the field of Molecular Dynamics especially in using Gromacs. > > I have several questions regarding mdp file and I'll be very grateful if > > you can help me with them. > > I'm using a membrane-protein system with Charmm36 ff. After I have > > constructed bilayer membrane by using CHARMM-GUI membrane builder I have > > run the README file as it, without changing the equilibration time (total > > equilibration time of 0.475ns). Followed by embedded protein into the > > membrane by using g_membed and performed solvation and minimization of > the > > entire system as was described in the KALP15-DPPC tutorial by Dr. Justin > > A.Lemkul. > > > > those are my questions: > > 1. Does the pre-equilibration of 0.475ns is enough before embedding > protein > > into the membrane and followed by long equilibration of the whole system > > for 200ns by using NVT followed by NPT equilibration? > > > > 2. I've read that when using CHARMM36 ff in gromacs is better to switch > the > > following parameters > > constraints = h-bonds > > cutoff-scheme = Verlet > > vdwtype = cutoff > > vdw-modifier = force-switch > > rlist = 1.2 > > rvdw = 1.2 > > rvdw-switch = 1.0 > > coulombtype = PME > > rcoulomb = 1.2 > > DispCorr = no > > > > I'm using the original mdout.mdp files produces by gromacs.Are those > > parameters optimal for a membrane-protein system or just for the lipids? > > > > Thank you all for your help. > > Olga > > -- > > 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. > > > > > -- > Shreyas Sanjay Kaptan > -- > 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] membrane-protein system by using charmm36 ff
Hi. Maybe you already know this but you can also build the whole embedded system with charmm-gui. Also, your parameters appear reasonable to me at first glance. As for the equilibration, that is a system specific question. If you have a "simple" uniform lipid content in the bilayer I would say from my experience, that the equilibration depends on the lipid heads and tails. Large heads and long tails generally imply a longer equilibration. Mixed lipids can require up to "microseconds" worth of equilibratio. I would take the saturation to a nearly fixed value of the Area per lipid and the bilayer thickness as an indication that it is safe to consider the "equilibration" enough. Do not use the 0.495 ns as some timescale. It is in fact quite short. On Sun, Jun 17, 2018 at 1:25 PM Olga Press wrote: > Dear Gromacs users, > I'm new in the field of Molecular Dynamics especially in using Gromacs. > I have several questions regarding mdp file and I'll be very grateful if > you can help me with them. > I'm using a membrane-protein system with Charmm36 ff. After I have > constructed bilayer membrane by using CHARMM-GUI membrane builder I have > run the README file as it, without changing the equilibration time (total > equilibration time of 0.475ns). Followed by embedded protein into the > membrane by using g_membed and performed solvation and minimization of the > entire system as was described in the KALP15-DPPC tutorial by Dr. Justin > A.Lemkul. > > those are my questions: > 1. Does the pre-equilibration of 0.475ns is enough before embedding protein > into the membrane and followed by long equilibration of the whole system > for 200ns by using NVT followed by NPT equilibration? > > 2. I've read that when using CHARMM36 ff in gromacs is better to switch the > following parameters > constraints = h-bonds > cutoff-scheme = Verlet > vdwtype = cutoff > vdw-modifier = force-switch > rlist = 1.2 > rvdw = 1.2 > rvdw-switch = 1.0 > coulombtype = PME > rcoulomb = 1.2 > DispCorr = no > > I'm using the original mdout.mdp files produces by gromacs.Are those > parameters optimal for a membrane-protein system or just for the lipids? > > Thank you all for your help. > Olga > -- > 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. > -- Shreyas Sanjay Kaptan -- 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] membrane-protein system by using charmm36 ff
Dear Gromacs users, I'm new in the field of Molecular Dynamics especially in using Gromacs. I have several questions regarding mdp file and I'll be very grateful if you can help me with them. I'm using a membrane-protein system with Charmm36 ff. After I have constructed bilayer membrane by using CHARMM-GUI membrane builder I have run the README file as it, without changing the equilibration time (total equilibration time of 0.475ns). Followed by embedded protein into the membrane by using g_membed and performed solvation and minimization of the entire system as was described in the KALP15-DPPC tutorial by Dr. Justin A.Lemkul. those are my questions: 1. Does the pre-equilibration of 0.475ns is enough before embedding protein into the membrane and followed by long equilibration of the whole system for 200ns by using NVT followed by NPT equilibration? 2. I've read that when using CHARMM36 ff in gromacs is better to switch the following parameters constraints = h-bonds cutoff-scheme = Verlet vdwtype = cutoff vdw-modifier = force-switch rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 coulombtype = PME rcoulomb = 1.2 DispCorr = no I'm using the original mdout.mdp files produces by gromacs.Are those parameters optimal for a membrane-protein system or just for the lipids? Thank you all for your help. Olga -- 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.
