Re: [gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Cheng, The paper you mentioned (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524983/) uses NAMD (http://www.ks.uiuc.edu/Research/namd/) has somewhat different scalability properties than GROMACS. Regards, Benson On Wed, Apr 8, 2020, at 7:14 AM, ZHANG Cheng wrote: > Dear Andre, > > > Thank you. We are trying to use an adenovirus as a vaccine. As it is > not stable, we want to simulate it to identify the unstable regions > (e.g. flexible), so as to either engineering (e.g. mutation) it, or > adding excipients. > > > Simulating only one protein of the capsid is of course doable. But do > you think simulating one protein without its neighbours could reflect > its dynamics? Would its boundary residues behave very differently > compared to with neighbours? > --Original-- > From:"ZHANG Cheng"<272699...@qq.com; > Date:Wed, Apr 8, 2020 11:02 AM > To:"gromacs.org_gmx-users" > Subject:Re:Simulate only one unit of the virus capsid while > fixing its surrounding units > > > > Dear Justin and Andre, > > > Thank you for the advice. So can I ask how commonly the very large > virus capsid is simulated? A recent paper "Physical properties of the > HIV-1 capsid from all-atom molecular dynamics simulations" is using > 3880 GPU accelerated Cray-XK nodes, which is impossible for our > university to provide. > > > > > -- Original -- > From:"ZHANG Cheng"<272699...@qq.com; > Date:Tue, Apr 7, 2020 10:10 PM > To:"ZHANG > Cheng"<272699...@qq.com;"gromacs.org_gmx-users" > Subject:Re:Simulate only one unit of the virus capsid while > fixing its surrounding units > > > > Dear Andre, Thank you for the advice. Can I ask, > > > 1) Could you please clarify the concepts? I know "constraint" and > "restraint" are two different things in gromacs. And "fix" is another > term? How about "freezegrps"? > > > 2) It is okay that the computational time is not reduced, as now only > several proteins are simulated. If I simulate all the several protein > without any fixing, I worry they will lose their conformation. So > fixing the neighbours and only focusing on the protein in the centre > could be the solution. > > > > > > -- Original -- > From:"ZHANG Cheng"<272699...@qq.com; > Date:Tue, Apr 7, 2020 09:41 PM > To:"gromacs.org_gmx-users" Cc:"ZHANG Cheng"<272699...@qq.com; > Subject:Simulate only one unit of the virus capsid while fixing > its surrounding units > > > > It is a challenge to simulate the entire virus as it is too big and I > do not have such computational resources. So I was thinking to only > simulate one coat protein and its surrounding neighbours, but keep the > neighbours relatively fixed. > > > Can I ask > > > 1) Is this a sensible idea to proceed? > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > 3) At which step should I start to introduce the fixation? > > > 4) If possible, is there a tutorial for this? I feel the information > here is still not straightforward to follow > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > Thank you! > > > Yours sincerely > Cheng > -- > 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Andre, Thank you. We are trying to use an adenovirus as a vaccine. As it is not stable, we want to simulate it to identify the unstable regions (e.g. flexible), so as to either engineering (e.g. mutation) it, or adding excipients. Simulating only one protein of the capsid is of course doable. But do you think simulating one protein without its neighbours could reflect its dynamics? Would its boundary residues behave very differently compared to with neighbours? --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Wed, Apr 8, 2020 11:02 AM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Cheng, maybe you should step back and begin the planification of your research project considering how much computer power you have available. If you cannot handle the whole capsid then you have to simplify the model either using some coarse grained force field (MARTINI, for instance) or studying a smaller part of the capsid. but these choices are up to you, they depend on what questions you are trying to answer. Andre On Wed, Apr 8, 2020 at 12:02 AM ZHANG Cheng <272699...@qq.com> wrote: > Dear Justin and Andre, > > > Thank you for the advice. So can I ask how commonly the very large virus > capsid is simulated? A recent paper "Physical properties of the HIV-1 > capsid from all-atom molecular dynamics simulations" is using 3880 GPU > accelerated Cray-XK nodes, which is impossible for our university to > provide. > > > > > --Original-- > From:"ZHANG Cheng"<272699...@qq.com; > Date:Tue, Apr 7, 2020 10:10 PM > To:"ZHANG Cheng"<272699...@qq.com;"gromacs.org_gmx-users"< > gromacs.org_gmx-users@maillist.sys.kth.se; > > Subject:Re:Simulate only one unit of the virus capsid while fixing > its surrounding units > > > > Dear Andre, Thank you for the advice. Can I ask, > > > 1) Could you please clarify the concepts? I know "constraint" and > "restraint" are two different things in gromacs. And "fix" is another term? > How about "freezegrps"? > > > 2) It is okay that the computational time is not reduced, as now only > several proteins are simulated. If I simulate all the several protein > without any fixing, I worry they will lose their conformation. So fixing > the neighbours and only focusing on the protein in the centre could be the > solution. > > > > > > -- Original -- > From:"ZHANG Cheng"<272699...@qq.com; > Date:Tue, Apr 7, 2020 09:41 PM > To:"gromacs.org_gmx-users" ; > Cc:"ZHANG Cheng"<272699...@qq.com; > Subject:Simulate only one unit of the virus capsid while fixing its > surrounding units > > > > It is a challenge to simulate the entire virus as it is too big and I do > not have such computational resources. So I was thinking to only simulate > one coat protein and its surrounding neighbours, but keep the neighbours > relatively fixed. > > > Can I ask > > > 1) Is this a sensible idea to proceed? > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > 3) At which step should I start to introduce the fixation? > > > 4) If possible, is there a tutorial for this? I feel the information here > is still not straightforward to follow > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > Thank you! > > > Yours sincerely > Cheng > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Justin and Andre, Thank you for the advice. So can I ask how commonly the very large virus capsid is simulated? A recent paper "Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations" is using 3880 GPU accelerated Cray-XK nodes, which is impossible for our university to provide. --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Tue, Apr 7, 2020 10:10 PM To:"ZHANG Cheng"<272699...@qq.com;"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Cheng, I also think that freezing introduces more artifacts than benefits, since you are probably beginning your simulation from a crystallographic structure and fixing most of the molecules will provide a crystal-like structure, not a relaxed structure closer to the typical physiological conditions. Andre On Tue, Apr 7, 2020 at 11:29 AM Justin Lemkul wrote: > > > On 4/7/20 10:10 AM, ZHANG Cheng wrote: > > Dear Andre, Thank you for the advice. Can I ask, > > > > > > 1) Could you please clarify the concepts? I know "constraint" and > "restraint" are two different things in gromacs. And "fix" is another term? > How about "freezegrps"? > > I would not use "fix" and "restrain" interchangeably. Fixing a quantity > means it cannot vary. With a restraint, movement is disfavored but not > prevented. Freezing is totally artificial and requires you to ignore > nonbonded interactions between the frozen groups. > > > > > 2) It is okay that the computational time is not reduced, as now only > several proteins are simulated. If I simulate all the several protein > without any fixing, I worry they will lose their conformation. So fixing > the neighbours and only focusing on the protein in the centre could be the > solution. > > > > Your approach assumes that the conformations of the proteins are not > dependent on their neighbors. I do not think that is a justifiable > assumption. If you simulate one protein freely and restrain its > neighbors, you're doing a glorified simulation of a crystal, which is > not reflective of biological reality for a virus capsid. > > -Justin > > > > > > > > > --Original-- > > From:"ZHANG Cheng"<272699...@qq.com; > > Date:Tue, Apr 7, 2020 09:41 PM > > To:"gromacs.org_gmx-users"< > gromacs.org_gmx-users@maillist.sys.kth.se; > > Cc:"ZHANG Cheng"<272699...@qq.com; > > Subject:Simulate only one unit of the virus capsid while fixing > its surrounding units > > > > > > > > It is a challenge to simulate the entire virus as it is too big and I do > not have such computational resources. So I was thinking to only simulate > one coat protein and its surrounding neighbours, but keep the neighbours > relatively fixed. > > > > > > Can I ask > > > > > > 1) Is this a sensible idea to proceed? > > > > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > > > > 3) At which step should I start to introduce the fixation? > > > > > > 4) If possible, is there a tutorial for this? I feel the information > here is still not straightforward to follow > > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > > > > Thank you! > > > > > > Yours sincerely > > Cheng > > -- > == > > 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 > > == > > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
On 4/7/20 10:10 AM, ZHANG Cheng wrote: Dear Andre, Thank you for the advice. Can I ask, 1) Could you please clarify the concepts? I know "constraint" and "restraint" are two different things in gromacs. And "fix" is another term? How about "freezegrps"? I would not use "fix" and "restrain" interchangeably. Fixing a quantity means it cannot vary. With a restraint, movement is disfavored but not prevented. Freezing is totally artificial and requires you to ignore nonbonded interactions between the frozen groups. 2) It is okay that the computational time is not reduced, as now only several proteins are simulated. If I simulate all the several protein without any fixing, I worry they will lose their conformation. So fixing the neighbours and only focusing on the protein in the centre could be the solution. Your approach assumes that the conformations of the proteins are not dependent on their neighbors. I do not think that is a justifiable assumption. If you simulate one protein freely and restrain its neighbors, you're doing a glorified simulation of a crystal, which is not reflective of biological reality for a virus capsid. -Justin --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Tue, Apr 7, 2020 09:41 PM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- == 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 == -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Andre, Thank you for the advice. Can I ask, 1) Could you please clarify the concepts? I know "constraint" and "restraint" are two different things in gromacs. And "fix" is another term? How about "freezegrps"? 2) It is okay that the computational time is not reduced, as now only several proteins are simulated. If I simulate all the several protein without any fixing, I worry they will lose their conformation. So fixing the neighbours and only focusing on the protein in the centre could be the solution. --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Tue, Apr 7, 2020 09:41 PM To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
Dear Cheng, Either fixing or constraining the other units will not decrease the computational cost of the simulation since you will still be computing the interactions between the unit that can move and all the other fixed/constrained units. Andre On Tue, Apr 7, 2020 at 10:41 AM ZHANG Cheng <272699...@qq.com> wrote: > It is a challenge to simulate the entire virus as it is too big and I do > not have such computational resources. So I was thinking to only simulate > one coat protein and its surrounding neighbours, but keep the neighbours > relatively fixed. > > > Can I ask > > > 1) Is this a sensible idea to proceed? > > > 2) To fix the neighbours, should I use "constraints" or "restraints"? > > > 3) At which step should I start to introduce the fixation? > > > 4) If possible, is there a tutorial for this? I feel the information here > is still not straightforward to follow > http://www.gromacs.org/Documentation/How-tos/Position_Restraints > > > Thank you! > > > Yours sincerely > Cheng > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Simulate only one unit of the virus capsid while fixing its surrounding units
It is a challenge to simulate the entire virus as it is too big and I do not have such computational resources. So I was thinking to only simulate one coat protein and its surrounding neighbours, but keep the neighbours relatively fixed. Can I ask 1) Is this a sensible idea to proceed? 2) To fix the neighbours, should I use "constraints" or "restraints"? 3) At which step should I start to introduce the fixation? 4) If possible, is there a tutorial for this? I feel the information here is still not straightforward to follow http://www.gromacs.org/Documentation/How-tos/Position_Restraints Thank you! Yours sincerely Cheng -- 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.
