Re: [gmx-users] Fwd: Probability of number of atomic contacts
Hi, When I use the tool, gmx analyze -dist, on the generated file from gmx mindist for the number of contact, I can get the probability of number of contacts. So I think if an appropriate index file and cut off distance are defined by using this approach, I can get the probability of the first shell coordination number for specific groups during the simulation time. Is this correct? because the coordination number from gmx rdf gives the average number of particles within a distance r. Best regards, Mahsa On Fri, Mar 1, 2019 at 12:11 PM Mahsa wrote: > Hi Mark, > > Thank you for your reply! Actually, I should clarify my last post because > it seems that I repeated my question :-) > When I use the tool that Justin suggested, gmx analyze -dist, on the > generated file from gmx mindist for the number of contact, I can get the > probability of number of contacts. So I think if an appropriate index file > and cut off distance are defined by using this approach, I can get the > probability of the first shell coordination number for specific groups > during the simulation time. Is this correct? because the coordination > number from gmx rdf gives the average number of particles within a distance > r. > > Best regards, > Mahsa > > On Fri, Mar 1, 2019 at 5:04 AM Mark Abraham > wrote: > >> Hi, >> >> Which GROMACS tools documentation did you check to see whether it can be >> done already? :-) I don't know the answer, but that's where to start! >> >> Mark >> >> On Thu., 28 Feb. 2019, 10:43 Mahsa, wrote: >> >> > Thank you very much for your comments! >> > >> > How would it be possible to get probability vs. number of contacts or >> > probability vs coordination number averaged across the simulations? Can >> it >> > be done directly with Gromacs tools or I need some scripts for that? >> > >> > Best regards, >> > Mahsa >> > >> > On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul wrote: >> > >> > > >> > > >> > > On 2/28/19 8:59 AM, Mahsa wrote: >> > > > Hi Justin, >> > > > >> > > > Could you please comment on my questions in the previous post? >> > > > >> > > > Best regards, >> > > > Mahsa >> > > > >> > > > -- Forwarded message - >> > > > From: Mahsa >> > > > Date: Sun, Feb 17, 2019 at 2:36 PM >> > > > Subject: Re: [gmx-users] Probability of number of atomic contacts >> > > > To: >> > > > >> > > > >> > > > Thank you very much, Justin! >> > > > >> > > > I tried this command: >> > > > >> > > > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg >> > > > >> > > > >> > > > and I got a histogram. Now the number of contacts between the ion >> and >> > the >> > > > polymer is between 160-180. I just want to be sure if I am doing >> this >> > > > analysis correct. When I use gmx mindist, from the index file I >> choose >> > a >> > > > group of the ion (including 46 ions) and then the polymer group (all >> > > > polymer chains in the box). I think maybe instead of choosing all >> > ions, >> > > I >> > > > should only select one of them and get the number of contact with >> the >> > > > polymers but then since I have 46 of this ion in the simulation box, >> > can >> > > it >> > > > be a good representative of the whole system? If not, what else can >> I >> > do >> > > in >> > > > this case? >> > > >> > > I don't see any point in doing per-ion analysis. You already have the >> > > answer you want with respect to contacts between the two species. >> > > Choosing one ion isn't necessarily going to be representative, either. >> > > >> > > > Besides, it is mentioned in the Gromacs manual, that if we use the >> > > > -group option >> > > > a contact of an atom in another group with multiple atoms in the >> first >> > > > group is counted as one contact instead of as multiple contacts. I >> want >> > > to >> > > > count all contact with a polymer chain as 1 contact and check the >> > number >> > > of >> > > > contacts with different polymer chains so by using -group and having >> > the >> > > > ion as the first group and polymer as the second group from the >> index >> > > file, >> > > > can I get this? >> > > >> > > This option is primarily used to avoid over-counting, e.g. the >> > > interaction between an ion and carboxylate oxygens will not be counted >> > > as two contact if each ion-oxygen distance satisfies the criterion; >> it's >> > > just one. >> > > >> > > > The last question, can I do the same approach to get the >> distribution >> > of >> > > > coordination number for the first coordination shell of ions and >> > special >> > > > atoms of the polymers? >> > > >> > > You can calculate coordination number by integrating an RDF. >> > > >> > > -Justin >> > > >> > > -- >> > > == >> > > >> > > 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 >> > >
Re: [gmx-users] Fwd: Probability of number of atomic contacts
Hi Mark, Thank you for your reply! Actually, I should clarify my last post because it seems that I repeated my question :-) When I use the tool that Justin suggested, gmx analyze -dist, on the generated file from gmx mindist for the number of contact, I can get the probability of number of contacts. So I think if an appropriate index file and cut off distance are defined by using this approach, I can get the probability of the first shell coordination number for specific groups during the simulation time. Is this correct? because the coordination number from gmx rdf gives the average number of particles within a distance r. Best regards, Mahsa On Fri, Mar 1, 2019 at 5:04 AM Mark Abraham wrote: > Hi, > > Which GROMACS tools documentation did you check to see whether it can be > done already? :-) I don't know the answer, but that's where to start! > > Mark > > On Thu., 28 Feb. 2019, 10:43 Mahsa, wrote: > > > Thank you very much for your comments! > > > > How would it be possible to get probability vs. number of contacts or > > probability vs coordination number averaged across the simulations? Can > it > > be done directly with Gromacs tools or I need some scripts for that? > > > > Best regards, > > Mahsa > > > > On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul wrote: > > > > > > > > > > > On 2/28/19 8:59 AM, Mahsa wrote: > > > > Hi Justin, > > > > > > > > Could you please comment on my questions in the previous post? > > > > > > > > Best regards, > > > > Mahsa > > > > > > > > -- Forwarded message - > > > > From: Mahsa > > > > Date: Sun, Feb 17, 2019 at 2:36 PM > > > > Subject: Re: [gmx-users] Probability of number of atomic contacts > > > > To: > > > > > > > > > > > > Thank you very much, Justin! > > > > > > > > I tried this command: > > > > > > > > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg > > > > > > > > > > > > and I got a histogram. Now the number of contacts between the ion and > > the > > > > polymer is between 160-180. I just want to be sure if I am doing this > > > > analysis correct. When I use gmx mindist, from the index file I > choose > > a > > > > group of the ion (including 46 ions) and then the polymer group (all > > > > polymer chains in the box). I think maybe instead of choosing all > > ions, > > > I > > > > should only select one of them and get the number of contact with the > > > > polymers but then since I have 46 of this ion in the simulation box, > > can > > > it > > > > be a good representative of the whole system? If not, what else can I > > do > > > in > > > > this case? > > > > > > I don't see any point in doing per-ion analysis. You already have the > > > answer you want with respect to contacts between the two species. > > > Choosing one ion isn't necessarily going to be representative, either. > > > > > > > Besides, it is mentioned in the Gromacs manual, that if we use the > > > > -group option > > > > a contact of an atom in another group with multiple atoms in the > first > > > > group is counted as one contact instead of as multiple contacts. I > want > > > to > > > > count all contact with a polymer chain as 1 contact and check the > > number > > > of > > > > contacts with different polymer chains so by using -group and having > > the > > > > ion as the first group and polymer as the second group from the index > > > file, > > > > can I get this? > > > > > > This option is primarily used to avoid over-counting, e.g. the > > > interaction between an ion and carboxylate oxygens will not be counted > > > as two contact if each ion-oxygen distance satisfies the criterion; > it's > > > just one. > > > > > > > The last question, can I do the same approach to get the distribution > > of > > > > coordination number for the first coordination shell of ions and > > special > > > > atoms of the polymers? > > > > > > You can calculate coordination number by integrating an RDF. > > > > > > -Justin > > > > > > -- > > > == > > > > > > 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. > > > > > -- > > 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
Re: [gmx-users] Fwd: Probability of number of atomic contacts
Hi, Which GROMACS tools documentation did you check to see whether it can be done already? :-) I don't know the answer, but that's where to start! Mark On Thu., 28 Feb. 2019, 10:43 Mahsa, wrote: > Thank you very much for your comments! > > How would it be possible to get probability vs. number of contacts or > probability vs coordination number averaged across the simulations? Can it > be done directly with Gromacs tools or I need some scripts for that? > > Best regards, > Mahsa > > On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul wrote: > > > > > > > On 2/28/19 8:59 AM, Mahsa wrote: > > > Hi Justin, > > > > > > Could you please comment on my questions in the previous post? > > > > > > Best regards, > > > Mahsa > > > > > > -- Forwarded message - > > > From: Mahsa > > > Date: Sun, Feb 17, 2019 at 2:36 PM > > > Subject: Re: [gmx-users] Probability of number of atomic contacts > > > To: > > > > > > > > > Thank you very much, Justin! > > > > > > I tried this command: > > > > > > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg > > > > > > > > > and I got a histogram. Now the number of contacts between the ion and > the > > > polymer is between 160-180. I just want to be sure if I am doing this > > > analysis correct. When I use gmx mindist, from the index file I choose > a > > > group of the ion (including 46 ions) and then the polymer group (all > > > polymer chains in the box). I think maybe instead of choosing all > ions, > > I > > > should only select one of them and get the number of contact with the > > > polymers but then since I have 46 of this ion in the simulation box, > can > > it > > > be a good representative of the whole system? If not, what else can I > do > > in > > > this case? > > > > I don't see any point in doing per-ion analysis. You already have the > > answer you want with respect to contacts between the two species. > > Choosing one ion isn't necessarily going to be representative, either. > > > > > Besides, it is mentioned in the Gromacs manual, that if we use the > > > -group option > > > a contact of an atom in another group with multiple atoms in the first > > > group is counted as one contact instead of as multiple contacts. I want > > to > > > count all contact with a polymer chain as 1 contact and check the > number > > of > > > contacts with different polymer chains so by using -group and having > the > > > ion as the first group and polymer as the second group from the index > > file, > > > can I get this? > > > > This option is primarily used to avoid over-counting, e.g. the > > interaction between an ion and carboxylate oxygens will not be counted > > as two contact if each ion-oxygen distance satisfies the criterion; it's > > just one. > > > > > The last question, can I do the same approach to get the distribution > of > > > coordination number for the first coordination shell of ions and > special > > > atoms of the polymers? > > > > You can calculate coordination number by integrating an RDF. > > > > -Justin > > > > -- > > == > > > > 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. > > > -- > 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] Fwd: Probability of number of atomic contacts
Thank you very much for your comments! How would it be possible to get probability vs. number of contacts or probability vs coordination number averaged across the simulations? Can it be done directly with Gromacs tools or I need some scripts for that? Best regards, Mahsa On Thu, Feb 28, 2019 at 7:17 PM Justin Lemkul wrote: > > > On 2/28/19 8:59 AM, Mahsa wrote: > > Hi Justin, > > > > Could you please comment on my questions in the previous post? > > > > Best regards, > > Mahsa > > > > -- Forwarded message - > > From: Mahsa > > Date: Sun, Feb 17, 2019 at 2:36 PM > > Subject: Re: [gmx-users] Probability of number of atomic contacts > > To: > > > > > > Thank you very much, Justin! > > > > I tried this command: > > > > gmx_seq analyze -f numcont.xvg -dist num_dist.xvg > > > > > > and I got a histogram. Now the number of contacts between the ion and the > > polymer is between 160-180. I just want to be sure if I am doing this > > analysis correct. When I use gmx mindist, from the index file I choose a > > group of the ion (including 46 ions) and then the polymer group (all > > polymer chains in the box). I think maybe instead of choosing all ions, > I > > should only select one of them and get the number of contact with the > > polymers but then since I have 46 of this ion in the simulation box, can > it > > be a good representative of the whole system? If not, what else can I do > in > > this case? > > I don't see any point in doing per-ion analysis. You already have the > answer you want with respect to contacts between the two species. > Choosing one ion isn't necessarily going to be representative, either. > > > Besides, it is mentioned in the Gromacs manual, that if we use the > > -group option > > a contact of an atom in another group with multiple atoms in the first > > group is counted as one contact instead of as multiple contacts. I want > to > > count all contact with a polymer chain as 1 contact and check the number > of > > contacts with different polymer chains so by using -group and having the > > ion as the first group and polymer as the second group from the index > file, > > can I get this? > > This option is primarily used to avoid over-counting, e.g. the > interaction between an ion and carboxylate oxygens will not be counted > as two contact if each ion-oxygen distance satisfies the criterion; it's > just one. > > > The last question, can I do the same approach to get the distribution of > > coordination number for the first coordination shell of ions and special > > atoms of the polymers? > > You can calculate coordination number by integrating an RDF. > > -Justin > > -- > == > > 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. > -- 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] Fwd: Probability of number of atomic contacts
On 2/28/19 8:59 AM, Mahsa wrote: Hi Justin, Could you please comment on my questions in the previous post? Best regards, Mahsa -- Forwarded message - From: Mahsa Date: Sun, Feb 17, 2019 at 2:36 PM Subject: Re: [gmx-users] Probability of number of atomic contacts To: Thank you very much, Justin! I tried this command: gmx_seq analyze -f numcont.xvg -dist num_dist.xvg and I got a histogram. Now the number of contacts between the ion and the polymer is between 160-180. I just want to be sure if I am doing this analysis correct. When I use gmx mindist, from the index file I choose a group of the ion (including 46 ions) and then the polymer group (all polymer chains in the box). I think maybe instead of choosing all ions, I should only select one of them and get the number of contact with the polymers but then since I have 46 of this ion in the simulation box, can it be a good representative of the whole system? If not, what else can I do in this case? I don't see any point in doing per-ion analysis. You already have the answer you want with respect to contacts between the two species. Choosing one ion isn't necessarily going to be representative, either. Besides, it is mentioned in the Gromacs manual, that if we use the -group option a contact of an atom in another group with multiple atoms in the first group is counted as one contact instead of as multiple contacts. I want to count all contact with a polymer chain as 1 contact and check the number of contacts with different polymer chains so by using -group and having the ion as the first group and polymer as the second group from the index file, can I get this? This option is primarily used to avoid over-counting, e.g. the interaction between an ion and carboxylate oxygens will not be counted as two contact if each ion-oxygen distance satisfies the criterion; it's just one. The last question, can I do the same approach to get the distribution of coordination number for the first coordination shell of ions and special atoms of the polymers? You can calculate coordination number by integrating an RDF. -Justin -- == 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.
[gmx-users] Fwd: Probability of number of atomic contacts
Hi Justin, Could you please comment on my questions in the previous post? Best regards, Mahsa -- Forwarded message - From: Mahsa Date: Sun, Feb 17, 2019 at 2:36 PM Subject: Re: [gmx-users] Probability of number of atomic contacts To: Thank you very much, Justin! I tried this command: gmx_seq analyze -f numcont.xvg -dist num_dist.xvg and I got a histogram. Now the number of contacts between the ion and the polymer is between 160-180. I just want to be sure if I am doing this analysis correct. When I use gmx mindist, from the index file I choose a group of the ion (including 46 ions) and then the polymer group (all polymer chains in the box). I think maybe instead of choosing all ions, I should only select one of them and get the number of contact with the polymers but then since I have 46 of this ion in the simulation box, can it be a good representative of the whole system? If not, what else can I do in this case? Besides, it is mentioned in the Gromacs manual, that if we use the -group option a contact of an atom in another group with multiple atoms in the first group is counted as one contact instead of as multiple contacts. I want to count all contact with a polymer chain as 1 contact and check the number of contacts with different polymer chains so by using -group and having the ion as the first group and polymer as the second group from the index file, can I get this? The last question, can I do the same approach to get the distribution of coordination number for the first coordination shell of ions and special atoms of the polymers? Best regards, Mahsa On Sun, Feb 17, 2019 at 1:39 PM Justin Lemkul wrote: > > > On 2/17/19 7:21 AM, Mahsa wrote: > > Dear Gromacs users, > > > > I want to get histograms of the number of polymer-ion contacts average > > across the simulation. For this I used, > > > > gmx mindist -f md.xtc -s topol.tpr -n index_traj.ndx -d 0.3 -od > mindist.xvg > > -on numcont.xvg -or mindistres.xvg -group > > > > and from the index file, I chose the ion first and then the polymer > group. > > The generated file numcont.xvg which is more related to what I am looking > > for, gives number of contacts vs time. How can I get the information > which > > I look for from this analysis? > > Post-process with gmx analyze -dist > > -Justin > > -- > == > > 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. > -- 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.
