Re: [gmx-users] Radial Density Profile
Hi Elham, In general to calculate the radial density profile of a droplet-like object one should do binning (histogram) in spherical coordinate along radius. That means you should define a series of shell each with thickness of dr and all centered on center of the vesicle. And then you could count how many atoms of your interest are withing each shell so that you would get something like \rho (r) at the end. Regards, Salman On Fri, Nov 29, 2019 at 4:52 AM elham wrote: > Dear all, I am working on vesicle structure of surfactants in water. I > want to calculate the radial density profile of surfactant headgroup atoms > versus r. The head group atoms are located on the vesicle surface.How can I > plot the radial density profile of headgroup atoms from the center of > vesicle versus r ? > Best regards > -- > 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] Fw: Radial Density Profile
Apologies for mis-reading your question. You need to look at the definition of what radial distribution function actually means and calculates, the atom density falls out of that. What they are asking for is the atom density, p(r)local, as a function of distance r from the center of the vesicle. You can do that from the radial distribution function, g(r). p(r)local = g(r) * p(bulk) Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Sat, 30 Nov 2019 at 03:37, elham wrote: > Dear Dr. Dallas Warren, > Many thanks for your response. I calculated the radial distribution > function of atoms on the surface of vesicles relative to the vesicle center > of mass. I submitted my paper and the referees asked me to calculate the > radial density profile instead of radial distribution function.I can plot > the density profile versus X, Y and Z direction.My question is, how can I > plot the density profile of an atom versus r?Best regards > > > >- Forwarded Message - From: Dallas Warren < > dallas.war...@monash.edu>To: GROMACS users ; elham > Sent: Friday, November 29, 2019, 11:41:07 AM > UTCSubject: Re: [gmx-users] Radial Density Profile > You want to calculate the RDF between the center of mass of an > appropriate group that will be at the center of the vesicle (probably the > surfactant, or alkane chain of the surfactant, and need to ensure that you > only have a single vesicle that perform the calculation on) to the center > of mass of each surfactant head group (or a particular atom of the head > group). Below link will help with the selection syntax required. > http://manual.gromacs.org/documentation/current/onlinehelp/selections.html > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > On Fri, 29 Nov 2019 at 20:52, elham wrote: > > Dear all, I am working on vesicle structure of surfactants in water. I > want to calculate the radial density profile of surfactant headgroup atoms > versus r. The head group atoms are located on the vesicle surface.How can I > plot the radial density profile of headgroup atoms from the center of > vesicle versus r ? > Best regards > -- > 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.
[gmx-users] Fw: Radial Density Profile
Dear Dr. Dallas Warren, Many thanks for your response. I calculated the radial distribution function of atoms on the surface of vesicles relative to the vesicle center of mass. I submitted my paper and the referees asked me to calculate the radial density profile instead of radial distribution function.I can plot the density profile versus X, Y and Z direction.My question is, how can I plot the density profile of an atom versus r?Best regards - Forwarded Message - From: Dallas Warren To: GROMACS users ; elham Sent: Friday, November 29, 2019, 11:41:07 AM UTCSubject: Re: [gmx-users] Radial Density Profile You want to calculate the RDF between the center of mass of an appropriate group that will be at the center of the vesicle (probably the surfactant, or alkane chain of the surfactant, and need to ensure that you only have a single vesicle that perform the calculation on) to the center of mass of each surfactant head group (or a particular atom of the head group). Below link will help with the selection syntax required. http://manual.gromacs.org/documentation/current/onlinehelp/selections.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 29 Nov 2019 at 20:52, elham wrote: Dear all, I am working on vesicle structure of surfactants in water. I want to calculate the radial density profile of surfactant headgroup atoms versus r. The head group atoms are located on the vesicle surface.How can I plot the radial density profile of headgroup atoms from the center of vesicle versus r ? Best regards -- 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] the a.u. unit in the RMS distribution graph
Hello Lalehan and Justin, Thanks for the suggestion! The following patch : https://gerrit.gromacs.org/c/gromacs/+/14542 does exactly that. Best, Christian On 2019-11-29 14:23, Justin Lemkul wrote: On 11/29/19 7:18 AM, Christian Blau wrote: Hello Lalehan, a.u. stands for "arbitrary units". The rmsd-dist contains a histogram over the distribution of rmsd values, you can read the a.u. as counts per length-interval. I would suggest that all histograms that GROMACS produces actually be labeled reasonably in the code - using a.u. is itself arbitrary because it has multiple possible meanings. If it's a raw histogram, we should be using "Frequency" and if normalized, "Probability." -Justin -- 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] Calculation of RMSF
Thank you for your answer. As Mala said, since it is called the reference structure, I was thinking that the RMSF was computed with respect to this structure and not the average structure. Is there any way with Gromacs to compute RMSF exactly with respect to a given structure? If I want to study a crystal of protein for force field validation (as in https://pubs.acs.org/doi/abs/10.1021/jp105813j), I would like to compute RMSF exactly with respect to the XRay structure first. If not with Gromacs, does someone know a way to do it with something else (cpptraj, mdanalysis, mdtraj?) Thank you Nicolas Le ven. 29 nov. 2019 à 14:22, Justin Lemkul a écrit : > > > On 11/29/19 5:53 AM, Mala L Radhakrishnan wrote: > > Hi, > > > > I am confused a bit by this answer -- isn't the file specified by -s used > > for defining the rmsf (this is what is called the "reference" structure > in > > the documentation, and I have found that my results do vary using a > > different "-s" file)...? Or is that just used for fitting and then the > > average of the resulting fitted structures is used for the rmsf? > > Specifically, what is the "-s" uased for in this case? > > It is used for fitting. RMSF is simply the standard deviation of > position, so an average structure is computed from the selected frames > and the RMSF is computed from it. > > -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] the a.u. unit in the RMS distribution graph
Hello Justin, thank you for the response. In that case I should use "frequency" if I plan to take it the way it is. Thanks, On Fri, Nov 29, 2019 at 4:25 PM Justin Lemkul wrote: > > > On 11/29/19 7:18 AM, Christian Blau wrote: > > Hello Lalehan, > > > > > > a.u. stands for "arbitrary units". > > > > The rmsd-dist contains a histogram over the distribution of rmsd > > values, you can read the a.u. as counts per length-interval. > > > > I would suggest that all histograms that GROMACS produces actually be > labeled reasonably in the code - using a.u. is itself arbitrary because > it has multiple possible meanings. If it's a raw histogram, we should be > using "Frequency" and if normalized, "Probability." > > -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] the a.u. unit in the RMS distribution graph
On 11/29/19 7:18 AM, Christian Blau wrote: Hello Lalehan, a.u. stands for "arbitrary units". The rmsd-dist contains a histogram over the distribution of rmsd values, you can read the a.u. as counts per length-interval. I would suggest that all histograms that GROMACS produces actually be labeled reasonably in the code - using a.u. is itself arbitrary because it has multiple possible meanings. If it's a raw histogram, we should be using "Frequency" and if normalized, "Probability." -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.
Re: [gmx-users] Calculation of RMSF
On 11/29/19 5:53 AM, Mala L Radhakrishnan wrote: Hi, I am confused a bit by this answer -- isn't the file specified by -s used for defining the rmsf (this is what is called the "reference" structure in the documentation, and I have found that my results do vary using a different "-s" file)...? Or is that just used for fitting and then the average of the resulting fitted structures is used for the rmsf? Specifically, what is the "-s" uased for in this case? It is used for fitting. RMSF is simply the standard deviation of position, so an average structure is computed from the selected frames and the RMSF is computed from it. -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.
Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer
On 11/29/19 3:27 AM, Mijiddorj B wrote: Dear Justin, As you suggested, I generated the charmm36 parameter using cgenff for single unit with two capping groups. After that, I created 3 residues based on the parameter of cgenff including N-ter side, Middle, and C-ter side residues. However, the net charges of these residues are not equal to zero as -0.002, -0.004, and -0.002, respectively. 1. How can I adjust the charge of these residue? Your model compound surely didn't have a net -0.008 charge, so make sure you're assigning charges correctly. Without seeing your actual residue definitions, there's nothing I (or anyone else) can suggest. 2. Is it possible to run simulation ignoring the grompp comments? When grompp tells you there's a problem, don't ignore it. If you're trying to simply override these unphysical charges, your simulation will be useless because your model does not reflect reality. -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.
Re: [gmx-users] Disulphide bonded cyclic peptides
The terminal selection should be NONE. First, you should have a CPN structure with disulfide bonds. https://www.tandfonline.com/doi/abs/10.1080/07391102.2019.1570341 -- 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] the a.u. unit in the RMS distribution graph
Hello Christian! Thank you for the valuable information :) Best, Lalehan On Fri, Nov 29, 2019 at 3:18 PM Christian Blau wrote: > Hello Lalehan, > > > a.u. stands for "arbitrary units". > > The rmsd-dist contains a histogram over the distribution of rmsd values, > you can read the a.u. as counts per > length-interval. > > > Best, > > Christian > > On 2019-11-29 12:57, Lalehan Ozalp wrote: > > Hello everyone, I ran a cluster analysis for a 10 ns simulation and > > produced rmsd-clust.xpm and rmsd-dist.xvg graphs. When I open the xvg > file, > > I see "a. u." in the y axis which I couldn't entirely understand. Is it > > supposed to stand for atomic unit for length or mass or something else? I > > provide the file as an example. > > > > Thank you in advance. > > > > Lalehan > > > -- > 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] the a.u. unit in the RMS distribution graph
Hello Lalehan, a.u. stands for "arbitrary units". The rmsd-dist contains a histogram over the distribution of rmsd values, you can read the a.u. as counts per length-interval. Best, Christian On 2019-11-29 12:57, Lalehan Ozalp wrote: Hello everyone, I ran a cluster analysis for a 10 ns simulation and produced rmsd-clust.xpm and rmsd-dist.xvg graphs. When I open the xvg file, I see "a. u." in the y axis which I couldn't entirely understand. Is it supposed to stand for atomic unit for length or mass or something else? I provide the file as an example. Thank you in advance. Lalehan -- 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] the a.u. unit in the RMS distribution graph
Hello everyone, I ran a cluster analysis for a 10 ns simulation and produced rmsd-clust.xpm and rmsd-dist.xvg graphs. When I open the xvg file, I see "a. u." in the y axis which I couldn't entirely understand. Is it supposed to stand for atomic unit for length or mass or something else? I provide the file as an example. Thank you in advance. Lalehan -- 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] Radial Density Profile
You want to calculate the RDF between the center of mass of an appropriate group that will be at the center of the vesicle (probably the surfactant, or alkane chain of the surfactant, and need to ensure that you only have a single vesicle that perform the calculation on) to the center of mass of each surfactant head group (or a particular atom of the head group). Below link will help with the selection syntax required. http://manual.gromacs.org/documentation/current/onlinehelp/selections.html Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 29 Nov 2019 at 20:52, elham wrote: > Dear all, I am working on vesicle structure of surfactants in water. I > want to calculate the radial density profile of surfactant headgroup atoms > versus r. The head group atoms are located on the vesicle surface.How can I > plot the radial density profile of headgroup atoms from the center of > vesicle versus r ? > Best regards > -- > 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] Calculation of RMSF
Hi, I am confused a bit by this answer -- isn't the file specified by -s used for defining the rmsf (this is what is called the "reference" structure in the documentation, and I have found that my results do vary using a different "-s" file)...? Or is that just used for fitting and then the average of the resulting fitted structures is used for the rmsf? Specifically, what is the "-s" uased for in this case? Thanks, Mala On Thu, Nov 28, 2019 at 9:24 PM Justin Lemkul wrote: > > > On 11/28/19 12:09 PM, Nicolas Cheron wrote: > > Dear all, > > > > I am puzzled by the way RMSF are computed. For a given trajectory > (nothing > > fancy, just a regular protein): > > (1) I have computed RMSF 5 times for two frames i.e. Frame 1/2, 3/4, 5/6, > > 7/8 and 9/10, each time using the same pdb reference (if I compute RMSF > for > > a single frame I sometimes have -nan, that's why I did it for couple of > > frames) > > The RMSF of one frame is always undefined, because there is no fluctuation. > > > (2) I have then computed RMSF for the 10 frames at the same time (1-10). > > > > I would expect that the average of RMSF^2 for (1) would equal RMSF^2 for > > (2), but that's not the case. To give you some numbers for 4 Calpha > carbons: > > Avg of case (1) case (2) > > 0,000722 0,001673 > > 0,000417 0,001197 > > 0,000400 0,001096 > > 0,000768 0,001910 > > It doesn't seem to be a rounding issue, neither a systematic difference. > > > > Can anyone please help me understand these differences? > > The average structure is different, so the RMSF is different as a > result. RMSF computes the fluctuation about an average structure, > computed from the coordinates in the frames you analyze. So if you > analyze 2 frames, the reference is the average of those two and you > return the RMSF about it. If you analyze 10 frames, your reference is > the average of those 10 and may not look anything like the average of > any 2 frames. > > -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. > -- Mala L. Radhakrishnan Associate Professor of Chemistry Director, Biochemistry Program Wellesley College 106 Central Street Wellesley, MA 02481 (781)283-2981 -- 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] Disulphide bonded cyclic peptides
Hi, On Fri, Nov 29, 2019 at 8:30 AM Sahil Lall wrote: > Hello, > > Thank you for your suggestions, gave me some insight into my own work. > However, the problem still persists. > > > With the option -ignh, you request pdb2gmx to add H atom. Thus, if you > have already H atoms in the pdb I suggest to remove the option -ignh. > > I had already tried removing the -ignh option before posting this here > but did not find success. > > Did you try also without -ter? > > Removing the -ter option does not work in any combination. It always > overrides everything else and breaks the cyclising peptide bond into > NH3+ and COO-. > > . > > > Another option could be to remove the extra H from gro/pdb file you got > from pdb2gmx, remove H, (if you want, fix the atom number using editconf), > then try to use the so obtained pdb/gro file as input to pdb2gmx (without > -ter -ignh) > > So this also does not work. pdb2gmx breaks the peptide bond without the > -ter option. > > I tried putting a new entry in the OPLS aminoacids.n.tdb file as you > suggested. I used the opls_910 planar hydrogen for secondary amines as > shown below > > [ CYS2-NH ] > [ replace ] > N opls_900 14.0027 -0.9 > CA opls_912B 12.011 0.12 > [ add ] > 1 1 H N CA C > opls_910 1.008 0.36 > [ delete ] > H > > You got a charged system, probably because you have generated a new entry without accounting for the partial charge. As atomic charge and atom types I suggest to use the one of the backbone for your new entry (since you do not have a real termini) for CYS-1 Nopls_238 -0.500 0 Hopls_2410.300 0 CAopls_224B 0.140 1 You could also directly change the charges in the top file. I hope this solve the problem Best regards Alessandra Now I can get the peptide bond correctly but the system is charged. > Output below: > > Identified residue CYS1 as a starting terminus. > Identified residue CYS6 as a ending terminus. > 2 out of 2 lines of specbond.dat converted successfully > Special Atom Distance matrix: > CYS1 CYS1 CYS1 CYS6 CYS6 > N1 C3 SG6 N87 C89 > CYS1 C3 0.244 > CYS1 SG6 0.312 0.419 > CYS6 N87 0.335 0.510 0.486 > CYS6 C89 0.136 0.373 0.322 0.239 > CYS6 SG92 0.387 0.482 0.205 0.420 0.365 > Linking CYS-1 N-1 and CYS-6 C-89... > Linking CYS-1 SG-6 and CYS-6 SG-92... > Select start terminus type for CYS-1 > 0: CYS2-NH > 1: NH3+ > 2: ZWITTERION_NH3+ (only use with zwitterions containing exactly one > residue) > 3: NH2 > 4: None > 0 > Start terminus CYS-1: CYS2-NH > Select end terminus type for CYS-6 > 0: COO- > 1: ZWITTERION_COO- (only use with zwitterions containing exactly one > residue) > 2: COOH > 3: None > 3 > End terminus CYS-6: None > Checking for duplicate atoms > Generating any missing hydrogen atoms and/or adding termini. > Now there are 6 residues with 96 atoms > Making bonds... > Number of bonds was 99, now 98 > Generating angles, dihedrals and pairs... > Before cleaning: 258 pairs > Before cleaning: 258 dihedrals > Keeping all generated dihedrals > Making cmap torsions...There are 258 dihedrals, 21 impropers, 174 angles > 255 pairs, 98 bonds and 0 virtual sites > Total mass 734.892 a.m.u. > Total charge -0.420 e > Writing topology > > Any ideas? > > Extremely thankful > > Sahil > > On 2019-11-28 20:15, Alessandra Villa wrote: > > > Hi again, > > > > On Thu, Nov 28, 2019 at 11:06 AM Sahil Lall wrote: > > > > Hello, > > > > I am extremely thankful for your suggestions, but I have a few concerns > > with your advice as stated below. > > > > Hi, > > Below some suggestion that may help you. > > > > On Wed, Nov 27, 2019 at 7:44 AM Sahil Lall wrote: > > > > Dear community, > > > > I want to use the OPLS-AA ff to understand the dynamics of a cyclic > > peptide with terminal Cystines that are disulphide linked. To cyclise > > the N- and C- termini, I used a special bond in a specbond.dat file > > placed in my working directory. > > > > 2 > > CYS N 1 CYS C 1 0.14 CYS CYS > > CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 > > > > and after the pdb2gmx command I get the following response > > > > Identified residue CYS2 as a starting terminus. > > Identified residue CYS7 as a ending terminus. > > 2 out of 2 lines of specbond.dat converted successfully > > Special Atom Distance matrix: > > CYS2CYS2CYS2CYS7CYS7 > > N1 C3 SG6 N45 C47 > > CYS2 C3 0.244 > > CYS2 SG6 0.312 0.419 > > CYS7 N45 0.335 0.510 0.486 > > CYS7 C47 0.136 0.373 0.322 0.239 > > CYS7SG50 0.387 0.482 0.205 0.420 0.365 > > Linking CYS-2 N-1 and CYS-7 C-47... > > Linking CYS-2 SG-6 and CYS-7 SG-50... > > > > However, the problem arises with the -ter flag in the pdb2gmx command > > > > pdb2gmx -f in.pdb -o out.gro -ter -ignh > > > > With the option -ignh, you request pdb2gmx to add H atom. Thus, if you > have already H atoms in the pdb I suggest to remove the option -ignh. > > I had already tried removing the -ignh option before posting this here > but did not find success. > > Did
[gmx-users] Radial Density Profile
Dear all, I am working on vesicle structure of surfactants in water. I want to calculate the radial density profile of surfactant headgroup atoms versus r. The head group atoms are located on the vesicle surface.How can I plot the radial density profile of headgroup atoms from the center of vesicle versus r ? Best regards -- 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] Calculation of young's modulus from stress-strain plot
Hi, On Thu, Nov 28, 2019 at 1:23 PM Pragati Sharma wrote: > Hello users, > > I am trying to plot stress-strain curve for natural rubber from NPT > simulations using the "deform" option. Deform along x direction at 1 bar > pressure. The parameters I gave in mdp file are: > > Pcoupl = Berendsen > Pcoupltype = semiisotropic > tau_p = 2 > compressibility= 0 4.5e-5 4.5e-5 > ref_p = 1 11 > deform = 0.01 0 0 0 0 0 > > Q. Should I give six values to ref_P and compressibility also. > Semiisotropic: Pressure coupling which is isotropic in the x and y direction, but different in the z direction. Two values each for compressibility and ref-p are required, for x/y and z directions respectively. Anisotropic: values are needed for xx, yy, zz, xy/yx, xz/zx and yz/zy components, respectively. When the off-diagonal compressibilities are set to zero, a rectangular box will stay rectangular. Beware that anisotropic scaling can lead to extreme deformation of the simulation box. Best regards Alessandra Q. If I give 'anisotropic' coupling, then the error is > "ERROR 1: Pressure coupling incorrect number of values (I need exactly 6)" > Should I give the next three values as zero or 1. OR I can just use > semiisotropic coupling only. > > Thanks in advance!! > -- > 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] Charmm27 and Charmm36 atomtypes assignments for polymer
Dear Justin, As you suggested, I generated the charmm36 parameter using cgenff for single unit with two capping groups. After that, I created 3 residues based on the parameter of cgenff including N-ter side, Middle, and C-ter side residues. However, the net charges of these residues are not equal to zero as -0.002, -0.004, and -0.002, respectively. 1. How can I adjust the charge of these residue? 2. Is it possible to run simulation ignoring the grompp comments? Best regards, Mijiddorj On 11/20/19 8:51 PM, Mijiddorj B wrote: > > Dear Prof. Justin, > > > > Thank you very much for your reply. I would like to use charmm27 because > my > > system contains a surface model, which were parametrized by INTERFACE > Force > > Field and compatible with charmm27. The polymer parameters of charmm27 > were > > AFAIK there's no reason to believe you have to use CHARMM27; INTERFACE > is generally compatible with CHARMM, which has a linear development > history so you should be able to combine it with any CHARMM potential. > > > generated by swissparam, and the server renamed the atomtypes. I would > like > > to assign those parameters with original charmm27. If possible, I would > > like to use original charmm27 parameters instead of the values of > > swissparam. I used charmm36 atomtypes for clarification. > > I do not know the atom type of the nitrogen which connected with three > > carbons. > > NG301. I still think it's best if you simply parametrize your monomer > units with CGenFF and use its parameters unless there are major penalties. > > -Justin > > -- 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.
