[gmx-users] farticle demanding about Small-Molecule Topologies
Dear Dr.Lemkul would you please send me full text of your below article : Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies unfortunately, i dont have accessible to full text of this article thanks a lot -- 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] how to remove water molecule inside micelle
Hello, It is not a really problem, since the water will move during the simulation (due to the hydrophobic effect), but It may take for that all the water left the micelle center. So I suggest you to use genbox with the following arguments -shell or -vdwd (see the genbox manual). An other approach if you use Packmol to construct your micelle is to reduce the space between the SDS alkyl chains during the construction process by palying with the value in the inside command in your packmol script # atoms 39 is the last Carbon of the C12 alkyl chain for CHARMM atoms 39 inside sphere 0. 0. 0. 3.0 --- 3 is the distance (in A) between the micelle center and the 12th carbon of the SDS alkyl chain. [1] end atoms [1] - 2-3 is a good value if you want to construct a SDS micelle with 60 monomers - You will need the minimize carrefully the micelle to remove steric clashes between SDS chains HTH -- Message: 3 Date: Mon, 29 Dec 2014 11:09:18 +0330 From: Mina Hashemi hashemi.mi...@gmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] how to remove water molecule inside micelle? Message-ID: CAFYjG+ad2XDVy3PEO9Xnd6E9=n6qsv9srgtkk8sjr0honoh...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Dear gromacs users I prepared my simulation system containing SDS. Then I added water molecules using genbox. Some water molecules entered in to the micelle. How to remove water molecules inside the micelle? Any help will highly appreciated. -- 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] -vsite hydrogen
Dear Users, I am simulating a membrane protein with charmm ff with a 2fs time step. How the results will be affected if I use a 5fs time step by using -vsite hydrogen option in pdb2gmx? Do my results loose their accuracy if I use this option? Best wishes, H.A -- 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] Obtaining PMF for change in domain position
Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which has two large domains connected by a flexible linker peptide (~10 aa). The two domains seem to interact with each other and have been crystallized in three different conformations. I want to calculate the change in binding energy of the two domains wrt change in their relative position, i.e. keeping position of one domain constant what is change in binding energy as the other domain moves from conformation 1, through conformation 2 to finally, conformation 3. What is the best way to do so? At first, I considered using umbrella sampling to address the problem. Here too, I was not sure how to write a pull code for such a complex reaction coordinate. Also, even if I can generate the conformations, what would be the ideal number of windows that would be needed to correctly generate a PMF ? My feeling is it would be a large number, but again it just a guess. Is there is a better way than this? Any help would be appreciated. Thanks in advance. Regards, Abhishek Acharya -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to remove water molecule inside micelle?
it's hard to say without knowing how you prepared and relaxed your micelle before adding water, so I can only provide you a few general comments: (1) a properly relaxed, well-packed micelle should not present any voids and water should not go inside the micelle (check the literature, this has already been done a number of times already for SDS and other surfactants) (2) increasing the value for -vdwd should decrease the number of water molecules inside the micelle, even if the preparation step was not accomplished so carefully. (3) maybe you could try Packmol: http://www.ime.unicamp.br/~martinez/packmol/ On Mon, Dec 29, 2014 at 5:39 AM, Mina Hashemi hashemi.mi...@gmail.com wrote: Dear gromacs users I prepared my simulation system containing SDS. Then I added water molecules using genbox. Some water molecules entered in to the micelle. How to remove water molecules inside the micelle? Any help will highly appreciated. -- 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] charge distribution
On 12/29/14 2:31 AM, elham tazikeh wrote: Dear Justin i really appricite for your help i want to tell all did work until now, again: 1.total charges in my topol.top was +2, then by genion, i added 2 CL to my comlex (HSA+Aspirin) 2.My .itp file (produce by PRODRG) was(consist of 11 atoms) : [ moleculetype ] ; Name nrexcl SAL 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OM 1 SAL O1' 1 -0.765 15.9994 ;' 2 C 1 SAL C1' 10.354 12.0110 ;' 3OM 1 SAL O2' 1 -0.765 15.9994 ;' 4 C 1 SAL C1 1 -0.027 12.0110 5 CH2 1 SAL C6 10.102 14.0270 6 CH2 1 SAL C5 10.101 14.0270 7 CR1 1 SAL C4 20.010 13.0190 8 CR1 1 SAL C3 20.010 13.0190 9 C 1 SAL C2 20.130 12.0110 10OA 1 SAL O2 2 -0.191 15.9994 11 H 1 SAL H2 20.041 1.0080 This explains your previous observations. This isn't aspirin. It's salicylic acid, albeit incorrect because it has two CH2 groups that should be aromatic. It also uses united aromatic carbons, which is incorrect. with topology file and .itp file, after grompp (for produce nvt.tpr) i encounted to below error : *system has non-zero total charge : -0.61* I don't know what could have happened here. The topology above sums to -1, as it should. 3.as yor re mentioned, Aspirin has 17 atoms. for charge distribution, i used of QM (NBO calculation) and my results was: 1 C -0.095205 2 C -0.077566 3 C -0.084684 4 C -0.028579 5 C -0.223106 6 C0.198041 7 H0.147099 8 H0.106100 9 H 0.101762 10 H 0.117238 11 C 0.443312 12 O -0.318010 13 H0.247465 14 O -0.341986 15 O -0.318846 16 C0.312765 17 O -0.320346 18 C -0.281115 19 H0.136126 20 H0.139768 21 H0.139765 these are estimated for* 2-acetoxy benzoic acid *alone (i dont know , must be calculate for complex HSA+Aspirin or Aspirin alone?) You can't do the whole complex with QM. Parametrization would be done on aspirin alone, but as I said, you probably don't need to use QM here; you can put the topology together from existing building blocks. 4. on the other hand, i tried to search in *aminoacids.rtp* file for *gromos* force field , but saw only charges for ACE group(other aminoacids and some solvents) and i could not find out the charges of all atoms in Aspirin molecule. Put it together from building blocks; it's very straightforward. The aromatic ring C-H are the same for PHE and TYR. The carboxylate is the same for anything with an acid (GLU, ASP, C-terminus). The ester parameters (and likely the C in the ring to which it is connected) you have to get from the literature, as this functional group is not included in the protein force field. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] farticle demanding about Small-Molecule Topologies
On 12/29/14 3:56 AM, elham tazikeh wrote: Dear Dr.Lemkul would you please send me full text of your below article : Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies unfortunately, i dont have accessible to full text of this article thanks a lot Contact me off-list for this request; there is no need to post this to the list. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] -vsite hydrogen
On 12/29/14 6:28 AM, h.aliza...@znu.ac.ir wrote: Dear Users, I am simulating a membrane protein with charmm ff with a 2fs time step. How the results will be affected if I use a 5fs time step by using -vsite hydrogen option in pdb2gmx? Do my results loose their accuracy if I use this option? Well, it's easy to test. The membrane properties that are expected to be observed are very easy to quantify. We didn't test our CHARMM36 port with virtual sites at all, so we cannot recommend such usage. Test thoroughly before doing any real production work. Membranes are extremely sensitive to alteration. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Obtaining PMF for change in domain position
On 12/29/14 6:57 AM, Abhi Acharya wrote: Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which has two large domains connected by a flexible linker peptide (~10 aa). The two domains seem to interact with each other and have been crystallized in three different conformations. I want to calculate the change in binding energy of the two domains wrt change in their relative position, i.e. keeping position of one domain constant what is change in binding energy as the other domain moves from conformation 1, through conformation 2 to finally, conformation 3. What is the best way to do so? You need to describe what these three conformations are. Do they involve rotations of the domains with respect to one another, or is it a simple linear distance that varies? At first, I considered using umbrella sampling to address the problem. Here too, I was not sure how to write a pull code for such a complex reaction coordinate. Also, even if I can generate the conformations, what would be the ideal number of windows that would be needed to correctly generate a PMF ? My feeling is it would be a large number, but again it just a guess. Is there is a better way than this? Hard to know a priori. You may need some trial and error here, but with umbrella sampling it's trivial to just go back and add windows, since the simulations are still all independent of one another. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] pdb information
Dear GMX users i d like to know about pdb information for instance, when i defined concentration of an ion by genion (-conc), gromacs added ion(s) to my structure Now, my question is: in a pdb e.g. (1ZE9: Amyloid beta peptide+Zn+2), there is only one cation in pdb file i want to know about its concentration? my mean is one Zn+2 ion equal *what concentration*? 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] pdb information
On 12/29/14 11:08 AM, elham tazikeh wrote: Dear GMX users i d like to know about pdb information for instance, when i defined concentration of an ion by genion (-conc), gromacs added ion(s) to my structure Now, my question is: in a pdb e.g. (1ZE9: Amyloid beta peptide+Zn+2), there is only one cation in pdb file i want to know about its concentration? my mean is one Zn+2 ion equal *what concentration*? regards Think back to general chemistry. Without a defined volume, you can't define concentration... -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Obtaining PMF for change in domain position
On Mon, Dec 29, 2014 at 8:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/29/14 6:57 AM, Abhi Acharya wrote: Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which has two large domains connected by a flexible linker peptide (~10 aa). The two domains seem to interact with each other and have been crystallized in three different conformations. I want to calculate the change in binding energy of the two domains wrt change in their relative position, i.e. keeping position of one domain constant what is change in binding energy as the other domain moves from conformation 1, through conformation 2 to finally, conformation 3. What is the best way to do so? You need to describe what these three conformations are. Do they involve rotations of the domains with respect to one another, or is it a simple linear distance that varies? Yes, there are significant rotations+translations along different axes involved which makes it challenging. Is there a way to model such movements using the pull code? At first, I considered using umbrella sampling to address the problem. Here too, I was not sure how to write a pull code for such a complex reaction coordinate. Also, even if I can generate the conformations, what would be the ideal number of windows that would be needed to correctly generate a PMF ? My feeling is it would be a large number, but again it just a guess. Is there is a better way than this? Hard to know a priori. You may need some trial and error here, but with umbrella sampling it's trivial to just go back and add windows, since the simulations are still all independent of one another. My concern is that since the domain movement from initial to final conformation is of about 10 nm, the number of windows required maybe too large. I read that the windows need to be spaced close enough so that each one samples some part of the next window. My system is also very large (200K atoms), so it seems to be computationally very expensive. I was just now thinking to reduce the problem to conducting umbrella sampling for each conformation, simply using COM distance of the two domains as the reaction coordinate to obtain the PMF in each case. From the PMF, the binding energy of the domains in each conformation can be obtain. This will allow me to circumvent the complications introduced by domain rotations and maybe reduce the number of simulations required a bit . Will this be a correct approach? Thank you. Abhishek Acharya -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Gromacs error regarding default gromos bond type and angle type
Dear Gromacs users we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial). This pdf file contains two cofactors including TPF and HEM. Our next step is to dock some antifungal drugs to this protein which is cytochrome of the fungi. As the TPF was not located in the active site and due to the lack of topology informtaion for this cofactor in gromos force fields, we omitted the TPF . Then we performed pdb2gmx on the protein along with the HEM cofactor. The pdb2gmx did not give error, so we were satisfied with the topology file. But when in the step of adding ions, we performed grommp command to get the ions.tpr file, we faced with 7 errors: these errors were saying that there are not gromos default bond type or angle type or dihedral type for specified lines in the topology file. I checked the atom numbers that were present in those bonds, angles and dihedrals and came to the conclusion hat all of them contain (Fe) atom which is present in the HEM cofactor. It seems that pdb2gmx command is not able to specify gromos default bond type or angle type whenever Fe is there. Now please guide us to solve the problem. what should I put in the vacancy spaces for these bond type or angle types. I mean what (gb_? or ga_?) and why the pdb2gmx did not gave error??? Thanks alot -- Dr. Delara Mohammad-Aghaie Assistant Professor of Physical Chemistry Department of Chemistry Shiraz University of Technology Shiraz Iran -- 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: Gromacs error regarding default gromos bond type and angle type
Dear Gromacs users we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial). This pdf file contains two cofactors including TPF and HEM. Our next step is to dock some antifungal drugs to this protein which is cytochrome of the fungi. As the TPF was not located in the active site and due to the lack of topology informtaion for this cofactor in gromos force fields, we omitted the TPF . Then we performed pdb2gmx on the protein along with the HEM cofactor. The pdb2gmx did not give error, so we were satisfied with the topology file. But when in the step of adding ions, we performed grommp command to get the ions.tpr file, we faced with 7 errors: these errors were saying that there are not gromos default bond type or angle type or dihedral type for specified lines in the topology file. I checked the atom numbers that were present in those bonds, angles and dihedrals and came to the conclusion hat all of them contain (Fe) atom which is present in the HEM cofactor. It seems that pdb2gmx command is not able to specify gromos default bond type or angle type whenever Fe is there. Now please guide us to solve the problem. what should I put in the vacancy spaces for these bond type or angle types. I mean what (gb_? or ga_?) and why the pdb2gmx did not gave error??? Thanks alot -- Dr. Delara Mohammad-Aghaie Assistant Professor of Physical Chemistry Department of Chemistry Shiraz University of Technology Shiraz Iran -- 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] -vsite hydrogen
We have tested virtual sites with CHARMM36 lipids; straightforward usage gives too ordered membranes. We have created custom virtual sites construction for lipid hydrogens and used them for pure membranes as well as for membrane proteins, and the differences between membrane properties with virtual sites and without are usually minor (but still noticeable). The parameters can be found here http://memphys.dk/node/71 and the paper http://pubs.acs.org/doi/abs/10.1021/ct500100f Wojciech Message: 1 Date: Mon, 29 Dec 2014 10:27:47 -0500 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] -vsite hydrogen Message-ID: 54a172f3.5040...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 12/29/14 6:28 AM, h.aliza...@znu.ac.ir wrote: Dear Users, I am simulating a membrane protein with charmm ff with a 2fs time step. How the results will be affected if I use a 5fs time step by using -vsite hydrogen option in pdb2gmx? Do my results loose their accuracy if I use this option? Well, it's easy to test. The membrane properties that are expected to be observed are very easy to quantify. We didn't test our CHARMM36 port with virtual sites at all, so we cannot recommend such usage. Test thoroughly before doing any real production work. Membranes are extremely sensitive to alteration. -Justin On Mon, Dec 29, 2014 at 8:52 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: -vsite hydrogen (Justin Lemkul) 2. Re: Obtaining PMF for change in domain position (Justin Lemkul) 3. pdb information (elham tazikeh) 4. Re: pdb information (Justin Lemkul) 5. Re: Obtaining PMF for change in domain position (Abhi Acharya) 6. Gromacs error regarding default gromos bond type and angle type (Negar Parvizi) -- Message: 1 Date: Mon, 29 Dec 2014 10:27:47 -0500 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] -vsite hydrogen Message-ID: 54a172f3.5040...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 12/29/14 6:28 AM, h.aliza...@znu.ac.ir wrote: Dear Users, I am simulating a membrane protein with charmm ff with a 2fs time step. How the results will be affected if I use a 5fs time step by using -vsite hydrogen option in pdb2gmx? Do my results loose their accuracy if I use this option? Well, it's easy to test. The membrane properties that are expected to be observed are very easy to quantify. We didn't test our CHARMM36 port with virtual sites at all, so we cannot recommend such usage. Test thoroughly before doing any real production work. Membranes are extremely sensitive to alteration. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Message: 2 Date: Mon, 29 Dec 2014 10:29:18 -0500 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Obtaining PMF for change in domain position Message-ID: 54a1734e.5000...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 12/29/14 6:57 AM, Abhi Acharya wrote: Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which has two large domains connected by a flexible linker peptide (~10 aa). The two domains seem to interact with each other and have been crystallized in three different conformations. I want to calculate the change in binding energy of the two domains wrt change in their relative position, i.e. keeping position of one domain constant what is change in binding energy as the other domain moves from conformation 1, through conformation 2 to finally, conformation 3. What is the best way to do so? You need to describe what these three conformations are. Do they involve rotations of the domains with respect to one
[gmx-users] charge distribution
Dear Justin thanks a lot for your response, your answers were very clear As you said,for building blocks i cant use of protein force field and i have to get from the literature(s) would you please recommend me some literature that i can use them? cheers -- 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] low performance 2 GTX 980+ Intel CPU Core i7-5930K 3.5 GHz (2011-3)
Dear gromacs users, I just recently bought a workstation that posees two GTX 980 plus an i7 (Intel CPU Core i7-5930K 3.5 GHz (2011-3)). In order to test it, i run a MD simulation of a system containing ~90k atoms. These are the performances: 2 GPU’s (1 job): 34ns/day (each cards were working about ~40%) 1 GPU (Nº1) (1 job): 37ns/day (~65% of performance) 1 GPU (Nº2) (1 job): 36ns/day (~65% of performance) 2 GPU’s (2 jobs simultaneously ) 16ns/day and 16ns/day respectively. (~20% of performance each) With respect to the last test, the .log file show the next message: Force evaluation time GPU/CPU: 3.177 ms/5.804 ms = 0.547 For optimal performance this ratio should be close to 1! NOTE: The GPU has 25% less load than the CPU. This imbalance cause performance loss. So probably, since all the cpu is splitting between each job, the ratio GPU/CPU will be worse. Is there a way i can solve this issue (is kind of sad that i’m getting a better performance with one GPU instead of two, since i saw that when i add a third or even a fourth one the performance start to decrease). Here’s my .mdp file: title = Protein-ligand complex MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 1500; 2 * 150 = 3 ps (30ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr output nstenergy = 1 ; save energies every 2 ps nstlog = 1 ; update log file every 2 ps nstxtcout = 15000 ; write .xtc trajectory every 2 ps energygrps = Protein non-Protein ; Bond parameters continuation= yes ; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) c lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 10 fs cutoff-scheme = Verlet rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.0 ; short-range electrostatic cutoff (in nm) rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electr pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermo tc-grps = Protein non-Protein; two coupling groups - more accur tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on f pcoupltype = isotropic ; uniform scaling of box ve tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in ba compressibility = 4.5e-5; isothermal compressibilit ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; assign velocities from Maxwell distribution Kind regards, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 798, Fax: 56-71-201 561 Email: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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] Obtaining PMF for change in domain position
On 12/29/14 11:34 AM, Abhi Acharya wrote: On Mon, Dec 29, 2014 at 8:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 12/29/14 6:57 AM, Abhi Acharya wrote: Hello GROMACS Users, This is a problem I am facing for the first time. Kindly guide be to the best options. I have a protein which has two large domains connected by a flexible linker peptide (~10 aa). The two domains seem to interact with each other and have been crystallized in three different conformations. I want to calculate the change in binding energy of the two domains wrt change in their relative position, i.e. keeping position of one domain constant what is change in binding energy as the other domain moves from conformation 1, through conformation 2 to finally, conformation 3. What is the best way to do so? You need to describe what these three conformations are. Do they involve rotations of the domains with respect to one another, or is it a simple linear distance that varies? Yes, there are significant rotations+translations along different axes involved which makes it challenging. Is there a way to model such movements using the pull code? Perhaps the enforced rotation options can be useful here. At first, I considered using umbrella sampling to address the problem. Here too, I was not sure how to write a pull code for such a complex reaction coordinate. Also, even if I can generate the conformations, what would be the ideal number of windows that would be needed to correctly generate a PMF ? My feeling is it would be a large number, but again it just a guess. Is there is a better way than this? Hard to know a priori. You may need some trial and error here, but with umbrella sampling it's trivial to just go back and add windows, since the simulations are still all independent of one another. My concern is that since the domain movement from initial to final conformation is of about 10 nm, the number of windows required maybe too large. I read that the windows need to be spaced close enough so that each one samples some part of the next window. My system is also very large (200K atoms), so it seems to be computationally very expensive. The number of windows needed is largely a function of the force constant, e.g. how strong the biasing potential is. But that's also a function of how strong the interactions are that are intrinsic to the system. I was just now thinking to reduce the problem to conducting umbrella sampling for each conformation, simply using COM distance of the two domains as the reaction coordinate to obtain the PMF in each case. From the PMF, the binding energy of the domains in each conformation can be obtain. This will allow me to circumvent the complications introduced by domain rotations and maybe reduce the number of simulations required a bit . Will this be a correct approach? Possibly, but COM distance can be a degenerate measure in the case of rotation. The PLUMED plugin may be useful here rather than standard Gromacs options, otherwise try to find an example in the literature and follow a known procedure. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] charge distribution
On 12/29/14 3:32 PM, elham tazikeh wrote: Dear Justin thanks a lot for your response, your answers were very clear As you said,for building blocks i cant use of protein force field and i have to get from the literature(s) would you please recommend me some literature that i can use them? http://lmgtfy.com/?q=gromos+ester+parameters :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] RDF does not reach 1 for bulk
Dear Gromacs users, I would like to know why the normalized RDF data from g_rdf does not reach 1 for bulk? As an alternative I tried using the raw data (i.e., by using the 'nonorm' flag) and normalized the values by dividing them by 'rho*volume of bin', which I believe is the standard method for normalization. Still I get the trend obtained from the normalized data, where the end of the RDF curve tapers downward, much below 1. Kindly suggest how I could deal with this issue. Thanks -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] pdb information
Dear Justin i choosed *Cubic* box for amyloid beta peptide+Zn ion simulation for this reason, my *volume* is defined if i suppose that, Zn ion = 1 mol its concentration will be calculated my assumption is correct? cheers -- 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.
