Re: [gmx-users] Scale Triclinic Box
Hi Salman, Tnx for the info, I actually want to do the cold-compression on my crystalline structure. So basically I need to both compress and expand the a and b parameters of the unit cell (the c parameter is already optimized)... so it's not just building a supercell, but rather scaling only 2 parameters of the unit cell simultaneously while remaping the new coordinates inside the scaled cell... could "gmx genconf -nbox ... ... ..." handle this? Best Maryam On Fri, Apr 3, 2020, 2:54 PM Salman Zarrini wrote: > Hi Maryam, > > The ``gmx genconf -nbox 2 2 1'' is your friend to generate a supercell, I > am just not sure if it could handle a triclinic cell. > Since your unit cell is not that large, you even can use Avogadro or > ASE-gui which both are good molecule editors and visualizers. > > Cheers, > Salman > > On Fri, Apr 3, 2020 at 3:55 PM Maryam Sadeghi > > wrote: > > > Dear All, > > > > I need to scale the a and b parameters of a triclinic crystalline unit > > cell. When I use the editconf command, only the cell parameters are > scaled > > while the coordinates of atoms are not remapped in the new cell. > > > > gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 > 0.5686 > > 1.9724 -angles 90.00 126.91 90.00 > > > > The unit cell consists of 4 polymer chains, each chain having 7 repeating > > (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 > bonds, > > 340 angles and 376 dihedrals. > > > > The original cell parameters are: > > a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, > > gamma: 90.00 > > > > Any suggestions how I can remap the coordinates (keeping the bonds and > > angles constant) together with scaling the box? > > > > Thanks, > > -- > > 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] How to parametrize a new molecule?
Thanks, Justin! Em sex., 3 de abr. de 2020 às 22:15, Justin Lemkul escreveu: > > > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: > > Dear users, > > > > I want to perform a simulation of a molecule inside DNA. I'm probably > going > > to use CHARMM for DNA. But how do I parametrize the molecule? > > http://cgenff.umaryland.edu/ > > -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] How to parametrize a new molecule?
On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: Dear users, I want to perform a simulation of a molecule inside DNA. I'm probably going to use CHARMM for DNA. But how do I parametrize the molecule? http://cgenff.umaryland.edu/ -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] How to parametrize a new molecule?
Dear users, I want to perform a simulation of a molecule inside DNA. I'm probably going to use CHARMM for DNA. But how do I parametrize the molecule? Thanks in advance. Yours, Herbert Georg -- 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] Scale Triclinic Box
Hi Maryam, The ``gmx genconf -nbox 2 2 1'' is your friend to generate a supercell, I am just not sure if it could handle a triclinic cell. Since your unit cell is not that large, you even can use Avogadro or ASE-gui which both are good molecule editors and visualizers. Cheers, Salman On Fri, Apr 3, 2020 at 3:55 PM Maryam Sadeghi wrote: > Dear All, > > I need to scale the a and b parameters of a triclinic crystalline unit > cell. When I use the editconf command, only the cell parameters are scaled > while the coordinates of atoms are not remapped in the new cell. > > gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686 > 1.9724 -angles 90.00 126.91 90.00 > > The unit cell consists of 4 polymer chains, each chain having 7 repeating > (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds, > 340 angles and 376 dihedrals. > > The original cell parameters are: > a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, > gamma: 90.00 > > Any suggestions how I can remap the coordinates (keeping the bonds and > angles constant) together with scaling the box? > > Thanks, > -- > 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] change the top file of a homodimer protein
On 4/3/20 5:12 PM, Qasim Pars wrote: Dear users, My protein has a homodimer structure. Here is the last part of the topology (.top) file: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 The topology (.itp) files of both chains are the same. My question is that can I change the last part of the topology file as follows? [ molecules ] ; Compound#mols Protein2 Not without modifying/removing #include statements and renaming the [moleculetype] in one of those #included .itp files to "Protein" -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] change the top file of a homodimer protein
Dear users, My protein has a homodimer structure. Here is the last part of the topology (.top) file: [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 The topology (.itp) files of both chains are the same. My question is that can I change the last part of the topology file as follows? [ molecules ] ; Compound#mols Protein2 Thanks in advance, -- Qasim Pars -- 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] Scale Triclinic Box
Dear All, I need to scale the a and b parameters of a triclinic crystalline unit cell. When I use the editconf command, only the cell parameters are scaled while the coordinates of atoms are not remapped in the new cell. gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686 1.9724 -angles 90.00 126.91 90.00 The unit cell consists of 4 polymer chains, each chain having 7 repeating (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds, 340 angles and 376 dihedrals. The original cell parameters are: a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, gamma: 90.00 Any suggestions how I can remap the coordinates (keeping the bonds and angles constant) together with scaling the box? Thanks, -- 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] PCA analysis with different atoms in -s and -f
Dear Eduardo, Many thanks for your detailed explanation. Sorry I am not an expert on the PCA. So I may need more explanations from you if you do not mind. Feel free to correct if I am wrong. I have done the common analysis to the MD run at different conditions, including RMSD, Rg, secondary structure, native contacts, etc. I can find some differences among those conditions. But I feel that there are infinite properties to choose to compare. So I am trying to find a more systematic way to quantify the difference. I found the "gmx anaeig -over" seems to be an ideal option. Can I ask, 1) How the "-ref" is used in the PCA analysis? i.e. How the "deviation" is used in the process of PCA? Do I need to fully understand the mathmatical equations in order to understand it? # -ref no (default) Use the deviation from the structure file (i.e. -s name.pdb) # -ref yes Use the deviation from the average of the trajectories 2) So far, I choose "MainChain" as the least square fit, and "C-alpha" for the PCA. I hope I can see the significant difference between the different conditions at the C-alpha level. But if not, I may choose "Backbone" or "MainChain" for the PCA. 3) Can you explain what is "long enough to have at least two halves of trajectory 0.pdb CA. 100% overlap of covariance matrices", and what is "block analysis to calculate overlap error as a function of time length"? Thank you! Yours sincerely Cheng --Original-- From:"ZHANG Cheng"<272699...@qq.com; Date:Wed, Apr 1, 2020 09:10 AM To:"gromacs.org_gmx-users"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.
