[gmx-users] TraPPE-EH in GROMACS
Dear gromacs users, I want to use TraPPE-EH force field parameters in GROMACS-2018.3. I have understood that in top file nbfunc=1, comb-rule=2,fudgeLJ=0.5,fudgeQQ=0.8333. But what will be the values of gen-pairs, nrexcl and [ pairs] section ? Any kind of help will be highly appreciated. Thanks and regards Dhrubajyoti Maji -- 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] choice of ?Qm Optimized Energy
thanks for your response Dr. Justin these all values are for same ligand submitted under different molid. All have net zero charge. only difference is in dQm optimized energy. I dont know weather i have to choose one with lowest value or the highest. Please check the link attached https://atb.uq.edu.au/molecule.py?molid=364968 *with regards* *Yogesh Sharma* -- 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] trjcat and trjconv performance
Hello all. I need to use trjcat and trjconv often and I am wondering if there is any way to speed up these utilities. They seem quite slow at the moment compared to the catdcd binary in the vmd distribution. Best, Miro -- 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] Correlation Functions
Hi, 1. Can we define a correlation function in GROMACS or we only can use those that are already defined? If we can do it I appreciate a useful hint. 2. When I use gmx velacc command I get "Not enough trajectory frames" error even though I used different nstvout. What frequency should I choose for data collection? I've read the manual but there is not a rule for it. Thank you. On Mon, 27 Jan 2020 at 15:23, Sina Omrani wrote: > Hi, > 1. Can we define a correlation function in GROMACS or we only can use > those that are already defined? If we can do it I appreciate a useful hint. > 2. When I use gmx velacc command I get "Not enough trajectory frames" > error even though I used different nstvout. What frequency should I choose > for data collection? I've read the manual but there is not a rule for it. > Thank you. > -- 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] Remove water molecules from .tpr file
On 1/27/20 12:15 PM, John Whittaker wrote: Hi Navneet, You can probably delete the water molecules and ions from your .gro file and run all the necessary files through grompp again. This should generate a new dummy .tpr file you can use that matches your trajectory file. It's even easier than that. Just use gmx convert-tpr with a matching index group and it will save a new .tpr file with the desired subset of atoms. -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] Remove water molecules from .tpr file
Hi Navneet, You can probably delete the water molecules and ions from your .gro file and run all the necessary files through grompp again. This should generate a new dummy .tpr file you can use that matches your trajectory file. Best, John > Hello Everyone! > > I want to calculate the g_mmpbsa (binding free energy) for a > protein+ligand > complex. > I want to delete the water molecules and other ions from the system. > I have removed the water molecules from the .xtc file. But how to > manipulate and remove the water molecules information from .tpr > (md_0_10.tpr)file. I want a new .tpr file which matches my new trajectory > file. How to do this? > > Regards > Navneet > -- > 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] Remove water molecules from .tpr file
Hello Everyone! I want to calculate the g_mmpbsa (binding free energy) for a protein+ligand complex. I want to delete the water molecules and other ions from the system. I have removed the water molecules from the .xtc file. But how to manipulate and remove the water molecules information from .tpr (md_0_10.tpr)file. I want a new .tpr file which matches my new trajectory file. How to do this? Regards Navneet -- 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] Assertion failed: Condition: bX
On 1/27/20 10:13 AM, Sadaf Rani wrote: Dear Gromacs users I am getting following message in my log file during MD simulation:-- --- Program: gmx mdrun, version 2018.1 Source file: src/gromacs/mdlib/minimize.cpp (line 582) Function:void write_em_traj(_IO_FILE *, t_commrec *, gmx_mdoutf *, int, int, const char *, gmx_mtop_t *, t_inputrec *, long, em_state_t *, t_state *, ObservablesHistory *) *Assertion failed:Condition: bX* The code below assumes that (with domain decomposition), x is collected to state_global in the call above. I could get a post regarding its fixing https://redmine.gromacs.org/issues/2554 Could you please suggest me why is this happening? and how should I fix it. Upgrade to a later version of GROMACS. The Redmine issue indicates 2018.2 has the problem, so clearly 2018.1 will, as well. At minimum, upgrade to the last version in the 2018 series but preferably just get the latest actual release. -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] Assertion failed: Condition: bX
Dear Gromacs users I am getting following message in my log file during MD simulation:-- --- Program: gmx mdrun, version 2018.1 Source file: src/gromacs/mdlib/minimize.cpp (line 582) Function:void write_em_traj(_IO_FILE *, t_commrec *, gmx_mdoutf *, int, int, const char *, gmx_mtop_t *, t_inputrec *, long, em_state_t *, t_state *, ObservablesHistory *) *Assertion failed:Condition: bX* The code below assumes that (with domain decomposition), x is collected to state_global in the call above. I could get a post regarding its fixing https://redmine.gromacs.org/issues/2554 Could you please suggest me why is this happening? and how should I fix it. Thanks & Regards. Sadaf -- 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] Diffusion Coefficient for hydration waters
Hi all, The diffusion coefficient can be calculated for the all the waters in the system, but how do calculate it for just the water molecules which are within 0.5 nm of the protein? Does anyone have any experience with this? I've tried to use gmx select to write an index file for the waters but as this is a dynamic selection, I would have to calculate each frame individually. Akash -- 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] gmx msd
On 1/27/20 6:20 AM, Maria Luisa wrote: Dear users, I'm using the command gmx msd but I found problem when I use the option -mol. Can u help me? Not without more information. What are you doing and what is your exact command? What is the problem you're facing, an error? Unexpected output? -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] Charmm to Gromacs itps
On 1/27/20 4:51 AM, atb files wrote: Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail Prepare the system with CHARMM-GUI and it will give you all the necessary inputs for running in GROMACS. -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] choice of ΔQm Optimized Energy
On 1/25/20 12:59 AM, Yogesh Sharma wrote: Greetings everyone, I was looking at the parameter files of a ligand. I found four files of ligand under the same name but differences were there in ΔQm Optimized Energy -1556371.3071 kJ.mol-1 -0.525 0.429 -0.250 which one should I use for my ligand interaction studies? There's no way to know based on the information provided. What did you download? To what do those values correspond? The first number looks like a configurational energy in absolute QM terms but that's not a physical value that an MM force field can reproduce. The other values could correspond to any different number of properties. What are they? -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] Build polymers with pdb2gmx
On 1/24/20 3:20 PM, Li, Shi wrote: Dear GMX users, I am new to polymer simulation and want to build a polymer system for Gromacs. I have followed Justin's instruction to make polyethylene by editing the rtp and hdb file. But I have a couple of questions regarding a larger polymer configuration: 1. The example system (polyethylene) only has one repeat unit, is there a way to define the number of repeat unit and then generate the PDB file? I GROMACS has no ability to build molecules. am also wondering if there is a way to make the configuration with random torsion? I currently use Gaussview to copy and paste, and the initial PDB is just a linear chain. Like this...^^O^^O^^O^^ Make the linear chain and run a Langevin simulation in the gas phase. 2. Since the PDB file is straightly from Gaussview, the atom names in the file are all in basic form (C, H, O...), in order for the pdb2gmx to work, I have to manually match and replace them according to the .rtp file. For larger repeat unit, is there a better way to do this? Unfortunately, no. Software that outputs repetitive atom names makes your life a nightmare when actually trying to do a simulation. -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] Protein pore collapse during simulation.
On 1/24/20 2:15 AM, Yogesh Sharma wrote: Sir, If i want to use charmm gui generated assembly for simulation in gromac forcefield. How can i extract berger lipid parameters (i.e lipid.itp according to yout tutorial) corresponding to charmm nomenclature? so that i can modify my forcefield in accordance. You would have to rename the atoms in the coordinate file. my ultimate aim is to simulate membrane protein with a ligand. whose parameters are only available in gromacff (ATB). #ligand contain metalloid atoms. You're making a big tradeoff here, as the Berger parameters are very inaccurate compared to modern lipid parameter sets. Metalloids are generally not available in biomolecular force fields, though. At least look at more recent GROMOS parameter sets rather than the Berger lipids. -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] gmx msd
Dear users, I'm using the command gmx msd but I found problem when I use the option -mol. Can u help me? Maria Luisa Maria Luisa Perrotta Ph.D Student, CNR-ITM via P.Bucci, 87036 Rende (Cs) Italy email: ml.perro...@itm.cnr.it -- 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] Correlation Functions
Hi, 1. Can we define a correlation function in GROMACS or we only can use those that are already defined? If we can do it I appreciate a useful hint. 2. When I use gmx velacc command I get "Not enough trajectory frames" error even though I used different nstvout. What frequency should I choose for data collection? I've read the manual but there is not a rule for it. Thank you. -- 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] gmx msd
Dear users, I'm using the command gmx msd but I found problem when I use the option -mol. Can u help me? Maria Luisa Maria Luisa Perrotta Ph.D Student, CNR-ITM via P.Bucci, 87036 Rende (Cs) Italy email: ml.perro...@itm.cnr.it -- 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] Charmm to Gromacs itps
Hi, have you tried gmx pdb2gmx -f ? Michele From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of atb files Sent: 27 January 2020 10:51 To: gromacs.org_gmx-users Subject: [gmx-users] Charmm to Gromacs itps Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail -- 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] Charmm to Gromacs itps
Hello users,I have .pdb, .psf and .crd file for one system. How to use them (convert to itp) in Gromacs? Thanks. YogesgSent using Zoho Mail -- 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] learning gromacs
Hi, I'm new to gromacs myself. Your best bet if you're new to Molecular dynamics is to do some tutorials and read best practices to try and understand what the computer is actually doing and why. http://www.mdtutorials.com/gmx/ I would recommend starting with the lysozyme in water tutorial as it is the simplest and then working through the ones that are relevant to your work. https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0 - best practice guide to help you better understand how not to waste computer time running meaningless simulations. Just because a simulation runs does not mean it is correct or useful. other handy resources. the documentation for the software. http://manual.gromacs.org/ also googling any error messages you find will usually bring up a research gate post or a message from this mailing list where someone has had the same problem. Hope this helps you getting started. Good luck. Best, Miro On Mon, Jan 27, 2020 at 6:24 PM Somdatta Chaudhari wrote: > Want to learn gromacs...plz help me out in this regards > > -- > Somdatta Y. Chaudhari > M.Pharm(Pharma.Chem) > Lecturer > Dept- Pharma.Chem > Modern College of Pharmacy, > Nigdi, Pune. (India) > -- > 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] Dipole moment and dielectric constant - gmx dipoles
Den 2020-01-27 kl. 01:28, skrev Iman Ahmadabadi:
Dear Philip,
Yes, you are right, thank you very much for your time and kindness.
gmx trjconv -pbc whole
Best regards,
Iman
On Sun, Jan 26, 2020 at 4:17 PM Iman Ahmadabadi
wrote:
Dear Gromacs users,
I'm trying to reproduce the gmx dipoles results via python code. In
calculating the fluctuations of total dipole moment, which is the sum on
dipole moment of individual molecules in the box, M = \sum q_{i}*R_{i}, in
which the charges q_{i} are in electron unit and position R_{i} are in nm.
For calculating M for each time step (frame), the x,y, and z component of
each atom is multiplied to their charges, and then summing on all atoms.
The average of M is on all trajectory frames, meaning that summing on M for
all frames and then dividing by the number of frames. Here, the acquired M
is divided by proper constant (0.020819434 e
·nm
) to set it in the Debye unit.
For M^{2}, M.M (dot product of M by M) is calculated for each frame and
then summing on all frames, followed by dividing by the number of frames.
But the results are larger than gmx dipoles, I wanted to ask that there is
something gmx dipoles is using in order to calculate the and ,
causing this difference? I appreciate any help in this regard.
Best regards,
Iman
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Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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