[gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out
Dear Gromacs Community, I have come across this problem during NVT equilibration of an all atom protein-ligand MD simulation. Fatal error: 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. I basically used the nvt and npt equilibration approach given in tutorial by Justin. I have tried changing the equilibration process by gradually increasing temperature to 100K. However it still shows the same error. I have tried with other conformation of ligand as initial structure also but no improvement. Could you advise how to go about this? Thank you all. Sincerely, Seke -- 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] Problem with mpirun
Dear Sir/Madam, We just installed gromacs 2019 today (MPI compiled) and we're currently testing the commands with MPI. The installations went fine however,we are having issues with the commands. $ echo $PATH /opt/vmd/1.9.3/bin:/opt/g_mmpbsa/bin:/opt/gromacs/2019.5/bin However, when we execute the commands we get the following response. mpirun -np 8 gmx_mpi mdrun -s md_0_10.tpr -o md_0_10.trr -cpi md_0_10.cpt -c md_0_10.gro -e md_0_10.edr -g md_0_10.log === = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = RANK 15 PID 23681 RUNNING AT biopo1 = KILLED BY SIGNAL: 4 (Illegal instruction) === We get the same error for 'mpirun -np 16 gmx_mpi mdrun -h' or ' mpirun -np 8 gmx_mpi mdrun -v -deffnm md_0_10' What are we missing here, please advise. Sincerely, Seket -- 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] RMSD of a single water molecule.
Dear User, I am trying to find the RMSD of a single water molecule which showed H-bond interaction with a ligand in a protein-ligand system simulation. The study was to explore the role of water in the binding of the ligand at the receptor. The RMSD of the water molecule (using the protein backbone for fitting) huge variation between 2 to 10 angstrom. VMD visualization showed that the water molecule was basically all over the simulation box and not at the vicinity of the ligand. Is it right to say from this observations that: 1. The H-bonds interaction of ligands with water molecule are transient ? 2. Water molecules are indeed all over the simulation box ? 3. gmx hbond analysis, gmx distance analysis led me to believe that there are interaction with water through out the simulation; just not the same water molecule . Would that be right ? Will appreciate if you can advise. Thank you. Sincerely, Seke -- 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] ERROR :: Atomtype LC3 not found : KALP-15 in water tutorial
Dear Expert, While doing the KALP15 in DPPC tutorial, I came across this error. I have tried google search for solutions but couldn't resolve it. Would appreciate if you would kindly let me know how to move forward: INPUT COMMAND: gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr OUTPUT ERROR: ERROR 1 [file dppc.itp, line 7]: Atomtype LC3 not found Full error message: gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr NOTE 1 [file minim_inflategro.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to -474520607 Generated 165 of the 1596 non-bonded parameter combinations ERROR 1 [file dppc.itp, line 7]: Atomtype LC3 not found There was 1 note --- Program: gmx grompp, version 2018.4 Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1390) Fatal error: There was 1 error in input file(s) Thank you - Seke -- 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] Tyrosine to phosphotyrosine conversion a must in phosphorylation protein ?
Dear expert, This is not a gromacs problem however I'm wondering if you can give some insight and direction to go look further. I have a protein phosphorylation protein kinase with a phosphotyrosine at a position 20 angstrom away from the binding site. I want to perform an MD to study the protein ligand interaction and binding energy calculations. I wonder if the modeling of the tyrosine to phophotyrosine is imperative for such studies. Is there any review or study done comparing such changes? I know newer force fields supports phosphorylation residues but wanted to know if failing to use phosphorylation structure would make the study useless. Your inputs will be appreciated. Thank you. Sincerely, Seke -- 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] Topology for phosphorylated protein in gromacs using Amber Forcefield
Dear Expert, I know this issue has been raised earlier by others but I'm still having trouble with generating topology files for a phosphorylated protein, phosphorylated at Tyrosine 1034 residue. I am using gromacs2018 and Amber99SB protein as FF. The residue in the PDB file is shown below. ATOM 1294 N PTR A1034 -2.670 -10.279 -15.822 1.00 16.60 N ATOM 1295 CA PTR A1034 -2.446 -9.183 -16.725 1.00 16.94 C ATOM 1296 C PTR A1034 -3.533 -8.144 -16.622 1.00 18.89 C ATOM 1297 O PTR A1034 -4.612 -8.406 -16.068 1.00 19.06 O ATOM 1298 CB PTR A1034 -2.291 -9.698 -18.159 1.00 18.90 C ATOM 1299 CG PTR A1034 -3.542 -10.337 -18.686 1.00 24.64 C ATOM 1300 CD1 PTR A1034 -3.802 -11.695 -18.501 1.00 22.99 C ATOM 1301 CD2 PTR A1034 -4.492 -9.556 -19.348 1.00 23.91 C ATOM 1302 CE1 PTR A1034 -4.980 -12.268 -18.990 1.00 23.96 C ATOM 1303 CE2 PTR A1034 -5.639 -10.107 -19.829 1.00 26.74 C ATOM 1304 CZ PTR A1034 -5.884 -11.455 -19.654 1.00 32.04 C ATOM 1305 OH PTR A1034 -6.953 -11.808 -20.159 1.00 41.31 O ATOM 1306 P PTR A1034 -7.810 -13.106 -19.896 1.00 46.59 P ATOM 1307 O1P PTR A1034 -9.076 -12.851 -20.613 1.00 45.47 O ATOM 1308 O2P PTR A1034 -8.107 -13.257 -18.394 1.00 55.84 O1- ATOM 1309 O3P PTR A1034 -6.994 -14.285 -20.476 1.00 42.59 O As advised in some previous letters, I copied residuetypes.dat and added "PTR" to it. I have also tried http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue Some experts mentioned modern amber FF can handle phosphorylated residues. But, I can't seem to find the right way to do it. query 1: Please advise how to go about this. I have never worked on Phosphorylated residues and have no like minded people to discuss with. A brief step wise instruction would really help me and others doing this for the first time (this problem has been asked frequently on Research gate and here too). query 2: should atom be treated at ATOM or HETATM ? Thanks. Sincerely, Keretsu -- 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] High pressure variation during NPT equilibration of Protein-ligand system.
Dear Experts, I am performing a protein-ligand stimulation in gromacs 2018. The pressure value showed wild variation between -800 to 500 bar and showed an average pressure value of -139 bar. The reference is 1 bar. I have used the "lysozyme in water" simulation tutorial by Justin A. Lemkul as a reference. The tutorial mentioned that 7.5 (+- 160) bar was reasonable for the system. I'm not sure if the value I am getting in my simulation results (-139 bar variation in pressure) are reasonable. Kindly advise. How do i justify this ? References and suggestions will be appreciated. Thank you. Regards, Seketoulie Note: The pressure values from the NPT are given below: # This file was created Tue May 14 21:24:43 2019 # Created by: # :-) GROMACS - gmx energy, 2018.4 (-: # # Executable: /usr/local/gromacs/bin/gmx # Data prefix: /usr/local/gromacs # Working dir: /home/biopo5/tutorial/Project4/JAK1/cmp49_jak1 # Command line: # gmx energy -f nvt.edr -o pressure.xvg # gmx energy is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title "GROMACS Energies" @xaxis label "Time (ps)" @yaxis label "(bar)" @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend "Pressure" 0.00 -3931.674805 1.00 528.706482 2.00 27.634497 3.00 -130.418900 4.00 -491.462982 5.003.087336 6.00 -246.631638 7.00 -86.932167 8.00 -453.551422 9.00 -46.325455 10.00 270.657562 11.00 -432.105682 12.00 -578.059326 13.00 -397.159760 14.00 180.598190 15.00 -159.344788 16.00 -122.911415 17.00 470.059418 18.00 -375.501251 19.00 -310.881561 20.00 68.639618 21.00 157.454422 22.00 -619.447388 23.00 -130.864059 24.00 58.016773 25.00 -132.054276 26.00 114.288574 27.00 -108.022186 28.00 -235.894424 29.00 -398.703217 30.00 252.965332 31.00 -269.996368 32.00 -58.096252 33.00 -291.578918 34.00 15.896652 35.00 53.429890 36.00 43.522858 37.00 -442.695190 38.00 111.608665 39.00 -12.626378 40.00 -136.936111 41.00 182.577164 42.00 -68.747620 43.00 121.546547 44.00 127.403526 45.00 -248.055176 46.00 184.869797 47.00 162.962906 48.00 -387.420013 49.00 228.167648 50.00 348.351471 51.00 -462.909180 52.00 -234.574936 53.00 -224.565689 54.00 311.879456 55.00 -404.242920 56.00 -740.461182 57.00 38.036850 58.00 -677.158447 59.00 -117.842407 60.00 -20.302151 61.00 -558.201233 62.00 218.174881 63.00 -269.575531 64.00 -153.398697 65.00 178.027954 66.00 -193.050797 67.00 -590.598694 68.00 -487.503754 69.00 171.980606 70.00 84.821785 71.00 -219.844803 72.00 -228.680954 73.00 -145.632614 74.00 47.675121 75.00 -310.033478 76.00 -705.341248 77.00 212.275406 78.00 24.035654 79.00 -221.810410 80.00 -189.725708 81.00 217.696289 82.00 427.632660 83.00 249.210770 84.00 -405.385956 85.00 78.898247 86.00 -19.268747 87.00 85.342247 88.00 155.808731 89.002.646250 90.00 -284.466888 91.00 152.030930 92.00 280.804352 93.00 -182.475830 94.00 -268.784149 95.00 -470.018829 96.00 -163.642685 97.00 291.026855 98.00 -982.940430 99.00 155.447800 100.00 77.415077 -- 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] g_mmpbsa parameter verify: using last 5ns of MD trajectory for binding energy calculation.
Dear Expert, Kindly apologise for putting up a question not exactly related to gromacs. I have a 30ns protein ligand simulation trajectory from Gromacs. I would like to use the last 5ns (i.e 25-30 ns) of the trajectory for binding energy calculation. As mentioned in the g_mmpbasa article i want to use 10ps snapshots. I assumed that the starting and ending frames and the 10ps snapshots conditions are passed in the option when calling the g_mmpbsa command. Kindly verify if I'm doing it right. g_mmpbsa -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i ../pbsa.mdp -pdie 2 -pbsa -decomp -b 25000 -e 3 -dt 10 here, -b 25000 is used to indicate that frame at 25ns is used as starting frame. Similarly -e 3 is used to indicate ending frame corresponding to 30ns. Also -dt 10 is use assuming 10ps snapshots will be used. Please correct me if I'm wrong. Any references will be appreciated. Thanks, Seke -- 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] is acpype compatible with amber 2018?? parmchk2 and not parmchk available
Dear Experts,
Has anyone with amber 2018 able to generate ligand topologies for
Gromacs simulation. I got an error reporting "parmchk failed" while
executing "acpype -i FFF.pdb". I noticed that there is no "parmchk"
installed in the system. The current version installed during
installation of amber is "parmchk2" and not "parmchk".
I have amber 2018 and gromacs 2018 installed on a centos7 system.
Again if you're able to generate a topology with the new amber2018
setup please let me know. Also if you have some suggestion how to
proceed, please let me know.
Error report:
[main@localhost try1]$ acpype -i Ligand.pdb
| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2018 AWSdS |
==> ... charge set to 0
==> ... converting pdb input file to mol2 input file
==> * Babel OK *
==> Executing Antechamber...
==> * Antechamber OK *
++start_quote+++
/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `which: no parmchk in
(/home/main/Downloads/amber18/bin:/home/main/Downloads/amber18/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/gromacs/bin:/home/main/.local/bin:/home/main/bin:/usr/local/gromacs/bin)
-i Ligand_bcc_gaff.mol2 -f mol2 -o Ligand_AC.frcmod'
++end_quote+
ERROR: Parmchk failed
ERROR: Tleap failed
==> ... trying Sleap
==> Executing Sleap...
++start_quote+++
++end_quote+
++start_quote+++
/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `which: no sleap in
(/home/main/Downloads/amber18/bin:/home/main/Downloads/amber18/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/local/gromacs/bin:/home/main/.local/bin:/home/main/bin:/usr/local/gromacs/bin)
-f sleap.in'
++end_quote+
ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'Ligand_AC.prmtop'
Total time of execution: 12m 43s
Thank you.
Sincerely, seke
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 176, Issue 11
Dear Thank you. "yum install numpy" worked for me. Surprised why i haven't tried that long back. On Fri, Dec 7, 2018 at 1:41 PM 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: numpy related problem in GROMACS protein-ligand file > preperation (Benson Muite) >2. How restrain the end-to-end distance in simulation? > (Mehdi Bagherpour) >3. Re: mdrun-adjusted cutoffs?! (Alex) >4. Re: mdrun-adjusted cutoffs?! (Mark Abraham) > > > -- > > Message: 1 > Date: Thu, 6 Dec 2018 12:51:35 + > From: Benson Muite > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Subject: Re: [gmx-users] numpy related problem in GROMACS > protein-ligand file preperation > Message-ID: <2709ee01-b64b-acd2-0595-298bd7cad...@ut.ee> > Content-Type: text/plain; charset="utf-8" > > Hi Seketoulie, > > If you have administrator rights on a CentOS system > > sudo yum search numpy > > will let you know what numpy versions have already been packaged. > > You can also use > > pip install --user numpy > > or build from source: > > https://docs.scipy.org/doc/numpy-1.10.1/user/install.html > > Regards, > > Benson > > On 12/6/18 1:57 PM, Seketoulie Keretsu wrote: > > Dear Experts, > > > > I am fairly new to gromacs (and linux CENTOS). I have recently > > installed the Gromacs18 successfully. However while doing the > > Protein-Lig tutorial I came across this problem while running the > > python script: > > > > Traceback (most recent call last): > > File "cgenff_charmm2gmx.py", line 46, in > > import numpy as np > > ImportError: No module named numpy > > > > > > I have python 2.7.5 installed on my system. I am unable to find > > solutions related to this. Kindly advise how to correct this? A hint > > on the possible cause will be awesome too. > > > > Note: I also have Amber18 installed on my the same system which > > apparently installs numpy. > > > > Thanking you. > > > > Sincerely, > > Seketoulie > > > -- > > Message: 2 > Date: Thu, 6 Dec 2018 15:58:04 +0100 > From: Mehdi Bagherpour > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] How restrain the end-to-end distance in > simulation? > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Dear all, > > I am new in Gromacs and would like to restrain the the end-to-end distance > of a bend DNA. I mean I want to restraint the distance between COM of end > base-pairs in simulation. > > I would appreciate if you could let me know how to do that. > > Cheer, > Mahdi > > > -- > > Message: 3 > Date: Thu, 6 Dec 2018 12:39:03 -0700 > From: Alex > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] mdrun-adjusted cutoffs?! > Message-ID: <8ffb83a0-4298-4dae-449a-65edad72b...@gmail.com> > Content-Type: text/plain; charset=utf-8; format=flowed > > I'm not ignoring the long-range contribution, but yes, most of the > effects I am talking about are short-range. What I am asking is how much > the free energy of ionic hydration for K+ changes in, say, a system that > contains KCl in bulk water -- with and without autotuning. Hence also > the earlier question about being able to turn it off at least temporarily. > > Alex > > On 12/6/2018 5:42 AM, Mark Abraham wrote: > > Hi, > > > > It sounds like you are only looking at the short-ranged component of the > > electrostatic interaction, and thus ignoring the way the long range > > component also changes. Is the validity of the PME auto tuning the question > > at hand? > > > > Mark > > > > On Thu., 6 Dec. 2018, 21:09 Alex > > >> More specifically, electrostatics. For the stuff I'm talking about, the > >> LJ portion contributes ~20% at the mo
[gmx-users] numpy related problem in GROMACS protein-ligand file preperation
Dear Experts, I am fairly new to gromacs (and linux CENTOS). I have recently installed the Gromacs18 successfully. However while doing the Protein-Lig tutorial I came across this problem while running the python script: Traceback (most recent call last): File "cgenff_charmm2gmx.py", line 46, in import numpy as np ImportError: No module named numpy I have python 2.7.5 installed on my system. I am unable to find solutions related to this. Kindly advise how to correct this? A hint on the possible cause will be awesome too. Note: I also have Amber18 installed on my the same system which apparently installs numpy. Thanking you. Sincerely, Seketoulie -- 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] gromacs.org_gmx-users Digest, Vol 175, Issue 95
Dear Alex Thank you for the "shameless self promotion". Have been looking for some classic gromacs products lately. Have seen some interesting methods in area of protein-ligand interactions. If you have some new and interesting gromacs papers related to Protein-ligand studies please suggest it here. Also came across this paper out of Stanford university. 400 micro sec simulations. Just blown my mind. https://www.nature.com/articles/s41467-016-0015-8 Will really appreciate if you can suggest . Appreciate you guys for all the help so far. Best, Seke On Tue, Nov 27, 2018 at 1:05 PM 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. Parameterizing N-terminal capping (Raji) >2. Re: Distance calculation (rose rahmani) >3. Re: Interaction energy (Mark Abraham) >4. shameless self-promotion (Alex) >5. Gromacs 2018.3 Exceeding Memory Issue (Peiyin Lee) >6. Re: Charge system simulation problem (Karpurmanjari Kakati) > > > -- > > Message: 1 > Date: Mon, 26 Nov 2018 12:50:05 -0600 > From: Raji > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Parameterizing N-terminal capping > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi > > I am trying to parameterize the N-terminal ?carboxybenzyl? capping for > peptide within CHARMM force field. Charges and bonded terms are transferred > by analogy from available amino acid and lipid parameters. Grompp throwing > errors for missing dihedral and bond terms of the linkage between ester > group and peptide backbone. I appreciate any ideas. > > > [image: image.png] > Thanks > Raji > > -- > > Message: 2 > Date: Mon, 26 Nov 2018 22:29:07 +0330 > From: rose rahmani > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Distance calculation > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Can i use -dist option? > Would you please help me? > On Mon, 26 Nov 2018, 00:48 rose rahmani > > Hi, > > > > My system contains 20 amino acids around nanotube. I want to know the > > adsorption amount of AA during simulation time; the adsorption occurs > > when the distance between one of non-hydrogen atoms of AA and the tube > > surface was less than 0.5 nm. So how can i calculate this property? > > > > Would you please help me? > > Best > > > > > -- > > Message: 3 > Date: Mon, 26 Nov 2018 21:51:50 +0100 > From: Mark Abraham > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Interaction energy > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Hi, > > On Mon, Nov 26, 2018 at 7:47 PM Nick Johans wrote: > > > On Mon, 26 Nov 2018, 21:28 Justin Lemkul > > > > > > > > > > On 11/26/18 10:51 AM, Nick Johans wrote: > > > > On Mon, 26 Nov 2018, 18:22 Justin Lemkul > > > > > > >> > > > >> On 11/22/18 11:41 AM, Nick Johans wrote: > > > >>> Hi > > > >>> > > > >>> I am beginner in MD. Maybe it is not a wise question but i want to > > > >>> calculate the interaction energy between protein and ligand and also > > > PMF > > > >> in > > > >>> different distances. But i don't know what is the didference between > > > >> PMF, i > > > >>> mean free energy in particular(by umbrella sampling) and the > > > interaction > > > >>> energy (by g_energy tool) in my case? > > > >> Interaction energy is a pairwise decomposition of short-range > > nonbonded > > > >> interaction energy in the system. This energy is usually not > > physically > > > >> meaningful, but if the force field has been parametrized in such a way > > > >> that it is, the interaction energy is a contribution to the enthalpy > > of > > > >> the system. > > > >> > > > > What forcefields embedded in GROMACS do, yes? > > > > > > AFAIK only CHARMM. > > > > > Interesting! You mean interaction energy calculated by for example AMBER > > may not be true? Why?? What makes CHARMM unique?? > > > > As Justin said, the difference is in the way it is parametrized. > Forcefields are generally built to be additive, but it does not follow that > they are decomposable. > > > > If coulomb energy is also existed between pairs, so the interaction > > > energy > > > > will be LJ+Coulomb yes? > > > > > > Pairs are 1-4 (intramolecular) interactions, so if you define > > > interaction energy between two nonbonded species, you'll get zeroes for > >
[gmx-users] preparing input file for GPU
I am running a protein ligand simulation for the first time after installation of GPU. When i execute mdrun i got this message, "Multiple energy groups is not implemented for GPUs, falling back to the CPU. ". I understand i have to remove the energy group in the .mdp file. But I am not sure how to do that. What are the changes i should do to make it compatible for GPU execution? Kindly suggest me a material or link where i can find the information. I have looked at some gromacs manual but could not really find for the specific problem. Suggestions on where to look will be appreciated too. Here is my .mdp file: title = Protein-ligand complex MD simulation ; Run parameters integrator = md; leap-frog integrator nsteps = 10; 2 * 10 = 200 ps (0.2 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; suppress .trr output nstvout = 0 ; suppress .trr output nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps nstxout-compressed = 5000 ; write .xtc trajectory every 10.0 ps compressed-x-grps = System energygrps = Protein UNK ; Bond parameters continuation= yes ; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_UNK Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; 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 x x xxx x x xxx Thanking you in anticipation. Seke -- 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] generic hardware assembling for gromacs simulation
Dear Benson, Thank you for answering . I am using Centos 6. My current simulation time for protein-ligand systems is about 1.6 ns/day. I am wondering if installing the GTX 1050 or GTX 970 can boost the output significantly (maybe 2 or 3 times more ?). I am installing just as mentioned below. tar xfz gromacs-2018.4.tar.gz cd gromacs-2018.4 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Do i need to pass some other options during the configuration for the GPU? Many thanks. Seke -- 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] gromacs.org_gmx-users Digest, Vol 175, Issue 63
Dear Benson, Thank you for answering . I am using Centos 6. My current simulation time for protein-ligand systems is about 1.6 ns/day. I am wondering if installing the GTX 1050 or GTX 970 can boost the output significantly (maybe 2 or 3 times more ?). I am installing just as mentioned below. tar xfz gromacs-2018.4.tar.gz cd gromacs-2018.4 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Do i need to pass some other options during the configuration for the GPU? Many thanks. Seke On Mon, Nov 19, 2018 at 11:33 PM 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. generic hardware assembling for gromacs simulation > (Seketoulie Keretsu) >2. Re: generic hardware assembling for gromacs simulation > (Benson Muite) >3. VMD visualization of clusters (Rahma Dahmani) >4. Re: VMD visualization of clusters (Benson Muite) >5. Re: generic hardware assembling for gromacs simulation > (pbusc...@q.com) > > > ---------- > > Message: 1 > Date: Mon, 19 Nov 2018 22:25:00 +0900 > From: Seketoulie Keretsu > To: gmx-us...@gromacs.org > Subject: [gmx-users] generic hardware assembling for gromacs > simulation > Message-ID: > > Content-Type: text/plain; charset="UTF-8" > > Dear Users. > > I apologise this this not exactly an GROMACs simulation question. > > I am a student and currently I trying to build a linux system for > gromacs simulation. I have seen some materials about utilizing GPUs > and multiprocessor but I can't fully understand some problems. I have > a system available with the configuration below: > > GPU: Zotac 1050ti 4gb GPU > > Processor: i5 quad core 3.10ghz > RAM: 8GB DDR 4 Corsair ram > Storage: 250 GB had > [also Gigabyte motherboard , 650w power supply, 500 GB external ] > > Would it be possible to utilize this GPUs to enhance the MD simulation > performance? If possible would you suggest/hint how to go about this? > Would it be possible to maximise the use of the resources if the OS is > installed with proper configurations? > > Thanking you. > > Sincerely, > Seke > > > -- > > Message: 2 > Date: Mon, 19 Nov 2018 13:29:12 + > From: Benson Muite > To: "gromacs.org_gmx-users@maillist.sys.kth.se" > > Subject: Re: [gmx-users] generic hardware assembling for gromacs > simulation > Message-ID: <357c7c1f-cd34-1423-3099-b1f85e04b...@ut.ee> > Content-Type: text/plain; charset="utf-8" > > This should probably work. What operating system are you using? Are you > using a later build of Gromacs, such as 2018.4 ? IF so have you tried > the instructions here: > > http://manual.gromacs.org/documentation/current/install-guide/index.html > > Have you tried building an CUDA example programs? > > On 11/19/18 2:25 PM, Seketoulie Keretsu wrote: > > Dear Users. > > > > I apologise this this not exactly an GROMACs simulation question. > > > > I am a student and currently I trying to build a linux system for > > gromacs simulation. I have seen some materials about utilizing GPUs > > and multiprocessor but I can't fully understand some problems. I have > > a system available with the configuration below: > > > > GPU: Zotac 1050ti 4gb GPU > > > > Processor: i5 quad core 3.10ghz > > RAM: 8GB DDR 4 Corsair ram > > Storage: 250 GB had > > [also Gigabyte motherboard , 650w power supply, 500 GB external ] > > > > Would it be possible to utilize this GPUs to enhance the MD simulation > > performance? If possible would you suggest/hint how to go about this? > > Would it be possible to maximise the use of the resources if the OS is > > installed with proper configurations? > > > > Thanking you. > > > > Sincerely, > > Seke > > -- > > Message: 3 > Date: Mon, 19 Nov 2018 14:57:32 +0100 > From: R
[gmx-users] generic hardware assembling for gromacs simulation
Dear Users. I apologise this this not exactly an GROMACs simulation question. I am a student and currently I trying to build a linux system for gromacs simulation. I have seen some materials about utilizing GPUs and multiprocessor but I can't fully understand some problems. I have a system available with the configuration below: GPU: Zotac 1050ti 4gb GPU Processor: i5 quad core 3.10ghz RAM: 8GB DDR 4 Corsair ram Storage: 250 GB had [also Gigabyte motherboard , 650w power supply, 500 GB external ] Would it be possible to utilize this GPUs to enhance the MD simulation performance? If possible would you suggest/hint how to go about this? Would it be possible to maximise the use of the resources if the OS is installed with proper configurations? Thanking you. Sincerely, Seke -- 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] related to box dimension : solvate protein-ligand complex
Dear All, I am doing he Protein-ligand complex tutorial on gromacs 5.0.7 (newly installed). I have successfully completed this tutorial earlier on gromacs 4.6. After the solvation step I found out that the protein-ligand complex solvated system had a cubic shape while my box dimension (shown using vmd command: pbc box) adopted a dodecahedron like shape. Please check the attachment for details. What could be the possible reason behind this? Kindly advise to rectify the problem. The was no error or warning uptill this. Thank you. Sincerely, Seke -- 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] KALP15 in DPPC: Bilayer out of solvation box
Dear Experts I am currently doing the gromacs tutorial for simulation of membrane protein (KALP15 in DPPC by Justin A. Lemkul). I came across several challenges most of which I could resolve. However, the result after solvation wasn't as expected. That is, a small portion of the DPPC bilayer was out of the solvation box and also the the water was no distributed over the system as mentioned in tutorial (or atleast it wasn't observable in VMD). I have done just as in the tutorial. I have no clue why the bilayer went outside the solvation box since i followed and executed just as mentioned in the tutorial. I suspect the later issue, that is, the distribution of water all over the system could be due to the step in which the changing of the value of C from 0.15 to 0.375 in vdwradii.dat wasn't effective. My questions are: 1. Are the other membrane protein simulation tutorials available. Perhaps more comprehensive ones? 2. After changing the value of C to 0.375 in the vdwradii.dat file at the working directory, should i copy the vdwradii.dat to /home//gromacs/top directory (where the file was originally located)? 3. The tutorial mentioned " Placing the new gromos53a6_lipid.ff directory in $GMXLIB will allow you to use this force field system-wide." I am unable to locate 'GMXLIB'. Does GMXLIB refer to the directory in which the forcefield files (eg. ffnonbonded.ipt) were located or should i create a GMXLIB directory. The problems seems trivial however I am unable to proceed beyond solvation. Kindly give suggestions. Thank you. Sincerely, Seke -- 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.
