Re: [gmx-users] cannot load the xtc file (without PBC) to VMD
Hey again, sorry for the late reply. I meant, I didn't have the chance to do that since a .trr file after the simulation was not generated. All I had was the em.trr. Later, I solved the problem by using editconf. Thank you for your attention. On Tue, Jan 14, 2020 at 2:51 PM wrote: > I didn't get you. So your problem is solved using trr file or not? > - Message from Lalehan Ozalp - > Date: Tue, 14 Jan 2020 12:53:54 +0300 > From: Lalehan Ozalp > Reply-To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] cannot load the xtc file (without PBC) to VMD > To: gmx-us...@gromacs.org > > > Thank you, but I haven't tried with a trr file and actually the last .trr > > file I've produced is em.trr. > > Thanks, > > > > On Mon, Jan 13, 2020 at 5:40 PM wrote: > > > >> Hii > >> Have you tried with the .trr file? Try the same procedure with .trr > file. > >> Thanks > >> - Message from Lalehan Ozalp - > >> Date: Mon, 13 Jan 2020 13:35:01 +0300 > >> From: Lalehan Ozalp > >> Reply-To: gmx-us...@gromacs.org > >> Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD > >> To: gmx-us...@gromacs.org > >> > >> Dear all, I have a question regarding loading .xtc file (with no > periodic > >> boundary conditions) to VMD which I generated before. To this end, I had > >> used the command: > >> trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol > >> -ur > >> compact -center > >> and selected *protein* for centering, and *system* for output. > >> However, when I load my corresponding gro file to VMD, and then loading > >> the > >> xtc file above, the following error occurs: > >> > >> ERROR) BaseMolecule: attempt to init atoms while structure building in > >> progress! > >> ERROR) Invalid number of atoms in file: 132259 > >> Info) Using plugin xtc for coordinates from file > >> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc > >> ERROR) Incorrect number of atoms (132259) in > >> ERROR) coordinate file > >> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc > >> ERROR) Mismatch between existing molecule or structure file atom count > >> and > >> coordinate or trajectory file atom count. > >> Info) Finished with coordinate file > >> /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc. > >> > >> This is especially strange since I carried out the same procedure > several > >> times before. Additionally, I have a parallel system (with an isoenzyme > >> of > >> the enzyme used here, with the same cofactor and the same ligand) and > the > >> same steps worked perfectly. As a side note, this happens when I load > xtc > >> file without PBC, while does not happen when I load xtc file in the > >> presence of PBC. > >> > >> Thank you so much in advance! > >> Lalehan > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests > >> visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > >> or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > >> - End message from Lalehan Ozalp - > >> -- > >> 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 > > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > send a mail to gmx-users-requ...@gromacs.org. > > - End message from Lalehan Ozalp - > -- > 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] cannot load the xtc file (without PBC) to VMD
Thank you, but I haven't tried with a trr file and actually the last .trr file I've produced is em.trr. Thanks, On Mon, Jan 13, 2020 at 5:40 PM wrote: > Hii > Have you tried with the .trr file? Try the same procedure with .trr file. > Thanks > - Message from Lalehan Ozalp - > Date: Mon, 13 Jan 2020 13:35:01 +0300 > From: Lalehan Ozalp > Reply-To: gmx-us...@gromacs.org > Subject: [gmx-users] cannot load the xtc file (without PBC) to VMD > To: gmx-us...@gromacs.org > > > Dear all, I have a question regarding loading .xtc file (with no periodic > > boundary conditions) to VMD which I generated before. To this end, I had > > used the command: > > trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol > -ur > > compact -center > > and selected *protein* for centering, and *system* for output. > > However, when I load my corresponding gro file to VMD, and then loading > the > > xtc file above, the following error occurs: > > > > ERROR) BaseMolecule: attempt to init atoms while structure building in > > progress! > > ERROR) Invalid number of atoms in file: 132259 > > Info) Using plugin xtc for coordinates from file > > /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc > > ERROR) Incorrect number of atoms (132259) in > > ERROR) coordinate file > /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc > > ERROR) Mismatch between existing molecule or structure file atom count > and > > coordinate or trajectory file atom count. > > Info) Finished with coordinate file > > /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc. > > > > This is especially strange since I carried out the same procedure several > > times before. Additionally, I have a parallel system (with an isoenzyme > of > > the enzyme used here, with the same cofactor and the same ligand) and the > > same steps worked perfectly. As a side note, this happens when I load xtc > > file without PBC, while does not happen when I load xtc file in the > > presence of PBC. > > > > Thank you so much in advance! > > Lalehan > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests > > visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > send a mail to gmx-users-requ...@gromacs.org. > > - End message from Lalehan Ozalp - > -- > 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] cannot load the xtc file (without PBC) to VMD
Dear all, I have a question regarding loading .xtc file (with no periodic boundary conditions) to VMD which I generated before. To this end, I had used the command: trjconv -f md_0_10.xtc -s md_30.tpr -n index.ndx -o noPBC.xtc -pbc mol -ur compact -center and selected *protein* for centering, and *system* for output. However, when I load my corresponding gro file to VMD, and then loading the xtc file above, the following error occurs: ERROR) BaseMolecule: attempt to init atoms while structure building in progress! ERROR) Invalid number of atoms in file: 132259 Info) Using plugin xtc for coordinates from file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc ERROR) Incorrect number of atoms (132259) in ERROR) coordinate file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc ERROR) Mismatch between existing molecule or structure file atom count and coordinate or trajectory file atom count. Info) Finished with coordinate file /home/habibe/lale/mao-MD/mao-a/20ns_extend/noPBC.xtc. This is especially strange since I carried out the same procedure several times before. Additionally, I have a parallel system (with an isoenzyme of the enzyme used here, with the same cofactor and the same ligand) and the same steps worked perfectly. As a side note, this happens when I load xtc file without PBC, while does not happen when I load xtc file in the presence of PBC. Thank you so much in advance! Lalehan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Thank you Justin, that saved me a lot of time. Best, Lalehan On Sun, Dec 1, 2019 at 3:45 PM Justin Lemkul wrote: > > > On 12/1/19 3:48 AM, Lalehan Ozalp wrote: > > Hello Christian, thank you for providing the patch. However I wonder if > > there is an easier way to convert a.u to frequency - as I need to install > > GROMACS from the start to install the patch. One more thing, I used > version > > 5.0, not 2019, and the patch is written for the version 2019. > > Change the axis label in the .xvg file with a text editor or re-label it > in XmGrace once the data are plotted. You don't need to run the analysis > again with the updated code. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Hello Christian, thank you for providing the patch. However I wonder if there is an easier way to convert a.u to frequency - as I need to install GROMACS from the start to install the patch. One more thing, I used version 5.0, not 2019, and the patch is written for the version 2019. Thank you again, Lalehan On Fri, Nov 29, 2019 at 7:34 PM Christian Blau wrote: > Hello Lalehan and Justin, > > > Thanks for the suggestion! The following patch : > https://gerrit.gromacs.org/c/gromacs/+/14542 does exactly that. > > > Best, > Christian > > On 2019-11-29 14:23, Justin Lemkul wrote: > > > > > > On 11/29/19 7:18 AM, Christian Blau wrote: > >> Hello Lalehan, > >> > >> > >> a.u. stands for "arbitrary units". > >> > >> The rmsd-dist contains a histogram over the distribution of rmsd > values, you can read the a.u. as counts per > >> length-interval. > >> > > > > I would suggest that all histograms that GROMACS produces actually be > labeled reasonably in the code - using a.u. is > > itself arbitrary because it has multiple possible meanings. If it's a > raw histogram, we should be using "Frequency" > > and if normalized, "Probability." > > > > -Justin > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Hello Justin, thank you for the response. In that case I should use "frequency" if I plan to take it the way it is. Thanks, On Fri, Nov 29, 2019 at 4:25 PM Justin Lemkul wrote: > > > On 11/29/19 7:18 AM, Christian Blau wrote: > > Hello Lalehan, > > > > > > a.u. stands for "arbitrary units". > > > > The rmsd-dist contains a histogram over the distribution of rmsd > > values, you can read the a.u. as counts per length-interval. > > > > I would suggest that all histograms that GROMACS produces actually be > labeled reasonably in the code - using a.u. is itself arbitrary because > it has multiple possible meanings. If it's a raw histogram, we should be > using "Frequency" and if normalized, "Probability." > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Hello Christian! Thank you for the valuable information :) Best, Lalehan On Fri, Nov 29, 2019 at 3:18 PM Christian Blau wrote: > Hello Lalehan, > > > a.u. stands for "arbitrary units". > > The rmsd-dist contains a histogram over the distribution of rmsd values, > you can read the a.u. as counts per > length-interval. > > > Best, > > Christian > > On 2019-11-29 12:57, Lalehan Ozalp wrote: > > Hello everyone, I ran a cluster analysis for a 10 ns simulation and > > produced rmsd-clust.xpm and rmsd-dist.xvg graphs. When I open the xvg > file, > > I see "a. u." in the y axis which I couldn't entirely understand. Is it > > supposed to stand for atomic unit for length or mass or something else? I > > provide the file as an example. > > > > Thank you in advance. > > > > Lalehan > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] the a.u. unit in the RMS distribution graph
Hello everyone, I ran a cluster analysis for a 10 ns simulation and produced rmsd-clust.xpm and rmsd-dist.xvg graphs. When I open the xvg file, I see "a. u." in the y axis which I couldn't entirely understand. Is it supposed to stand for atomic unit for length or mass or something else? I provide the file as an example. Thank you in advance. Lalehan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error of missing atoms due to an incorrectness in the .hdb file
Thank you Justin, I worked more on the format of hydrogen names and I don't see those errors anymore. However, the only error I now see is: "Atom H5'1 not found in rtp database in residue FAD, it looks a bit like H01". Which is weird, because there is no atom named H5'1 anywhere! Not in the pdb, not in the rtp, not itp nor hdb file. This is absolutely a black box to me. Thanks again! On Thu, May 23, 2019 at 12:07 AM Justin Lemkul wrote: > > > On 5/22/19 4:14 PM, Lalehan Ozalp wrote: > > Hello all, > > > > I am trying to run a simulation with a protein involving a covalently > bound > > FAD cofactor. I followed the steps provided on the website > > > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > > and -I think- added the hydrogens in the .hdb file accordingly. While > doing > > this, I specifically used the atom types that gromacs would recognize (I > > also added relevant .rtp and .itp file to the forcefield in the current > > working directory). > > > > However, several warnings and subsequently a fatal error occurs when I > run > > pdb2gmx. I don't prefer using -missing option in this case as it'll > > probably give a wrong topology. > > > > How to come around this? Any help would be appreciated. I provide the > > warnings and the error message below; as well as the constitution of the > > hydrogens in the .hdb file: > > (.hdb file) > > FAD 6 > > 2 3 H N2CA NC > > 3 4 HC CT CA CA > > 1 1 HC CA CA CT > > 1 1 H5 CQ NC CA > > 1 1 H5 CQ NA CT > > 1 1 HA CA CA CT > > > > This entry cannot be correct, because the same atoms are defined in > multiple ways. Note that the .hdb file requires atom *names*, not types. > The errors listed below indicated you have 30 more hydrogens that are > unaccounted for. FAD is a big molecule, you have to include all the > hydrogens in the isoalloxazine, adenosine, and ribitol. > > -Justin > > > WARNING: atom H01 is missing in residue FAD 600 in the pdb file > > You might need to add atom H01 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H02 is missing in residue FAD 600 in the pdb file > > You might need to add atom H02 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H03 is missing in residue FAD 600 in the pdb file > > You might need to add atom H03 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H04H is missing in residue FAD 600 in the pdb file > > You might need to add atom H04H to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H05 is missing in residue FAD 600 in the pdb file > > You might need to add atom H05 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H06H is missing in residue FAD 600 in the pdb file > > You might need to add atom H06H to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H07 is missing in residue FAD 600 in the pdb file > > You might need to add atom H07 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H08H is missing in residue FAD 600 in the pdb file > > You might need to add atom H08H to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H09 is missing in residue FAD 600 in the pdb file > > You might need to add atom H09 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H10 is missing in residue FAD 600 in the pdb file > > You might need to add atom H10 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H11 is missing in residue FAD 600 in the pdb file > > You might need to add atom H11 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H
[gmx-users] error of missing atoms due to an incorrectness in the .hdb file
Hello all, I am trying to run a simulation with a protein involving a covalently bound FAD cofactor. I followed the steps provided on the website http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field and -I think- added the hydrogens in the .hdb file accordingly. While doing this, I specifically used the atom types that gromacs would recognize (I also added relevant .rtp and .itp file to the forcefield in the current working directory). However, several warnings and subsequently a fatal error occurs when I run pdb2gmx. I don't prefer using -missing option in this case as it'll probably give a wrong topology. How to come around this? Any help would be appreciated. I provide the warnings and the error message below; as well as the constitution of the hydrogens in the .hdb file: (.hdb file) FAD 6 2 3 H N2CA NC 3 4 HC CT CA CA 1 1 HC CA CA CT 1 1 H5 CQ NC CA 1 1 H5 CQ NA CT 1 1 HA CA CA CT WARNING: atom H01 is missing in residue FAD 600 in the pdb file You might need to add atom H01 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H02 is missing in residue FAD 600 in the pdb file You might need to add atom H02 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H03 is missing in residue FAD 600 in the pdb file You might need to add atom H03 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H04H is missing in residue FAD 600 in the pdb file You might need to add atom H04H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H05 is missing in residue FAD 600 in the pdb file You might need to add atom H05 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H06H is missing in residue FAD 600 in the pdb file You might need to add atom H06H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H07 is missing in residue FAD 600 in the pdb file You might need to add atom H07 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H08H is missing in residue FAD 600 in the pdb file You might need to add atom H08H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H09 is missing in residue FAD 600 in the pdb file You might need to add atom H09 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H10 is missing in residue FAD 600 in the pdb file You might need to add atom H10 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H11 is missing in residue FAD 600 in the pdb file You might need to add atom H11 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H12 is missing in residue FAD 600 in the pdb file You might need to add atom H12 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H13 is missing in residue FAD 600 in the pdb file You might need to add atom H13 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H14 is missing in residue FAD 600 in the pdb file You might need to add atom H14 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H15 is missing in residue FAD 600 in the pdb file You might need to add atom H15 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H16 is missing in residue FAD 600 in the pdb file You might need to add atom H16 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H17 is missing in residue FAD 600 in the pdb file You might need to add atom H17 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H18 is missing in residue FAD 600 in the pdb file You might need to add atom H18 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H19 is missing in residue FAD 600 in the pdb file You might need to add atom H19 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H21 is missing in residue FAD 600 in the pdb file You might need to add atom H21 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H22 is missing in residue FAD 600 in the pdb file
[gmx-users] Best method to calculate binding free energy with GROMACS version 2016.3
Hi everyone, I've run several simulations with a set of 6 ligands and an enzyme (30 ns) in water. I want to employ a method to calculate binding free energy of the ligands but I'm aware that MMPBSA is not compatible with version 2016.3. The forcefield I've used is charmm36-nov2018.ff. I know I have options like PMF, BAR, FEP and LIE. However, I cannot be sure which one to use. From the manual (or other materials) readings I've made so far, they all seem to make sense. Any help would be appreciated. Thanks, Lalehan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS
Dear Szilárd, They most certainly are clear! I originally thought the GPU of the terminal would be very useful. Your suggestions are of great help. Thank you so much! Best wishes, Lalehan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS
Dear Szilárd, There is indeed one GPU. And please keep in mind I used to exploit the -nt 72 option BEFORE the 2019-dev version. It looks like it employs GPU by default and I don't know how to efficiently use it, apparently. Here is the info you asked for: System size: 130655 atoms .mdp file: ; Run parameters integrator = md; leap-frog integrator nsteps = 1500 ; 2 * 1500 = 3 ps (30 ns) dt = 0.002 ; 2 fs ; Output control nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps nstxout-compressed = 5000 ; save coordinates every 10.0 ps ; Bond parameters continuation= yes ; continuing from NPT constraint_algorithm= lincs ; holonomic constraints constraints = h-bonds ; bonds to H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighbor searching and vdW cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 20; largely irrelevant with Verlet rlist = 1.2 vdwtype = cutoff vdw-modifier= force-switch rvdw-switch = 1.0 rvdw= 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb= 1.2 pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_nap_16 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 my command: gmx mdrun -deffnm md_0_30 -ntmpi 4 -ntomp 18 -npme 1 -pme gpu -nb gpu and what the program prints in the log file once I run it: GROMACS version:2019-dev Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support:CUDA SIMD instructions: NONE FFT library:fftw-3.3.8 RDTSCP usage: disabled TNG support:enabled Hwloc support: disabled Tracing support:disabled Built on: 2019-01-22 13:53:24 Build CPU vendor: Unknown Build CPU brand:Unknown Build CPU family: 0 Model: 0 Stepping: 0 Build CPU features: Unknown C compiler: /usr/local/bin/gcc GNU 5.3.0 C++ compiler flags: -std=c++11 -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations -Wall -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Tue_Jan_10_13:22:03_CST_2017;Cuda compilation tools, release 8.0, V8.0.61 Running on 1 node with total 36 cores, 72 logical cores, 1 compatible GPU Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E5-2699 v3 @ 2.30GHz Family: 6 Model: 63 Stepping: 2 GPU info: Number of GPUs detected: 1 #0: NVIDIA Quadro K2200, compute cap.: 5.0, ECC: no, stat: compatible Highest SIMD level requested by all nodes in run: AVX2_256 SIMD instructions selected at compile time: None This program was compiled for different hardware than you are running on, which could influence performance. The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Hardware: Architecture: x86_64 CPU op-mode(s):32-bit, 64-bit Byte Order:Little Endian CPU(s):72 On-line CPU(s) list: 0-71 Thread(s) per core:2 Core(s) per socket:18 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family:6 Model: 63 Model name:Intel(R) Xeon(R) CPU E5-2699 v3 @ 2.30GHz Stepping: 2 CPU MHz: 1200.000 BogoMIPS: 4589.66 Virtualization:VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 46080K NUMA node0 CPU(s): 0-17,36-53 NUMA node1 CPU(s): 18-35,54-71 GPU: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107GL [Quadro K2200]
Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS
Dear Carsten, thank you for your advice. I'd tried gmx mdrun -deffnm md_0_30 -ntmpi 4 -ntomp 18 -npme 1 -pme gpu -nb gpu, then tried -ntmpi 8 -ntomp 9, later tried -ntmpi 12 -ntomp 6 (the rest of the command being the same) and I feel like neither of them make much of a difference. The CPU performance doesn't seem bad, but the steps are not flowing fast enough. My system involves 130655 atoms and I'm absolutely sure I ran simulation with the very same system a month ago, finishing within 2-3 days by only using option -nt 72. It was the 2016.3 version in which GPU support was disabled. I'm afraid I don't know how to exploit GPU in the most possible efficient way. Anyways, thank you for your suggestion! Lalehan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS
Dear Szilárd, Thank you for your response. I'm basically simulating an enzyme including a cofactor and a ligand that is of my interest. I'm trying to observe the ligand's behaviour through a 30 ns trajectory. I'm confused by what you said. I used to employ the -nt option according to the old versions' manuals. It basically advised to enter the number that is the number of cores in a computer. Which reminds me of the fact that things have must be changed with the new versions (e.g. CUDA compiling). I'll be very glad to hear some guidance as I'm trying to learn how to employ GPUs efficiently just now. Thank you, best regards, Lalehan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to increase GMX_OPENMP_MAX_THREADS
Thank you for your reply. Next time I build GROMACS I'll keep that in mind. The funny thing is; nobody in the lab upgraded GROMACS. Hence the complications. Best regards, -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to increase GMX_OPENMP_MAX_THREADS
Hello all, I'd been running simulation with GROMACS 2018 using 72 open mpi threads without problem until (I assume) it was updated to 2019 version. When I execute mdrun with option -nt 72 (which is the number of cores of my terminal) it says: "you are using 72 openmp threads, which is larger than GMX_OPENMP_MAX_THREADS (64). Decrease the number of OpenMP threads or rebuild GROMACS with a larger value for GMX_OPENMP_MAX_THREADS." In the documentation of GROMACS 2019 release, it's written: "mdrun can run with more than GMX_OPENMP_MAX_THREADS threads." Could you please help me how to get around this issue? Thank you in advance. Lalehan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
