Re: [gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0
Hi, I've had problems in the past with syntax requirements for CMAKE_PREFIX_PATH. Try putting the path in quotes and separating with a semicolon instead of a colon. Kevin On Sat, Apr 4, 2020 at 1:40 PM Wei-Tse Hsu wrote: > *Message sent from a system outside of UConn.* > > > Dear gmx users, > Recently I've been trying to install GROMACS 2020.1. However, I encounter a > compilation error while using the make command. The error is as follows: > > > > > > */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find > /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit > statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: *** > [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2* > From the error above, it seemed that GROMACS was unable to find library > like libpthread.so.0 and libpthread_nonshared.a. After checking I found > that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and > libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/ > x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add > the paths of the libraries for GROMACS to search for. Specifically, the > command I was using is: > *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd > build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON > -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7 > -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make > > gmx_compile.log* > However, it turned out that I still got the same error. I'm confused right > now since I thought that gromacs should be able to find the files. I'm > wondering if I missed something. Could someone please tell me what I can do > or share some relevant experience? Any help is much appreciated! > > Best, > Wei-Tse > -- > 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] Scale Triclinic Box
On 4/4/20 5:07 PM, Maryam Sadeghi wrote: Hi Justin, I actually want to scale the box (both moving the chains apart and close to each other by changing the a and b parameters of the cell). I don't want to run any dynamics at this point as I have already done quantum mechanics minimization on this structure. When I use the editconf command the cell parameters change but the coordinates of the atoms remain unchanged, i.e. by compression the polymer chains remain outside of the cell... I was wondering if editconf could scale the coordinates proportionally with the cell parameters without distorting the bonds lengths? You can apply a scaling vector with editconf -scale as I suggested in my last message, but I do not think it will do what you want. That's the only GROMACS tool that has any such capability, so if that doesn't work, GROMACS isn't going to do what you want. -Justin gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686 1.9724 -angles 90.00 126.91 90.00 The original cell parameters are: a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, gamma: 90.00 The unit cell consists of 4 polymer chains, each chain having 7 repeating (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds, 340 angles and 376 dihedrals. Best Maryam On Sat, Apr 4, 2020, 4:54 AM Justin Lemkul wrote: On 4/3/20 11:16 PM, Maryam Sadeghi wrote: Hi Salman, Tnx for the info, I actually want to do the cold-compression on my crystalline structure. So basically I need to both compress and expand the a and b parameters of the unit cell (the c parameter is already optimized)... so it's not just building a supercell, but rather scaling only 2 parameters of the unit cell simultaneously while remaping the new coordinates inside the scaled cell... could "gmx genconf -nbox ... ... ..." handle this? It sounds like you need to actually perform a simulation in which high pressure is applied to compress the box. genconf is for duplicating a box N times in each dimension, and while you can change box vectors and scale coordinates with editconf (-scale option), this is not the same as compressing them and bond lengths, etc. will become distorted. -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. -- == 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] Scale Triclinic Box
Hi Justin, I actually want to scale the box (both moving the chains apart and close to each other by changing the a and b parameters of the cell). I don't want to run any dynamics at this point as I have already done quantum mechanics minimization on this structure. When I use the editconf command the cell parameters change but the coordinates of the atoms remain unchanged, i.e. by compression the polymer chains remain outside of the cell... I was wondering if editconf could scale the coordinates proportionally with the cell parameters without distorting the bonds lengths? gmx editconf -f CONTCAR.pdb -o scl0.2.pdb -bt triclinic -box 0.3560 0.5686 1.9724 -angles 90.00 126.91 90.00 The original cell parameters are: a: 0.79620 nm, b: 1.27140 nm, c: 1.9724 nm, alpha: 90.00, beta: 126.91, gamma: 90.00 The unit cell consists of 4 polymer chains, each chain having 7 repeating (C-O-C) units. The system has 3 atom types (C, H, O), 196 atoms, 192 bonds, 340 angles and 376 dihedrals. Best Maryam On Sat, Apr 4, 2020, 4:54 AM Justin Lemkul wrote: > > > On 4/3/20 11:16 PM, Maryam Sadeghi wrote: > > Hi Salman, > > > > Tnx for the info, I actually want to do the cold-compression on my > > crystalline structure. So basically I need to both compress and expand > the > > a and b parameters of the unit cell (the c parameter is already > > optimized)... so it's not just building a supercell, but rather scaling > > only 2 parameters of the unit cell simultaneously while remaping the new > > coordinates inside the scaled cell... could "gmx genconf -nbox ... ... > > ..." handle this? > > It sounds like you need to actually perform a simulation in which high > pressure is applied to compress the box. genconf is for duplicating a > box N times in each dimension, and while you can change box vectors and > scale coordinates with editconf (-scale option), this is not the same as > compressing them and bond lengths, etc. will become distorted. > > -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.
[gmx-users] Unable to compile GROMACS 2020.1 using GNU 7.5.0
Dear gmx users, Recently I've been trying to install GROMACS 2020.1. However, I encounter a compilation error while using the make command. The error is as follows: */usr/bin/ld: cannot find /lib/libpthread.so.0/usr/bin/ld: cannot find /usr/lib/libpthread_nonshared.acollect2: error: ld returned 1 exit statusmake[2]: *** [lib/libgromacs.so.5.0.0] Error 1make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2make: *** [all] Error 2* >From the error above, it seemed that GROMACS was unable to find library like libpthread.so.0 and libpthread_nonshared.a. After checking I found that instead of in /lib/ and /usr/lib/, the files libpthread.so.0 and libpthread_nonshared.a are in /lib/x86_64-linux-gnu and /usr/lib/ x86_64-linux-gnu. Therefore, I used the option DCMAKE_PREFIX_PATH to add the paths of the libraries for GROMACS to search for. Specifically, the command I was using is: *tar xfz gromacs-2020.1.tar.gz && cd gromacs-2020.1 && mkdir build && cd build && rm -rf * && cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_CXX_COMPILER=g++-7 -DCMAKE_C_COMPILER=gcc-7 -DCMAKE_PREFIX_PATH=/usr/lib/x86_64-linux-gnu:/lib/x86_64-linux-gnu && make > gmx_compile.log* However, it turned out that I still got the same error. I'm confused right now since I thought that gromacs should be able to find the files. I'm wondering if I missed something. Could someone please tell me what I can do or share some relevant experience? Any help is much appreciated! Best, Wei-Tse -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] How to parametrize a new molecule?
Hello Herbert, Not related to your question, but be careful if you are going to use CHARMM36 force field for DNA, as a recent study ( https://pubs.acs.org/doi/10.1021/acs.jpcb.9b09106) shows that this ff does not preserve DNA stability at a longer time scale, in case you are going to do so. Best, Mahdi On Sat, Apr 4, 2020 at 3:21 AM Herbert de Castro Georg wrote: > Thanks, Justin! > > > > Em sex., 3 de abr. de 2020 às 22:15, Justin Lemkul > escreveu: > > > > > > > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote: > > > Dear users, > > > > > > I want to perform a simulation of a molecule inside DNA. I'm probably > > going > > > to use CHARMM for DNA. But how do I parametrize the molecule? > > > > http://cgenff.umaryland.edu/ > > > > -Justin > > > > -- > > == > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > == > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- 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 use GROMACS license?
Den 2020-04-04 kl. 16:18, skrev Nikhil Maroli: Dear GMX team, The GROMACS license allows one to use the codes inside a proprietary software? Basically, building a GUI and selling it for a higher price? Yes. As long as modifications to gromacs are available under the LGPL license as well. -- David van der Spoel, Ph.D., Professor of Biology Uppsala University. http://virtualchemistry.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] How to use GROMACS license?
Dear GMX team, The GROMACS license allows one to use the codes inside a proprietary software? Basically, building a GUI and selling it for a higher price? -- Regards, Nikhil Maroli -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Scale Triclinic Box
On 4/3/20 11:16 PM, Maryam Sadeghi wrote: Hi Salman, Tnx for the info, I actually want to do the cold-compression on my crystalline structure. So basically I need to both compress and expand the a and b parameters of the unit cell (the c parameter is already optimized)... so it's not just building a supercell, but rather scaling only 2 parameters of the unit cell simultaneously while remaping the new coordinates inside the scaled cell... could "gmx genconf -nbox ... ... ..." handle this? It sounds like you need to actually perform a simulation in which high pressure is applied to compress the box. genconf is for duplicating a box N times in each dimension, and while you can change box vectors and scale coordinates with editconf (-scale option), this is not the same as compressing them and bond lengths, etc. will become distorted. -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] Calculate probability of presence of water around a residues
Dear Users, I have two queries 1. I have tried using the select command to Calculate probability of presence of water around a residues by creating an a group in my index analyze.ndx contains a group named ser76 which has the atom position near which i want to find this water (say atom 1313) *gmx select -s md_0_1.tpr -f md_0_1_center.xtc -os no_solv.xvg -select 'name OW and within 0.3 of group ser76' -n analyze.ndx* This command gives an error Error in user input: Selection 'name OW and within 0.3 of group ser76' never matches any atoms. 2. Regarding *MMPBSA calculation* for my protein-ligand simulation. i m using GROMACS 2018 version on the server. What is the procedure for doing the same. Thanks & Regards, Dr. Pooja Kesari Post Doctoral Fellow Department Of Biosciences and Bioengineering Indian Institute of Technology Bombay 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.
