[gmx-users] Quick and Dirty Installation Error
Hello, I am trying to install GROMACS 2020 on my Windows laptop using Cygwin 3.1.4. I have run the steps outlined in the installation guide (http://manual.gromacs.org/documentation/2020/install-guide/index.html) before the command "make", version 4.3,. The command cmake in the build folder executed properly. When I try to execute "make", it returns the following error: /gromacs-2020/src/external/thread_mpi/src/tmpi_init.cpp:476:42: error: 'strdup' was not declared in this scope; did you mean 'strcmp'? 476 | threads[i].argv[j] = strdup( (*argv)[j] ); | ^~ | strcmp The error has to do with the C++ compiler I installed (g++ from gcc version 9.2.0) not recognizing the object 'strdup'. Is there a way to fix this error? Best, Vinu Harihar -- 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] Electric field
Dear GMX users, I would like to perform MD simulations with external electric field. I would like to control the frequency. In the manual, I found that we should use ω 2.45 GHz, like microwave, and it was defined as ω=2πc/λ. I think that λ is equal to 0.1224 m. Finally, I think that ω = 2*3.14*3e10^8 / 0.1224 = 0.0154 /ps Is it right? Thank you very much for any advice. Best regards, Mijiddorj -- 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 unusual unit
Thank you Justin and David, that's very helpful -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of David van der Spoel Sent: 16 March 2020 17:13 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] gmx msd unusual unit CAUTION: This email came from outside of the University. To keep your account safe, only click on links and open attachments if you know the person who sent the email, or you expected to receive this communication. Den 2020-03-16 kl. 15:10, skrev Justin Lemkul: > > > On 3/16/20 10:07 AM, Joe Paul-Taylor wrote: >> Hello >> >> With running gmx msd I am told in the output the y axis unit is nm/ >> S2/ N, which is unexpected. Is this simply an print error or is there >> an error within the calculation? I have provided a copy of the output >> below, noting the units of the self-diffusion coefficient are >> sensible. Any insight would be much appreciated. > > The unit is correct. GROMACS does all distance calculations in terms > of nm. You get an interpreted output of the MSD in traditional units > for the diffusion constant. The confusion maybe about the xmgrace formatting :) nm^2 if you use the right software... > > -Justin > >> # Created by: >> # :-) GROMACS - gmx msd, 2019.2 (-: >> # Command line: >> # gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o >> msd_IRMOF-NHPr_3OCT_8_run_1.xvg >> # gmx msd is part of G R O M A C S: >> # >> # Gromacs Runs One Microsecond At Cannonball Speeds # >> @title "Mean Square Displacement" >> @xaxis label "Time (ps)" >> @yaxis label "MSD (nm\S2\N)" >> @TYPE xy >> # MSD gathered over 1 ps with 1001 restarts # Diffusion constants >> fitted from time 1000 to 9000 ps # D[ UNK] = 0.0031 (+/- >> 0.0004) (1e-5 cm^2/s) >> >> Thank you >> >> Joe >> >> > -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] makes sense for Ryckaert Bellemans dihs. only.
Dear Gromacs users I am calculating a dihedral angle between certain atoms by following command:- gmx angle -type dihedral -f md_1000ps.xtc -n dihedral.ndx -ov group.xvg -of trans.xvg Group 0 ( dihedral1) has 4 elements Group 1 ( dihedral2) has 4 elements Group 2 ( dihedral3) has 4 elements Select a group: 2 Selected 2: 'dihedral3' I get a warning as below:- Warning: calculating fractions as defined in this program makes sense for Ryckaert Bellemans dihs. only. Ignoring -of What does it mean? Can anyone please help me to understand? I am using gromacs 2020 Thanks. 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.
Re: [gmx-users] gmx msd unusual unit
Den 2020-03-16 kl. 15:10, skrev Justin Lemkul: On 3/16/20 10:07 AM, Joe Paul-Taylor wrote: Hello With running gmx msd I am told in the output the y axis unit is nm/ S2/ N, which is unexpected. Is this simply an print error or is there an error within the calculation? I have provided a copy of the output below, noting the units of the self-diffusion coefficient are sensible. Any insight would be much appreciated. The unit is correct. GROMACS does all distance calculations in terms of nm. You get an interpreted output of the MSD in traditional units for the diffusion constant. The confusion maybe about the xmgrace formatting :) nm^2 if you use the right software... -Justin # Created by: # :-) GROMACS - gmx msd, 2019.2 (-: # Command line: # gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o msd_IRMOF-NHPr_3OCT_8_run_1.xvg # gmx msd is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @ title "Mean Square Displacement" @ xaxis label "Time (ps)" @ yaxis label "MSD (nm\S2\N)" @TYPE xy # MSD gathered over 1 ps with 1001 restarts # Diffusion constants fitted from time 1000 to 9000 ps # D[ UNK] = 0.0031 (+/- 0.0004) (1e-5 cm^2/s) Thank you Joe -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] energy minimization in vacuum
Hi, If u minimise the protein in vaccum...the bad contact within the protein atoms will be removed After solvation if u do...then both the bad water contact and steric clashes within the protein will be removed. On Mon 16 Mar, 2020, 8:37 PM Deepanshi ., wrote: > Dear all, > > I am trying to simulate an all atom protein in water. I wanted to ask that > what is the importance of minimizing the protein in a vacuum. It is not > mentioned in the lysozyme tutorial. > > Thanks. > > Regards, > Deepanshi > -- > 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] energy minimization in vacuum
Dear all, I am trying to simulate an all atom protein in water. I wanted to ask that what is the importance of minimizing the protein in a vacuum. It is not mentioned in the lysozyme tutorial. Thanks. Regards, Deepanshi -- 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 unusual unit
Hello With running gmx msd I am told in the output the y axis unit is nm/ S2/ N, which is unexpected. Is this simply an print error or is there an error within the calculation? I have provided a copy of the output below, noting the units of the self-diffusion coefficient are sensible. Any insight would be much appreciated. # Created by: # :-) GROMACS - gmx msd, 2019.2 (-: # Command line: # gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o msd_IRMOF-NHPr_3OCT_8_run_1.xvg # gmx msd is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title "Mean Square Displacement" @xaxis label "Time (ps)" @yaxis label "MSD (nm\S2\N)" @TYPE xy # MSD gathered over 1 ps with 1001 restarts # Diffusion constants fitted from time 1000 to 9000 ps # D[ UNK] = 0.0031 (+/- 0.0004) (1e-5 cm^2/s) Thank you Joe -- 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 unusual unit
On 3/16/20 10:07 AM, Joe Paul-Taylor wrote: Hello With running gmx msd I am told in the output the y axis unit is nm/ S2/ N, which is unexpected. Is this simply an print error or is there an error within the calculation? I have provided a copy of the output below, noting the units of the self-diffusion coefficient are sensible. Any insight would be much appreciated. The unit is correct. GROMACS does all distance calculations in terms of nm. You get an interpreted output of the MSD in traditional units for the diffusion constant. -Justin # Created by: # :-) GROMACS - gmx msd, 2019.2 (-: # Command line: # gmx msd -s topol.tpr -f npt.xtc -b 3000 -e 13000 -o msd_IRMOF-NHPr_3OCT_8_run_1.xvg # gmx msd is part of G R O M A C S: # # Gromacs Runs One Microsecond At Cannonball Speeds # @title "Mean Square Displacement" @xaxis label "Time (ps)" @yaxis label "MSD (nm\S2\N)" @TYPE xy # MSD gathered over 1 ps with 1001 restarts # Diffusion constants fitted from time 1000 to 9000 ps # D[ UNK] = 0.0031 (+/- 0.0004) (1e-5 cm^2/s) Thank you Joe -- == 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] Fatal error: Too many warnings (3) ; WARNING * [file lig.prm, line **] :: How to overcome this error -> simply delete the lines which give warnings?
On 3/15/20 6:39 PM, Adarsh V. K. wrote: Dear all, How to overcome this error ? How to overcome this error. Simply delete the lines which give warnings? *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1* The above command returns following 'error message' while using with " ions.mdp " This run will generate roughly 13 Mb of data There were 3 notes There were 3 warnings - Fatal error: Too many warnings (3). WARNING 1 [file lig.prm, line 11]: Overriding U-B parameters. WARNING 2 [file lig.prm, line 14]: Overriding U-B parameters. WARNING 3 [file lig.prm, line 17]: Overriding U-B parameters. - You have parameters in your .prm file that are already present in ffbonded.itp, which happens due to the CGenFF server version (4.0) being behind that of the CHARMM36 port (CGenFF 4.1). Remove the offending parameters from the .prm file. -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] (no subject)
Download and use the forcefield files from the ATB server website, and then make that you correctly point to it in your top file. On Sat, 14 Mar. 2020, 7:32 pm FAISAL NABI, wrote: > Hi, > I have been a new user and i was following the protein-ligand complex > tutorial for MD. I have used GROMOS96 54a7 FF and to build ligand topology > i have used ATB webserver. I did download the .itp and .pdb file from there > and converted that to .gro file. The problem i am facing is it shows an > error while i add ions that "Atomtype CAro not found", although i have > added the atomtypes in the gromacs topology file still it's showing the > same error. I request if somebody could provie me a stepwise protocol i > could follow. > > Thank you > > -- > > Faisal Nabi > > *Pre-Doctoral Fellow (CSIR-JRF)* > C/o Professor Rizwan Hassan Khan > Interdisciplinary Biotechnology Unit, > Aligarh Muslim University, Aligarh, UP, INDIA. > Email-*fn...@myamy.ac.in * > * faisalbioc...@gmail.com * > Contact no. - *+91-8923713214* > -- > 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] Can you help regarding this
What specifically do you need help with? Both the error messages there are explicit about what the issues are, first you have failed to correctly adjust the number of molecules of the topology (.top) to match the coordinate file. You also have a +10 net charge, which is unlikely to be a good idea. On Sat, 14 Mar. 2020, 4:58 pm Kushal Roy, wrote: > GROMACS is written by: > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. > Berendsen > Par BjelkmarAldert van Buuren Rudi van Drunen Anton Feenstra > Gerrit GroenhofAleksei Iupinov Christoph Junghans Anca Hamuraru > Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus > Carsten Kutzner Per Larsson Justin A. LemkulViveca Lindahl > Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola > Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov >Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen > Christian WennbergMaarten Wolf >and the project leaders: > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2017, The GROMACS development team at > Uppsala University, Stockholm University and > the Royal Institute of Technology, Sweden. > check out http://www.gromacs.org for more information. > > GROMACS is free software; you can redistribute it and/or modify it > under the terms of the GNU Lesser General Public License > as published by the Free Software Foundation; either version 2.1 > of the License, or (at your option) any later version. > > GROMACS: gmx grompp, version 2018.1 > Executable: /usr/bin/gmx > Data prefix: /usr > Working dir: /mnt/c/Users/kushal/Desktop/New folder (10) > Command line: > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr > > Ignoring obsolete mdp entry 'title' > > NOTE 1 [file ions.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 -694988524 > Generated 165 of the 1596 non-bonded parameter combinations > Excluding 3 bonded neighbours molecule type 'Protein_chain_X' > Excluding 2 bonded neighbours molecule type 'SOL' > > NOTE 2 [file topol.top, line 11469]: > System has non-zero total charge: 10.00 > Total charge should normally be an integer. See > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > for discussion on how close it should be to an integer. > > > > > --- > Program: gmx grompp, version 2018.1 > Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 619) > > Fatal error: > number of coordinates in coordinate file (solv.gro, 45034) > does not match topology (topol.top, 44947) > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > kushalrajroy@DESKTOP-RVURRJU:/mnt/c/Users/kushal/Desktop/New folder (10)$ > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr > :-) GROMACS - gmx grompp, 2018.1 (-: > > GROMACS is written by: > Emile Apol Rossen Apostolov Paul Bauer Herman J.C. > Berendsen > Par BjelkmarAldert van Buuren Rudi van Drunen Anton Feenstra > Gerrit GroenhofAleksei Iupinov Christoph Junghans Anca Hamuraru > Vincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus > Carsten Kutzner Per Larsson Justin A. LemkulViveca Lindahl > Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola > Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov >Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen > Christian WennbergMaarten Wolf >and the project leaders: > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > Copyright (c) 2001-2017, The GROMACS development team at > Uppsala University, Stockholm University and > the Royal Institute of Technology, Sweden. > check out http://www.gromacs.org for more information. > > GROMACS is free software; you can redistribute it and/or modify it > under the terms of the GNU Lesser General Public License > as published by the Free Software Foundation; either version 2.1 > of the License, or (at your option) any later version. > > GROMACS: gmx grompp, version 2018.1 > Executable: /usr/bin/gmx > Data prefix: /usr > Working dir: /mnt/c/Users/kushal/Desktop/New folder (10) > Command line: > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr >
Re: [gmx-users] Creating a simple water box
Is the "close contact" really an issue? As soon as you start any sort of MD that will quickly adjust itself. On Sat, 14 Mar. 2020, 7:23 pm dodia, wrote: > Dear gromacs users, > > I was trying a simple gmx solvate test on a water box of size 25*20*20 > angstrom, creating a water box of density 1 g/cm^3. By my calculations > the no. of water molecules in the box should by 332 (each water molecule > has a volume of (3.11 angstrom)^3). When I use the solvate command: > > gmx solvate -cs spc216 -box 2.5 2 2 -o test2.pdb -maxsol 332 > > with gromacs 5.0.7, I get 291 water molecules in the box, and the > density as 0.87 g/cm^3 > > with gromacs 2016.1, I get 295 water molecules in the box, and the > density as 0.88 g/cm^3 > > When I try using the -scale option: > > gmx solvate -cs spc216 -scale 0.40 -box 2.5 2 2 -o test.pdb -maxsol 332 > > I can get a density of 0.993 g/cm3, however when I visualize the > structure, I can notice a lot of close contact between O-O atoms (the > distance between O-O atoms becomes lower than 1.49 angstroms, the O-O > bond length). So is there any other way to fine tune the gmx solvate > command so as to generate the water box with density close to 1 g/cm^3, > without the close contact problem? > > Best Regards, > Mayank Dodia > -- > 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] Fwd: Problems with Non-equilibrium MD
Hi all, I am using non-equilibrium MD to calculate the viscosity of the liquid by applying a shear on xy direction. My problem is that when I observe the trajectory of the simulation, I find only the box deformed and particles did not change correspondingly, as shown in the attached image. I also attached my mdp file, can anyone give me some suggestions? Thanks. Regards -- *Jun ZHOU* Postgraduate Student , Room 117, Building 36 Department of Civil Engineering, Monash University, Victoria 3800, Australia. -- 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] Fwd: Problems with Non-equilibrium MD
Hi Jun, Can you add a link to your image online rather than attaching it? Benson On Mon, Mar 16, 2020, at 10:25 AM, Jun Zhou wrote: > Hi all, > > I am using non-equilibrium MD to calculate the viscosity of the liquid by > applying a shear on xy direction. My problem is that when I observe the > trajectory of the simulation, I find only the box deformed and particles > did not change correspondingly, as shown in the attached image. > > I also attached my mdp file, can anyone give me some suggestions? Thanks. > > Regards > > -- > *Jun ZHOU* > Postgraduate Student , > Room 117, Building 36 > Department of Civil Engineering, > Monash University, > Victoria 3800, Australia. > > -- > 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] no subject
Hello Faisal, Easiest way to do this is by navigating to the MD files tab and download the "Gromacs 4.5.x-5.x.x 54a7" below this warning - "*Warning!* This molecule contains non-standard atom types not included in the standard GROMOS 54A7 forcefield..." The folder contains the procedure to modify the 54a7 forcefield to include the non-standard atomtypes. However the easiest way to just include the whole folder in your working directory (wd) and when you prepare gro from pdb in the first step, you can choose the option 1 (you will see that you receive a prompt saying this ff is from the wd). Hope it helps. If you are interested in Ligand- protein interaction studies. I would suggest you to use Amber or Charmm ff. This is because GROMOS is a united atom ff and an all atom ff might be better in helping you understand these interactions. Please go through the last part of this thread - https://www.researchgate.net/post/How_can_I_use_a_Topology_file_generated_by_an_ATB_server If you want to use Amber ff. you can use ACPYPE which works in conjunction with AMBER to prepare files necessary in gromacs compatible format. As antechamber (part of AMBER) is a semi qm/mm technique the parametrization happens faster , plus it can be done directly on your system. All the best -- Regards, Prasanth. -- 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.
