[gmx-users] Buckingham parameters to Lennard Jones Parameters
Hello Group, Can anyone please tell me as how can i convert Buckingham potential parameters into Lennard Jones parameters? Thanks in advance. -- 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] Using different sets of parameters with the same functional form for a single dihedral
Hello Group, I want to define dihedral potential for a particular dihedral in GROMACS. My problem is that i have eight sets of parameters with *different multiplicity (n)* and f*orce constant value (k)* for the same dihedral of *functional form 1*. I am thinking that may be i can define all these parameters one by one with different dihedral type code in the *bonded.itp and .rtp* file and use *functional form 1 *for all of them. But i don't know whether this is the correct way to do this or i have to use *functional form 9*. Please help me guys. Cheers -- 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] Doubt regarding gmx msd
Dear gmx users, I want to calculate mean square displacement (MSD) for three chains in my system. And for this i have prepared separate index file for all the three chains in my system. And i am running the gmx msd command using these index file. But i am confused as how i can interpret the data in the output .xvg file which i got after running the gmx msd command. In the output file there are msd values for different times separated by the interval of 5 ps (the time interval i used to store the data in .xtc file). I went through some of the post related to gmx msd command. And i am confused with the option -trestart. If i am giving suppose -trestart as 1 ns for a trajectory file of 240 ns. Then in my output file i should get data points separated with the time interval of 1 ns rather than 5 ps? I am clear that msd results are averaged over all the atoms but how they are averaged over different restart times for each time in the output file i.e. i my case 0,5 ps etc. and at last i am getting in my output file data points separated by an interval of 5 ps instead of 1 ns (trestart time). Looking forward to you all for clearing my doubt Cheers -- 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 post a reply on user list?
Respected Sir, I wanted to know that after posting a question on the list and getting a answer for that, from where i can post a reply on the user list if i want to discuss some more issues related to that particular question. I know that the question is silly but i am not able to find how to reply? Thanking You, SK -- 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] Criteria used to get DIHEDRAL DISTRIBUTION at discrete points
Hello List, I wanted to know that when we calculate dihedral distribution in GROMACS using gmx angle, it gives us values at discrete points like -180,-179 etc then what happens to the angles that falls in between -180 and -179? And what criteria is used to decide that a value lying in between -180 and -179 will be counted as either -180 or -179? Thanks in advance, SK -- 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] Easiest way to calculate the POTENTIAL ENERGY of a single isolated chain in GROMACS
Hello list, Can anyone please tell me about how can i calculate the POTENTIAL ENERGY of a single isolated chain in the most easiest way in GROMACS. Cheers, SK -- 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 LENNARD JONES 9-6 potential form in GROMACS
Hello List, Can anyone tell me regarding how can i use Lennard Jones 9-6 potential form in GROMACS. Thanks, SK -- 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 decide the PRESSURE COUPLING CONSTANT VALUES and TEMPERATURE COUPLING CONSTANT VALUES
Hello list, I am preparing an amorphous sample using GROMACS but i am not able to get the required density of the amorphous polymer. I am having reasonable force field parameters and compressibility factors values. So i am thinking that there must be some error with the coupling constant values of Temperature and pressure but i don't know how to set them. Glad if someone could help me out. Cheers, SK -- 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 166, Issue 49
FFTW=ON -DGMX_GPU=ON > >>> -DCMAKE_INSTALL_PREFIX=/--PATH--/Programs/Gromacs2018 > >>> > >>> I am confused here that the old compilers worked but the new ones did > >>> not, > >>> while the error message suggests to use newer compilers. > >>> Could some one help me with fixing it? Thanks a lot! > >>> > >>> > >>> All the best, > >>> Qinghua > >>> -- > >>> 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. > > > > > > -- > Elton Carvalho > > > -- > > Message: 3 > Date: Fri, 9 Feb 2018 23:36:57 +0100 > From: Qinghua Liao > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Gromacs 2018 installation failed > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed > > Hello Elton, > > Thanks a lot for your help! I just tried to load a binutils library (it > was installed on the cluster) and install Gromacs 2018 again, > it works now! > > > All the best, > Qinghua > > > On 02/09/2018 11:33 PM, Elton Carvalho wrote: > > If you are in a hurry, you can download the binutils package from here > > https://www.gnu.org/software/binutils/ and compile it on your own, > setting > > the PREFIX to a directory in your home, then use $PATH to make your > binary > > the highest priority. > > > > Cheers, > > Elton > > > > On Fri, Feb 9, 2018 at 8:17 PM, Qinghua Liao > wrote: > > > >> Hello Elton, > >> > >> Thanks a lot for your information, I already sent an e-mail to the > >> administrator, > >> hopefully they will fix it. > >> > >> > >> All the best, > >> Qinghua > >> > >> > >> On 02/09/2018 08:03 PM, Elton Carvalho wrote: > >> > >>> Hello, Qinghua, > >>> > >>> The error message refers to the standard library. I believe the package > >>> that provides this in ubuntu is glibc. Check that it's a current enough > >>> version. > >>> > >>> Another thing is that the liker (ld) needs to support C++11. That's the > >>> binutils package. I've had success with version 2.29. Not sure which is > >>> the > >>> lowest version required. > >>> > >>> Good luck, > >>> Elton > >>> > >>> On Fri, Feb 9, 2018 at 12:25 PM, Qinghua Liao > >>> wrote: > >>> > >>> Dear GMX developers, > >>>> I am trying to install Gromacs2018 with cuda on clusters, the > >>>> installation > >>>> was successful on one cluster, > >>>> but failed on the other cluster. I guess there might be some library > >>>> missing on the other cluster. > >>>> > >>>> For the succeeded one, the operating system is openSUSE 42.2 > (GNU/Linux > >>>> 4.4.27-2-default), the compilers are gcc and c++ 4.8.5, > >>>> the CUDA version is 9.0.176, the MPI is openMPI 1.10.3 > >>>> > >>>> For the failed one, the operating system is Ubuntu 16.04.3 (GNU/Linux > >>>> 4.4.0-109-generic x86_64), I tried CUDA 9.1.85 and 9.0.176, > >>>> together with gcc/c++ version 6.4, icc/icpc 2017.4, all were failed. > The > >>>> error is the same: > >>>> > >>>> > >>>> -- Performing Test CXX11_STDLIB_PRESENT > >>>> -- Performing Test CXX11_STDLIB_PRESENT - Failed > >>>> CMake Error at cmake/gmxTestCXX11.cmake:210 (message): > >>&
[gmx-users] Do i need to put POSITION RESTRAINT DURING EQUILIBRATION STAGE ( NVT&NPT ) if i am preparing an amorphous sample?
Thank you Krzysztof Makuch for your valuable suggestion. Regards SK -- 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] Do i need to put POSITION RESTRAINT DURING EQUILIBRATION STAGE ( NVT&NPT ) if i am preparing an amorphous sample?
Hi list, I am preparing an amorphous sample using GROMACS but i am in doubt that during the equilibration stage ( NVT & NPT ) do i need to put position restraint on my polymer as there are no solvent in my system and if i have to use position restraint then why i should do that? THANKS, SK -- 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] Finding out the RDF between the COM of all the residues present in Group 1 with the COM of all the residues present in Group 2
Dear all, Can anyone please tell me the proper command in GROMACS to calculate the RDF between the COM of all the residues present in Group 1 with the COM of all the residues present in Group 2. Thanks & Regards, Sanjeet -- 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] Running no periodic boundary condition simulation in GROMACS
Dear all, I want to run no pbc simulation for a single chain in GROMACS inorder to find out the forcefield applied potential energy of the chain. Can anyone please tell me how to do it? Thanks in advance -- 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.
