[gmx-users] Regarding continuation of mdrun

Hello everyone I have a doubt regarding the extension of simulation in newer version of gromacs (4.0.4). 1) If simulation has completed and one wants to extend it further the option used is tpbconv -s full_part3.tpr -extend timetoextendby -o full_part4.tpr and then mdrun as usual with an additi

[gmx-users] Compiler and OS issue in gromacs

Hello everyone, There is following warning given in the GROMACS home page, WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc. Can anyone please tell me that whet

[gmx-users] OS - Compiler - GROMACS compatibility

Hi, Since the following warning is given in the GROMACS home page, WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These compilers come with recent Linux distrubutions like Fedora 5/6 etc. is the problem only with the 4.1.x series or

[gmx-users] Re: Re:Re:g_mindist option

Thanks a lot for your reply Actually "maximum internal distance" is not a separate concept it is what i am getting in the mindist.xvg file shown below This is the mindist.xvg file: @ title "Minimum distance to periodic image" @xaxis label "Time (ps)" @yaxis label "Distance (nm)" @TY

[gmx-users] Re:g_mindist option

Hi I am doing a 5 peptide simulation in a 6nm box. Now to check the correctness of my simulation i m calculating the minimum periodic distance using g_mindist to find out the distance between molecule and its periodic images.Following is the command i have used g_mindist -s full.tpr -f full.xtc -

[gmx-users] Re: Energy minimization output

Hi I am doing a 5 peptide simulation. I have done energy minimization using this command 1.grompp -v -f em.mdp -c b4em_sol_mov1.gro -p gnnqqny.top -o em.tpr -nice 19 2.mdrun -v -s em.tpr -e em.edr -c after_em.gro -o em.trr -g em.log -nice 19 After energy minimization (steep, 5000 steps, emto

[gmx-users] Re: Putting more than one peptide

Hi I am doing 5 peptide simulation. 1. First i am defining a box using editconf editconf -f 1st.gro -o box1.gro -bt cubic -box 6 -d 1.1 then for inserting the next peptide i am using genbox genbox -cp box1.gro -ci 2nd.gro -nmol 1 -o box2.gro -seed 24 -try 100 and same for the subsequent 3 pep

[gmx-users] RE: value of d in editconf

Hi I am doing a 5 peptide(7 residue) simulation in a 5 nm cubic box. but during editconf i haven't given the option -d to specify the distance between the solute and the box. Now some of the atoms of my peptides are out of the box also is it normal? Does not applying -d is going to effect in any w

[gmx-users] Re: tpr file problem with analysis and merged trajectories

sorry the mail was not complete and accidentally sent i m sending it again Hi I am running a simulation for 60 ns but due to power cutt it stopped at different time intervals and i continued the run with following command 1. tpbconv -s full.tpr -f full.trr -e full.edr -o full_part1.tpr -until

[gmx-users] Re:continuation of run

Hi I am running a simulation for 60 ns but due to power cutt it stopped at different time intervals and i continued the run with following command 1. tpbconv -s full.tpr -f full.trr -e full.edr -o full_part1.tpr -until 6 2. nohup mpirun -np 2 mdrun_mpi -v -s full_part1.tpr -e full_part1.edr

[gmx-users] (no subject)

Hi all I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2. so check i tried to to do speptide tutorial in /usr/local/gromacs/share/gromacs/tutor/speptide But when i m running grompp for position restraint with the command grompp -f pr -o pr -c after_em -r after_em -p speptide i

[gmx-users] Re: Removal of pbc for analysis

Hi All, I am doing a 5 peptide simulation, and i want to analyze some of the basic properties like radius of gyration, distance between peptides etc. but i wanted to do it in a situation when all my peptides are inside the box. Due to pbc i am getting artifacts. i tried all the -pbc option (inbox,

[gmx-users] Re Re Re: charge group in topology file

Thanks for the reply but if you see the charge group which include N and H is not an integer 10 opls_238 2ASN N 3 -0.514.0067 ; qtot 0.5 11 opls_241 2ASN H 30.3 1.008 ; qtot 0.8 24 opls_238 3ASN

[gmx-users] Re: charge group in topology file

Hi, All I am running gromacs for simulation of 5 peptides. I have a problem with the topology file in which the charge on each and every charge group is not coming whole but in some of them it is in fraction which is not correct. I have used G43a1 as well as OPLS but i am getting the same problem

[gmx-users] Re: merging two trajectory files

Hi i have carried out simulation for 6 ns which stopped after 3 ns due to some problem, i further continues from that point of time to the final time. now i want to see the trajectory as a whole combining these two trajectories but by applying trjcat -o complete_full.trr full.trr full1.trr i am

[gmx-users] (no subject)

Hi i have carried out simulation for 6 ns which stopped after 3 ns due to some problem, i further continues from that point of time to the final time. now i want to see the trajectory as a whole combining these two trajectories but by applying trjcat -o complete_full.trr full.trr full1.trr i am