Re: [gmx-users] WHAM

Dear Justin,I don't have special computers to be compatible with these softwares and run complex calculations.So i have to connect to some computers which is not mine and the old version is installed there.i can't update them because i'm just a normal user and not a root one! So there are two choic

Re: [gmx-users] my minimization structure looks like a messy box?

Hello, You need to use -pbc mol in your command for viewing the trajectory, then this issue will be solved. Sent with Mailtrack

Re: [gmx-users] set computer time on REMD simulation

Hello, If I understand correctly, it terminates at 0.99*t, t is the time you set in hour. In you case, you simulation should be terminated at 0.1*0.99 = 0.099 h, which is 5.94 minutes. PS: 0.1 h is not 10 minutes, but 6 minutes. All the best, Qinghua On 12/18/2017 08:05 AM, YanhuaOuyang wro

[gmx-users] set computer time on REMD simulation

Dear gromacs user, The computing workstation I used has a limited time: 6 hours, namely the REMD will be terminated after 6 hours. So I add option "-maxh 0.1" in the MD commands to test. The md commands are as below: mdrun_mpi -s remd_.tpr -multi 20 -replex 1000 -x remd_.xtc -cpo rem

[gmx-users] Measuring distance to the nearest image

Hi all, I am trying to measure the distance between the COM of two side chain functional groups across the periodic boundary to their nearest image rather than across the unit cell itself. I have tried several gromacs distance commands with no success and more at random as I trawl through the

Re: [gmx-users] Complication of errors, .itp file regarding

On Mon, 18 Dec 2017 at 1:27 AM, Justin Lemkul wrote: > > > On 12/17/17 2:54 PM, RAHUL SURESH wrote: > > Dear all > > > > I managed to overcome above errors by manually creating an .itp file from > > the parameter file of ffTK. But i end up with 139 warnings stating > > > > > > > > > > *"Too few p

Re: [gmx-users] WHAM

Rose, Although in my opinion Justin does know everything, the problem is with your question. You've posted the same thing over and over (and over), and noone replied -- this could be an indicator that people simply have nothing to say. We don't know anything about your system, we don't know w

Re: [gmx-users] WHAM

On 12/17/17 3:39 PM, Rose wrote: Why you don't answer me?is there anything wrong in my question? Contrary to popular opinion, I don't know everything :) If I don't reply to a question, it is because I have nothing useful to contribute. But since you asked, diagnosing what appears to be bug

Re: [gmx-users] WHAM

Why you don't answer me?is there anything wrong in my question? Thank you Sent from my iPhone > On Dec 17, 2017, at 17:36, rose rahmani wrote: > > Hi, > > I try to use umbrella sampling for calculating PMF. i change distance between > protein and ZNS nanosheet. I use gomacsV4.5.4 > > after m

Re: [gmx-users] WHAM

Why you don't answer me?is there anything wrong in my question? Thank you Sent from my iPhone > On Dec 17, 2017, at 17:36, rose rahmani wrote: > > Hi, > > I try to use umbrella sampling for calculating PMF. i change distance > between protein and ZNS nanosheet. I use gomacsV4.5.4 > > after mi

Re: [gmx-users] Complication of errors, .itp file regarding

On 12/17/17 2:54 PM, RAHUL SURESH wrote: Dear all I managed to overcome above errors by manually creating an .itp file from the parameter file of ffTK. But i end up with 139 warnings stating *"Too few parameters on line (source file /home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/g

Re: [gmx-users] Complication of errors, .itp file regarding

Dear all I managed to overcome above errors by manually creating an .itp file from the parameter file of ffTK. But i end up with 139 warnings stating *"Too few parameters on line (source file /home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp, line 1841) "* Going

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

Thanks Justin. One component I mean system of only one type atom, each atom has two charged virtual sites. So I can not see from VMD any breaking. On Dec 17, 2017 8:10 PM, "Justin Lemkul" wrote: On 12/17/17 8:22 AM, Faezeh Pousaneh wrote: > Dear Justin, > > How can I check that ''input confi

Re: [gmx-users] Complication of errors, .itp file regarding

On 12/17/17 8:18 AM, RAHUL SURESH wrote: Dear all Let me put forth the thing first. I have generated the parameter file using fftk(structure.par) and derived the respective topology file(structure.top) using topotools of vmd. Now to get the itp fiule, I manually copied the necessary data from

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

On 12/17/17 8:22 AM, Faezeh Pousaneh wrote: Dear Justin, How can I check that ''input configuration is "broken" across PBC'' ? From vmd it is hard to say, since I only have one component system. What is that one component? If a group of atoms is supposed to be in a charge group, and it is

Re: [gmx-users] Complication of errors, .itp file regarding

Dear all I managed to overcome above errors by manually creating an .itp file from the parameter file of ffTK. But i end up with 139 warnings stating *"Too few parameters on line (source file /home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp, line 1841) "* Going

[gmx-users] WHAM

Hi, I try to use umbrella sampling for calculating PMF. i change distance between protein and ZNS nanosheet. I use gomacsV4.5.4 after minimization and equilibration. i use: grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -o pull.tpr this is md_pull.mdp: integrator = md

Re: [gmx-users] The sum of the two largest charge group radii (X) is larger than rlist

Dear Justin, How can I check that ''input configuration is "broken" across PBC'' ? >From vmd it is hard to say, since I only have one component system. Best regards On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh wrote: > > The sum of the two largest charge group radii (7.984601) is larger

[gmx-users] Complication of errors, .itp file regarding

Dear all Let me put forth the thing first. I have generated the parameter file using fftk(structure.par) and derived the respective topology file(structure.top) using topotools of vmd. Now to get the itp fiule, I manually copied the necessary data from structure.top and made structure.itp file. F