Re: [gmx-users] energy minization mdp

2017-07-28 Thread Justin Lemkul
On 7/28/17 2:54 PM, Mohammad Zahidul Hossain Khan wrote: Dear User I have protein-ligand system. I have basic idea for energy minimization.mdp parameter. ; integrator = steep emtol = 10.0 emstep = 0.01 nsteps = 500 energygrps = Protein OAI ; nstlist= 1 cutoff-scheme = Verlet ns_type=

[gmx-users] TIP4P-D Water itp file

2017-07-28 Thread atanu das
Hi All, Does anyone have the itp file for TIP4P-D water (J. Phys. Chem. B, 2015, 119  (16), pp 5113–5123) and also the parameters that are needed to be added to the ffnonbonded.itp file for this water model?  ThanksAtanu -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] About the QM/MM MD of Gromacs

2017-07-28 Thread Clinton King
In case anyone is interested, here is a copy of the script I am currently using to interface Gromacs 2016.1 with Gaussian 09 without altering the source code of Gaussian 09. It is based on Gerrit Groenhoef's script, available at wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian, with some alterations so

[gmx-users] energy minization mdp

2017-07-28 Thread Mohammad Zahidul Hossain Khan
Dear User I have protein-ligand system. I have basic idea for energy minimization.mdp parameter. ; integrator = steep emtol = 10.0 emstep = 0.01 nsteps = 500 energygrps = Protein OAI ; nstlist= 1 cutoff-scheme = Verlet ns_type= grid rlist= 1.0 coulombtype= PME rcoulomb= 1.0

Re: [gmx-users] error message: Invalid transform ...

2017-07-28 Thread Mark Abraham
Hi, The QM/MM code is essentially untested and unmaintained and wasn't developed for that version of GAUSSIAN, so you're dicing with death. Death looks like he's rolling well. ;-) I recommend using either the exact software versions used in published work, or some other package. Mark On Fri, 28

Re: [gmx-users] concatenate 2 trajectory files

2017-07-28 Thread Mark Abraham
Hi, On Fri, 28 Jul 2017 17:49 Atila Petrosian wrote: > Dear gromacs users, > > I had done a md simulation for 100 ns. I continued that for another 50 ns. > > gmx grompp -f 100.mdp -c eq.gro -p system.top -o 100.tpr -n index.ndx > gmx mdrun -nb gpu -v -deffnm 100 > >

Re: [gmx-users] error message: Invalid transform ...

2017-07-28 Thread Clinton King
No, I haven't been changing the code. I have been doing mixed qm/mm (using Gaussian 09 for the qm calculations) with some frozen atoms in the qm region. There were two changes I made to this run that altered it from previously successful runs: I increased the time step slightly, and I added a

[gmx-users] concatenate 2 trajectory files

2017-07-28 Thread Atila Petrosian
Dear gromacs users, I had done a md simulation for 100 ns. I continued that for another 50 ns. gmx grompp -f 100.mdp -c eq.gro -p system.top -o 100.tpr -n index.ndx gmx mdrun -nb gpu -v -deffnm 100 gmx grompp -f 50.mdp -c 100.gro -p system.top -o 50.tpr -n index.ndx gmx mdrun -nb gpu -v -deffnm

[gmx-users] On the modeling of a shear flow

2017-07-28 Thread Gleb Novikov
Dear GROMACS Users, I am interesting in the work-flow of the shear flow modeling in GROMACS. I am dealing with a complex MARTINI CG membrane system consisted of several proteins embedded within big POPC-cholesterol bi-layer solvated in non-polarizable water. Within this system I would like to

[gmx-users] How to define (or modify) a new potential function in Gromacs?

2017-07-28 Thread lan hoa Trinh
Dear Gromacs community, I am attemping to use Gromacs for a Coarse - grained simulation. In our model, we have a term similar to the angle harmonic potential term, but the variable is not angle but the volume created by three consecutive vectors. I don't know if there is a way to implement that

[gmx-users] ATOMTYPES directive

2017-07-28 Thread lan hoa Trinh
Dear Gromacs community, In the [ atomtypes ] directive, according to Gromacs manual, it should have 7 seperated fields, which are name, at.num, mass, charge, ptype, c6, c12. However, when I remove the field of at.num, Gromacs still works without notifying any error. If I insert 2 fields more, it

Re: [gmx-users] gmx check

2017-07-28 Thread Dawid das
Thank you for explaining. Best wishes, Dawid 2017-07-28 15:11 GMT+02:00 Mark Abraham : > Hi, > > Seems like the extremes of normal variation of unconstrained bonds. As gmx > help check suggests, the feature exists as a quick sanity check. The use of > "correct" is in

Re: [gmx-users] gmx check

2017-07-28 Thread Mark Abraham
Hi, Seems like the extremes of normal variation of unconstrained bonds. As gmx help check suggests, the feature exists as a quick sanity check. The use of "correct" is in the sense of "between sensible atom indices" rather than suggesting that only one length is valid. Mark On Fri, 28 Jul 2017

Re: [gmx-users] gmx check

2017-07-28 Thread Dawid das
Hi, No, those bonds I get the message were not constrained and virtually in every frame there is different bunch of bonds for which I get this message. Because the whole output from gmx check is 1.1 GB, I just give you a few examples. Reading frame 0 time0.000 # Atoms 24884 Precision

Re: [gmx-users] gmx check

2017-07-28 Thread Mark Abraham
Hi, It's hard to tell without seeing the messages and knowing whether those bonds were constrained. Mark On Fri, 28 Jul 2017 13:19 Dawid das wrote: > Dear Gromacs Users, > > I get a bunch of communicates when I run > gmx check -f npt-md2.xtc -s1 npt-md2.tpr >&

[gmx-users] gmx check

2017-07-28 Thread Dawid das
Dear Gromacs Users, I get a bunch of communicates when I run gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out saying that I get different bond lengths than they should be. Can that be caused by only 0.001 nm precision of my results? Also I am not exactly sure if I understand correctly

Re: [gmx-users] Using external force field with GROMACS

2017-07-28 Thread Qinghua Liao
Hello, You can also set the variable of GMXLIB so that pdb2gmx can find the force field you want to use, like: GMXLIB=/ path /charmm36m.ff Best, Qinghua On 07/28/2017 10:53 AM, Souparno Adhikary wrote: Hi, I want to use the latest CHARMM36m force field which I downloaded from MacKerell

Re: [gmx-users] Using external force field with GROMACS

2017-07-28 Thread David van der Spoel
On 28/07/17 10:53, Souparno Adhikary wrote: Hi, I want to use the latest CHARMM36m force field which I downloaded from MacKerell group's website. I use a common HPC system and do not have an administrator account. Can you give me an idea how I can add this forcefield to the pdb2gmx options? We

Re: [gmx-users] Using external force field with GROMACS

2017-07-28 Thread Mark Abraham
Hi, On Fri, 28 Jul 2017 10:53 Souparno Adhikary wrote: > Hi, > > I want to use the latest CHARMM36m force field which I downloaded from > MacKerell group's website. I use a common HPC system and do not have an > administrator account. > > Can you give me an idea how I can

Re: [gmx-users] How to increase the volatile gpu-util

2017-07-28 Thread Mark Abraham
Hi, On Fri, 28 Jul 2017 10:37 leila karami wrote: > Dear gromacs users, > > I am running CG MD simulation on a Rocks cluster using the following > command: > > gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 16 -gpu_id 0>& md.job & > > I tried the different value for the

[gmx-users] Using external force field with GROMACS

2017-07-28 Thread Souparno Adhikary
Hi, I want to use the latest CHARMM36m force field which I downloaded from MacKerell group's website. I use a common HPC system and do not have an administrator account. Can you give me an idea how I can add this forcefield to the pdb2gmx options? We are using quite an old version of GROMACS-

[gmx-users] How to increase the volatile gpu-util

2017-07-28 Thread leila karami
Dear gromacs users, I am running CG MD simulation on a Rocks cluster using the following command: gmx_mpi mdrun -nb gpu -v -deffnm gpu_md -ntomp 16 -gpu_id 0>& md.job & I tried the different value for the -ntomp option. With -ntomp 16 run will finish sooner than the other values for -ntomp. In

Re: [gmx-users] Performance values

2017-07-28 Thread Maureen Chew
You might find this reference handy - it has a really nice explanation for how to look at a log file Topology preparation, "What's in a log file", basic performance improvements: Mark Abraham, Session 1A

Re: [gmx-users] gmx complains of mismatch between index and trajectory file

2017-07-28 Thread Mark Abraham
Hi, Your xtc file has only the group you wrote, so it isn't valid to index into it with an index file that was made for a conformation with many other atoms. That's the mismatch the message mentions. For your xtc, "System" is the subset of *it* that you seem to want for your analysis. Note that

Re: [gmx-users] error message: Invalid transform ...

2017-07-28 Thread Mark Abraham
Hi, That's a new one for me ;-) So new that I assume you were changing the code? Mark On Fri, 28 Jul 2017 00:51 Clinton King wrote: > Has anybody ever seen the following error message before? > > > Program: gmx mdrun, version 2016.1 > Source file: