[gmx-users] Local pressure of water

Dear all,I am simulating polarizable water with Gromacs 5.0.5. I am wondering if it is possible to calculate the pressure profiles along z axis.I do not find corresponding programs from the manual. Instead, I find some discussions 4 years ago from the mailing list, but they do not make much

Re: [gmx-users] Pdb file

I created the pdb file by genconf but the system was not minimized, i got positive potential energy. What may be the problem? On 11 Aug 2015 19:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, gmx genconf on a small box with a single argon is a useful starting point. Mark On Tue, Aug

Re: [gmx-users] Preparation of simulation system for GdmCl and protein simulation.

Hi, Maybe they made a mistake. You could try asking them, rather than some strangers on the internet :-D Mark On Tue, Aug 11, 2015 at 5:53 AM dipak sanap dipak94sa...@gmail.com wrote: Hi all, Thank you very much for your reply Mark, Still if i see little variation of few molecules here

[gmx-users] Proton transfer reaction in gromacs

Hello, I want to study proton transfer reaction in a protein channel using gromacs. I read in the literature that it is not possible to do this by classical MD, then what are the other ways to perform it in gromacs..?? -- *Padmani sandhu* *Research Scholar,* *Center for Computational Biology

[gmx-users] Unexpected free energy values.

Dear all, I am studying the CH4-CO2-H2O mixture at low T(270K) and high P (20 bar). Forcefields used: CH4 : Single point LJ site; CO2 : EPM2 (Rigid with two virtual sites); H2O: TIP4P. I computed the free energy of solvation for a CH4 molecule in H2O in the presence of CO2 at different

Re: [gmx-users] MD simulation using TFE

On Tue, Aug 11, 2015 at 4:26 AM Bikash Ranjan Sahoo bikash.bioinformat...@gmail.com wrote: Dear All, I want to simulate my protein in 85 and 15 % water and TFE, respectively. Start simpler. Make sure you can simulate pure water, and water-TFE mixture first. One of your problems right now is

Re: [gmx-users] 2. Proton transfer reaction in gromacs (Padmani Sandhu)

Hi, Since bonds break and form upon proton transfer it requires quantum mechanics, both for the electrons and the proton(s). To avoid the heavy computational burden, one can opt to use classical dynamics for the proton and semi-empirical methods, which are accessible in Gromacs (5) through

[gmx-users] Pdb file

How can i create the .pdb file for 1600 atoms of argon ? -- 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

[gmx-users] Distance restrain with dummy atom

Dear Gromacs users, I am working with membrane simulations and I would like to put distance restrain along Z-axis between a dummy atom I generated at the centre of box and all the water molecules. For this, I first generated a dummy atom at the centre of box and also made a simple .itp file for

[gmx-users] Charmm 36 parameter file for gromacs

Dear Gromacs users, On the .itp file on the charmm36 force field, I see the DOPC and other lipid which have the [atom][bond] and [ impropers] parameter. I wonder where is the parameter for [dihedrals]. please help me! Thank in advance Tuong Vy -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Pdb file

Hi, gmx genconf on a small box with a single argon is a useful starting point. Mark On Tue, Aug 11, 2015 at 3:16 PM Sunil Ghimire ghimiresuni...@gmail.com wrote: How can i create the .pdb file for 1600 atoms of argon ? -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Distance restrain with dummy atom

Dear Justin, Thanks for your quick reply. I am trying to run membrane protein simulation with slab geometry and EW3DC method (ewald-geometry = 3dc), due to ion asymmetry in the system. Following the article http://www.cell.com/biophysj/abstract/S0006-3495%2803%2974458-0?mobileUi=0 , I have set

Re: [gmx-users] Distance restrain with dummy atom

On 8/11/15 8:30 AM, anu chandra wrote: Dear Gromacs users, I am working with membrane simulations and I would like to put distance restrain along Z-axis between a dummy atom I generated at the centre of box and all the water molecules. For this, I first generated a dummy atom at the centre of

Re: [gmx-users] Charmm 36 parameter file for gromacs

On 8/11/15 10:01 AM, Vy Phan wrote: Dear Gromacs users, On the .itp file on the charmm36 force field, I see the DOPC and other lipid which have the [atom][bond] and [ impropers] parameter. I wonder where is the parameter for [dihedrals]. Angles and dihedrals are automatically generated

[gmx-users] Regarding positive potential energy

Hai gromacs users I am trying to run the simulation of rna with urea as solvent. I have added 300 molecules of water using genbox command and while runnning the energy minimization step, the total potential energy is coming as positive. please help me to solve this

[gmx-users] Add new integrator

Hello GROMACS users, I am interested in adding a fifth/sixth order predictor/corrector integrator to GROMACS. Is this possible? If so, any guidance on which files need to be updated is much appreciated. Best, Eric -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Add new integrator

Adding an integrator for your own work is hard but doable, especially if you don't need it parallelized. Look at the do_update_X routines for examples. It will be harder for 5th/6th order since you probably need values of the forces for times in the past, which are not automatically stored in

[gmx-users] DPPC benchmark has different behavior on different machines

Hello, I am benchmarking a new cluster and also learning the ropes of GROMACS. I am using the dppc benchmark from http://www.gromacs.org/About_Gromacs/Benchmarks On the first cluster, which contains 8 processors per node, I have the scaling one might expect # n ranks [performance (ns/day)

[gmx-users] charged group problem

Dear users, My system contains peptide + TFE + water in an octahedron box. I am using oplsaa.ff I am trying to do EM but running this command grompp -f em.mdp -c C22_TFE-W.gro -p topol.top -o em.tpr the next error message come up WARNING 1 [file em.mdp]: The sum of the two largest charge

Re: [gmx-users] Charmm 36 parameter file for gromacs

Dear Dr. Justin and Gromacs User, Thank you so much for your helps. When I use charmm36 ff to generate the topology for lipid (DOPC). I got many warning Warning :Long bond And after get the topology, the total charge is very high (+888 e for DOPC bilayer have 516 molecular). When I used grompp

[gmx-users] pdb file for united atom force fields

Dear Gromacs users, I need to work with a united atom FF, but I have defined all the Hydrogens in my pdb file. Does it cause any problem in MD procedure? Truly yours, Farideh -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Distance restrain with dummy atom

On 8/11/15 11:06 AM, anu chandra wrote: Dear Justin, Thanks for your quick reply. I am trying to run membrane protein simulation with slab geometry and EW3DC method (ewald-geometry = 3dc), due to ion asymmetry in the system. Following the article