[gmx-users] Pme on gpu performance

Dears, I would like to ask what performance improvement is expected for future releases (e.g. 4.6) for PME calculations on gpu cards. Last week I sent benchmark results for dhfr to the list, which show no performance gain when the newest versions of tesla cards vs intel xeon R are used (m

[gmx-users] Adding ions using "genion"

Dear, I create a box of water with 10 MIBC molecules on two opposite surfaces. then I used the command "grompp -f input_min.mdp -o min.tpr -c box1.g96" to creat .tpr file before using the command "genion -s min.tpr -o add.gro -nname Cl -pname NA -nn 20 -np 20" to add 20 Na+ and 20 Cl- into this bo

Re: [gmx-users] Adding ions using "genion"

On Thu, Nov 24, 2011 at 5:16 PM, cuong nguyen wrote: > Dear, > I create a box of water with 10 MIBC molecules on two opposite surfaces. > then I used the command "grompp -f input_min.mdp -o min.tpr -c box1.g96" to > creat .tpr file before using the command "genion -s min.tpr -o add.gro > -nname Cl

Re: [gmx-users] Adding ions using "genion"

On 24/11/2011 8:16 PM, cuong nguyen wrote: Dear, I create a box of water with 10 MIBC molecules on two opposite surfaces. then I used the command "grompp -f input_min.mdp -o min.tpr -c box1.g96" to creat .tpr file before using the command "genion -s min.tpr -o add.gro -nname Cl -pname NA -nn 2

Re: [gmx-users] do remd in the npt ensemble:Warning: pressure scaling more than 1%, mu: 333821 333821 333821

On 24/11/2011 6:31 PM, 杜波 wrote: dear teacher, when i do remd in the npt ensemble. =md.mdp=== ; Start time and timestep in ps tinit = 0 dt = 0.01 nsteps = 5000 ; For exact run continuation or redoing part of a run ; Temperature coupling Tcoupl = nose-hoover ; Gro

[gmx-users] centroid clustering

On 24/11/2011 5:07 PM, Robel Teklebrhan wrote: Dear gmx users, Is centroid to centroid clustering method available in Gromacs? I want to use this method to cluster my molecules? When asking for help, please start a new email with a descriptive subject so that the people who you hope

[gmx-users] Umbrella Sampling tutorial

Hey Gmx Users, I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm: Time COM distance 0 - 0.5 208 - 0.7 218 - 0.92 225 - 1.119 231 - 1.41 235 - 1.61 239 - 1.81 246 - 2.09 253 - 2.3 261 - 2.51 268 - 2.71 276 - 2.91 289 - 3.11 307 - 3.3 325 - 3.5 348 - 3.7 359 - 3.93 3

Re: [gmx-users] grompp line too long error

Here is the detailed info about my setup: System:64-bit Linux GMX version:4.5.4 I know that windows and linux have different line end format and I didn't edit my text files using editor on windows,but all on linux. My goal is to simulate membrane protein embeded in lipid bilayer,I don't have expe

[gmx-users] Regarding KALP-15 Simulation

Dear All, *Sorry folks* without following the subsequent lines I came to wrong conclusion. But I got stuck with some other problem. After concatenating the dppc128 periodicity corrected box and kalp box the numbers indices of the atoms are not continuos so when I run the grompp command

Re: [gmx-users] grompp line too long error

Here is the detailed info about my setup: System:64-bit Linux GMX version:4.5.4 I know that windows and linux have different line end format and I didn't edit my text files using editor on windows,but all on linux. Which editor? Problems in principle could arise from your encodings setup, even

[gmx-users] mdrun -rerun (not reproducible energy values?)

Dear Gromacs Users, I am using the -rerun option of mdrun to re-analyze a trajectory. Thus, I tried to rerun the same trajectory (md.xtc) with exactly the same md.tpr.  But the bonded interactions are not computed or written to the log file or to the .edr file, resulting to completely different

[gmx-users] Reg : Simulating heterologous protein complex with bound ligand

Dear Gromacs Users, I am working on a protein complex with two subunits which are heterologous and I docked them using HADDOCK. Now, to one of the subunit I built a ligand covalently attached to one of the residue, which enters into the active site of the another subunit in the complex. Now

[gmx-users] multiple molecules simulations

Dear all, I have performed a simulation on eight identical peptides (composed by 11 residues) embedded in explicit water. Box dimensions (cube of 7.92nm) have been chosen to get a high concentration to accelerate the aggregation process. PME has been used and rvdw=rcoulomb=0.9. The trajectory

[gmx-users] Time step problem on coarse-grained LJ chain

Dear all I am trying to simulate a Lennard-Jones coarse-grained polymer melt. Until know I simulated only one chain, in order to check if the parameters I used are OK. I simulated one chain of 50 LJ particles with *ε=1KJ/mol, m=1gr/mol, σ=1nm*. This means that my characteristic time of the system

Re: [gmx-users] 2. Re: GROMACS/ORCA QMMM (Jose Tusell)

Dear Jose, I just installed the 4.5.5. version and the calculation runs ok for me! But I did change the ORCAINFO file: First of all you should clean your ORCAINFO file. Remove !QMMMOpt COPT and remove !EnGrad Otherwise the program might get confused about doing a single point and gradient calc

Re: [gmx-users] pyroglutamate in gromos53a6

Thank you Tsjerk, I am now trying with amber99.ff but have encountered the following problem: My PCA is at the N-terminus. I have an entry for [ NPCA ] in aminoacids.rtp and have updated aminoacids.r2b to include NPCA and I've even added an entry in aminoacids.hdb for NPCA. Yet when I g

Re: [gmx-users] Time step problem on coarse-grained LJ chain

Hi Chrysostomos, To understand this, you have to understand how jumps are removed. I explained that before, and it's in the archive somewhere. The bottom line is that jumps can't be removed properly when intervals between frames are too large, or the changes in position are too large relative to t

Re: [gmx-users] pyroglutamate in gromos53a6

Hi Henry, Apparently NPCA is not listed as being protein, so pdb2gmx assumes that the chain begins with GLY. Add NPCA to the file residuetypes.dat one directory up, with the designation 'Protein'. I think that should solve it. Groetjes, Tsjerk On Thu, Nov 24, 2011 at 6:59 PM, Henry Hocking wro

Re: [gmx-users] pyroglutamate in gromos53a6

Thank you Tsjerk, Now it works ! Cheers, Henry On 24 Nov 2011, at 23:11, Tsjerk Wassenaar wrote: Hi Henry, Apparently NPCA is not listed as being protein, so pdb2gmx assumes that the chain begins with GLY. Add NPCA to the file residuetypes.dat one directory up, with the designation 'Protein

Re: [gmx-users] Umbrella Sampling tutorial

Steven Neumann wrote: Hey Gmx Users, I went through Justin tutorial of umbrella sampling with spacing of 0.2 nm: Time COM distance 0 - 0.5 208 - 0.7 218 - 0.92 225 - 1.119 231 - 1.41 235 - 1.61 239 - 1.81 246 - 2.09 253 - 2.3 261 - 2.51 268 - 2.71 276 - 2.91 289 - 3.11 307 - 3.3 325

Re: [gmx-users] Regarding KALP-15 Simulation

Ravi Kumar Venkatraman wrote: Dear All, *Sorry folks* without following the subsequent lines I came to wrong conclusion. But I got stuck with some other problem. After concatenating the dppc128 periodicity corrected box and kalp box the numbers indices of the atoms are not conti

Re: [gmx-users] Reg : Simulating heterologous protein complex with bound ligand

Rohit Farmer wrote: Dear Gromacs Users, I am working on a protein complex with two subunits which are heterologous and I docked them using HADDOCK. Now, to one of the subunit I built a ligand covalently attached to one of the residue, which enters into the active site of the another subunit

[gmx-users] Reg : Simulating heterologous protein complex with bound ligand

Dear Gromacs Users, I am working on a protein complex with two subunits which are heterologous and I docked them using HADDOCK. Now, to one of the subunit I built a ligand covalently attached to one of the residue, which enters into the active site of the another subunit in the complex. Now I wa

Re: [gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

Hi Oliver, Apologies for the late reply. The comparison you have showed us has been done for a DNA fragment. Do you believe that negligible errors can also be obtained for proteins using the amber99sb force field? thanks, Thomas On 22 November 2011 11:58, Oliver Grant wrote: > Hi there, > >

Re: [gmx-users] mdrun -rerun (not reproducible energy values?)

On 25/11/2011 2:28 AM, Vasileios Tatsis wrote: Dear Gromacs Users, I am using the -rerun option of mdrun to re-analyze a trajectory. Thus, I tried to rerun the same trajectory (md.xtc) with exactly the same md.tpr. But the bonded interactions are not computed or written to the log file or to

[gmx-users] Pressure stabilization during NPT phase

Dear Gromacs Users! At the present time I'm simulating small peptide (11 a.c in coiled conformation) in water. I've desided to use parameters from Lysozyme simmulation ( opls ff for parametrisation and all mdp parameters from that simulation). Because my peptide was smaller than typical globula

[gmx-users] about relaxation protocol

Dear all: I am a new Gromacs user and I would like to relax my membrane system by linear force constant: NPT with protein and ligand heavy atoms annealing, force constant was removed from 10.0-->0 Kal/mol during 10 ns. Is it possible for Gromacs to introduced such kind of relaxation in

Re: [gmx-users] about relaxation protocol

Hi Albert, You can use the free energy perturbation stuff. Check the manual. Cheers, Tsjerk On Nov 25, 2011 7:43 AM, "Albert" wrote: Dear all: I am a new Gromacs user and I would like to relax my membrane system by linear force constant: NPT with protein and ligand heavy atoms annealing,

Re: [gmx-users] Pressure stabilization during NPT phase

On 25/11/2011 5:22 PM, James Starlight wrote: Dear Gromacs Users! At the present time I'm simulating small peptide (11 a.c in coiled conformation) in water. I've desided to use parameters from Lysozyme simmulation ( opls ff for parametrisation and all mdp parameters from that simulation).

Re: [gmx-users] Pressure stabilization during NPT phase

Hi James, There have been extensive discussions about this on the list. Check the archives. In short, smaller systems give larger fluctuations, and shorter simulations give larger deviations from the expected average. Cheers, Tsjerk On Nov 25, 2011 7:23 AM, "James Starlight" wrote: Dear Groma

Re: [gmx-users] Pressure stabilization during NPT phase

Mark, Tsjerk thanks! I've check my uncompleated produced MD run by G_energy and find that average pressure is 1.1 Bar that is most close to ref. By the way could you tell me about extra possible ways of checking running simmulation? ( E.g I'm calculating long produce trajectory and want to check

Re: [gmx-users] Pressure stabilization during NPT phase

On 25/11/2011 6:38 PM, James Starlight wrote: Mark, Tsjerk thanks! I've check my uncompleated produced MD run by G_energy and find that average pressure is 1.1 Bar that is most close to ref. By the way could you tell me about extra possible ways of checking running simmulation? ( E.g I'm ca

Re: [gmx-users] multiple molecules simulations

Dear all, I did not get an answer yet. I really want know your opinion. If you need other details about the simulation I'm willing to give it to you. Thank you in advance, Gloria Da: Gloria Saracino A: "gmx-users@gromacs.org" Inviato: Giovedì 24 Novembre

Re: [gmx-users] Pressure stabilization during NPT phase

This way I've already used but is this possible to extract Gro and trp files from uncompleated runs and not stopping this simulation ? James 2011/11/25 Mark Abraham > On 25/11/2011 6:38 PM, James Starlight wrote: > > Mark, Tsjerk thanks! > > I've check my uncompleated produced MD run by G_ene