Re: [gmx-users] Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

On 2012-10-08 09:05, Emma Eriksson wrote: Thank you David for your response. Please see my reply below. On 2012-10-04 11:50, Emma Eriksson wrote: Dear all, I am using the pull code in Gromacs 4.5.5 to constrain the distance in one direction (z) between a small molecule and a lipid bilayer. I

[gmx-users] Nucleotide terminal problems in GORMOS96 force field

I am going to simulate a tRNA molecule using GROMOS96 force field, which contain some modified nucleotide. I've build the .rtp entry for each modified residues like this . But pdb2gmx prompt out such error mess

Re: [gmx-users] generation of .itp file

Hi, That's essentially what pdb2gmx is for. Erik 9 okt 2012 kl. 06.50 skrev Shine A: > sir, > > I want to generate .itp from a pdb file. Is there any option in > gromacs. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Pleas

[gmx-users] Re: Re: Pull code with pull_geometry = cylinder generates error: Distance of pull group 1 (4.030185 nm) is larger than 0.49 times the box size (3.012310)

On 2012-10-08 09:05, Emma Eriksson wrote: > Thank you David for your response. Please see my reply below. > > On 2012-10-04 11:50, Emma Eriksson wrote: >> Dear all, >> >> I am using the pull code in Gromacs 4.5.5 to constrain the distance in one >> direction (z) between a small molecule and a lipi

[gmx-users] Do I need to repeat my MD simulation ?

Dear all, I did a MD simulation (GROMACS 4.5 G53a6 force field) on protein-peptide complex for 5ns and got an interesting conformational change of T-loop. However, when I rerun my script using the same input file in the same machine, I can not observe the same or similar conformational change.

[gmx-users] pull=constraint gives zero forces

But for GMX 4.0.7 there are forces in the pullf.xvg. The forces which arise rom the contraint the hold the two groups fixed. I use them for thermodynamic integration... I use the following mdp-parameters, probably this gives you an idea what you might make different: ; AFM OPTIONS pull

[gmx-users] Re: pull=constraint gives zero forces

Sorry - forgot to mention that before crashing, the run with all other constraints removed produces a single line of pullf output: 0. -812.401-4002.84482.04 1951.47 138.953 -1806.55 -601.0072644.79 447.018 1768.6 -214.64 -199.829-2746.97 1177.7

Re: [gmx-users] Do I need to repeat my MD simulation ?

Well, 5 ns is not a long time in the life of a protein-peptide complex. I would start several (5-10?) runs with different (random) starting impulse to get more reliable data. If the conformational change is connected to crossing a significant energy barrier, it will be a rare event... which m

Re: [gmx-users] Re: pull=constraint gives zero forces

Hi, Do you know there are issues with using pull=constraint on molecules that have constrained bonds? It's mentioned in the manual somewhere. Erik 9 okt 2012 kl. 11.39 skrev alex.bjorling: > Sorry - forgot to mention that before crashing, the run with all other > constraints removed produces a

Re: [gmx-users] Martini lipid bilayer...

Well ... it always depends on what you want to do but the file on the link you give are the official website and they should be reliable :)) On Oct 9, 2012, at 12:04 PM, rama david wrote: Hi Gromacs friends, I am interested in Martini force-field and application in lipid bilayer. I foun

Re: [gmx-users] average velocity

On 2012-10-09 13:09, Dr. Vitaly Chaban wrote: Dear All - Is there a handy utility, which would give me an average velocity of a given particle during the simulation? g_traj -ov followed by g_analyze Thank you! Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Phys

Re: [gmx-users] distance between protein and ligand

On 10/9/12 12:48 AM, Archana Sonawani wrote: Hi, I have simulated a protein-ligand complex for 5ns. I checked distance between the important residues of protein and the ligand using g_dist. My question is can the distance between the two groups decrease from the initial distance (docked compl

Re: [gmx-users] Nucleotide terminal problems in GORMOS96 force field

On 10/9/12 3:34 AM, 史卜吉 wrote: I am going to simulate a tRNA molecule using GROMOS96 force field, which contain some modified nucleotide. Gromos96 parameters are rather poor for nucleotides. AMBER or CHARMM parameter sets are far better suited for simulations of nucleic acids. I've bu

[gmx-users] pull=constraint gives zero forces

For me it seems that the problem with the constraints iteration is only relevant if both groups are connected with contraints over the rest of the system. It seems that your pull-code parameters are essentially the same like mine (apart from the fact that you have more groups). In my case the sy

Re: [gmx-users] EM & MD

On 10/9/12 9:45 AM, Ali Alizadeh wrote: Dear All users I ran energy minimization and mdrun for my system with EM was a good run : Run parameters integrator = steep dt = 0.002 nsteps= 5 emtol =100

Re: [gmx-users] Polarisablity of water using Gromacs

On 2012-10-09 14:26, Deepak Ojha wrote: Dear Gmx_users, I want to calculate instantaneous polarizability of water using GROMACS.I found there exists a water model which polarisable in gromacs with the itp file sw.itp. Is it possible to get the above mentioned using the sw water model in gromacs

[gmx-users] Could not converge NPT constraints

I have not much experience with Gromacs, although I have worked for years on molecular simulations. I am trying to run a NPT simulation of 1000 SPCE water molecules at 293 K with the opls force field. I equilibrated the system first during 1 ns using a velocity rescale thermostat, a Berendsen

[gmx-users] About Em and Equlibration With Lincs Algorithim

Dear Justin Than you for your previous Reply  I am doing EM for My cyclic peptide using following EM. MDP ; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator  = steep    ; Algorithm (steep = steepest descent min

[gmx-users] Re: Distance between Centre of Mass!

Please keep all Gromacs-related correspondence on the gmx-users list. I am not a private tutor. I am CC'ing this message to the list and will ask that all further correspondence be addressed there. On 10/9/12 12:26 PM, Arman Mahboubi Soufiani wrote: Dear Justin, I have two layers of PLA a

Re: [gmx-users] Could not converge NPT constraints

On 10/9/12 11:31 AM, juan-manuel.casti...@mv.uni-kl.de wrote: I have not much experience with Gromacs, although I have worked for years on molecular simulations. I am trying to run a NPT simulation of 1000 SPCE water molecules at 293 K with the opls force field. I equilibrated the system first

Re: [gmx-users] single precision to double precision version

On 10/9/12 12:21 PM, Ali Alizadeh wrote: Dear All users How to convert my single precision version of gromacs to double precision? Is it possible? You don't; you re-install Gromacs with the desired precision. Note that single- and double-precision installations can exist side-by-side wit

Re: [gmx-users] About Em and Equlibration With Lincs Algorithim

On 10/9/12 12:38 PM, vidhya sankar wrote: Dear Justin Than you for your previous Reply I am doing EM for My cyclic peptide using following EM. MDP ; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep

[gmx-users] RB parameters for the OPLSAA force field.

Dear all, Does anyone know where I can find reference of how to calculate the RB parameters (C0-C5) for proper dihedrals? I have got some undefined dihedrals in my top file and I am not sure where to start. What kind of information do i need to calculate those parameters? any package that does

Re: [gmx-users] distance between protein and ligand

Hi, Did u repeat your MD simulation of your docked complex ? I also asked the similar question. Alex replied :" I would start several (5-10?) runs with different (random) starting impulse to get more reliable data." Best Shiyong On Tue, Oct 9, 2012 at 12:48 PM, Archana Sonawani wrote: > Hi,

Re: [gmx-users] Interaction study for peptide-receptor..

Hi, Your expectation from MD is too much than reality. Peptide design is an open problem. Lots of elegant protocols are available. However, to my understanding, the core problem is still about protein-peptide docking and scoring. MD simulation only helps on some special cases. It is impossible th

Re: [gmx-users] Interaction study for peptide-receptor..

On 10/9/12 8:43 PM, Liu Shiyong wrote: Hi, Your expectation from MD is too much than reality. Peptide design is an open problem. Lots of elegant protocols are available. However, to my understanding, the core problem is still about protein-peptide docking and scoring. MD simulation only helps

Re: [gmx-users] Interaction study for peptide-receptor..

Justin, Single mutation for four residue. The number of mutants is 4x19=76 Of course , that is a tiny peptide library. Best Shiyong On Wed, Oct 10, 2012 at 9:06 AM, Justin Lemkul wrote: > > > On 10/9/12 8:43 PM, Liu Shiyong wrote: >> >> Hi, >> >> Your expectation from MD is too much than rea

Re: [gmx-users] Interaction study for peptide-receptor..

On 10/9/12 9:17 PM, Liu Shiyong wrote: Justin, Single mutation for four residue. The number of mutants is 4x19=76 Of course , that is a tiny peptide library. Of course one can design many different mutants with a 4-residue peptide (far more than 76 in fact, considering all possible combi

Re: [gmx-users] single precision to double precision version

On Tue, Oct 9, 2012 at 12:07 PM, Justin Lemkul wrote: > > > On 10/9/12 12:21 PM, Ali Alizadeh wrote: >> >> Dear All users >> >> How to convert my single precision version of gromacs to double precision? >> >> Is it possible? >> > > You don't; you re-install Gromacs with the desired precision. Not

Re: [gmx-users] Interaction study for peptide-receptor..

Hi, Yes it is possible to screen peptides as ligand. But for these following information is needed 1. Binding site of peptide and ligand 2. Which residues in peptide are important for binding. After you simply do the mutation on the desired peptide.Performed the MD upto 50 ns Find the intera

Re: [gmx-users] distance between protein and ligand

Hi Liu Shiyong, No, I didn't repeat any simulation. My intention is to compare two large compounds with our designed molecule which is comparatively smaller. On Wed, Oct 10, 2012 at 6:01 AM, Liu Shiyong wrote: > Hi, > > Did u repeat your MD simulation of your docked complex ? > > I also asked

[gmx-users] TPI run

Dear users, I want to run TPI of water in a binary mixture of water DMSO system. My question is, how to add the extra water or extra DMSO molecule, or precisely, how to get the NEW set of coordinates for one water OR one DMSO molecule? I will appreciate your reply. Rikg -- View this message i