Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 27

thank you for the reply Justin. though the APL looks close to the acceptable range, I am afraid the SN1 and SN2 acyl chain parameters are not in the range as reported by Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888?3903 and also the membrane thickness increases. > > > > >

Re: [gmx-users] Charge groups in poly methyl methacrylic acid

Den 2018-06-06 kl. 05:01, skrev Debadutta Prusty: Hi everyone, I am new to gromacs and hence, this question might be naive. How does one go about assigning charge groups while creating new monomer topologies in .rtp files? What I gather from looking at similar posts is that the net charge of a c

Re: [gmx-users] Charge groups in poly methyl methacrylic acid

I would try to double-check with topology generators like http://erg.biophys.msu.ru/tpp/ on a short polymer chain (e.g. three links, termini passivated by H), or do a CHELPG calculation to look at the charge distribution within the central unit (OPLS and AMBER rely on CHELPG charges) to get an

[gmx-users] Charge groups in poly methyl methacrylic acid

Hi everyone, I am new to gromacs and hence, this question might be naive. How does one go about assigning charge groups while creating new monomer topologies in .rtp files? What I gather from looking at similar posts is that the net charge of a charge group should be an integer (zero for a neutral

Re: [gmx-users] Virtual sites causing npt simulation instabilities

On 6/5/18 9:28 PM, Eisenhart, Andrew (eisenhaw) wrote: Sorry about that, he’s a another link to the same files with the fixed em.mdp. I hope the 7zip format is ok. Please use tgz or just upload a plain-text em.mdp. -Justin https://files.fm/u/r65e3kzq Andrew E. Eisenhart Graduate Researc

Re: [gmx-users] Virtual sites causing npt simulation instabilities

Sorry about that, he’s a another link to the same files with the fixed em.mdp. I hope the 7zip format is ok. https://files.fm/u/r65e3kzq Andrew E. Eisenhart Graduate Research Assistant | University of Cincinnati 330.383.5061 From: gromacs.org_gmx-users-boun...@ma

Re: [gmx-users] mdp-settings for charmm36 and lipid apl values

On 6/5/18 1:03 PM, Muthukumaran Rajagopalan wrote: Dear Gromacs Users, I have recently started performing membrane simulations in gromacs 5.01 version, I have started running simulations with pure POPE bilayer constructed from charmm-gui membrane builder with XY dimension 70 angs (84 lipids

Re: [gmx-users] total energy of a protein

On 6/5/18 5:12 PM, Saumyak Mukherjee wrote: Dear All, Is there any way of obtaining the total energy of a protein from GROMACS (including bond stretch, angle bend, dihedral, Coulomb, LJ, Coulomb-14 and LJ-14) other than using gmx mdrun rerun? ‌ No, because there's no built-in way to decompo

Re: [gmx-users] Virtual sites causing npt simulation instabilities

On 6/5/18 7:02 PM, Eisenhart, Andrew (eisenhaw) wrote: Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations. em.mdp is some corrupted binary file. Plea

Re: [gmx-users] Virtual sites causing npt simulation instabilities

Here's the link to the files, if there's anything else I can send let me know. I've been using 5.1.1 for the initial set up and energy minimization, and 5.1.2 for the nvt and npt simulations. https://files.fm/u/c9uef9qh Thanks Andrew _

[gmx-users] total energy of a protein

Dear All, Is there any way of obtaining the total energy of a protein from GROMACS (including bond stretch, angle bend, dihedral, Coulomb, LJ, Coulomb-14 and LJ-14) other than using gmx mdrun rerun? ‌ ​Regards, Saumyak​ -- Gromacs Users mailing list * Please search the archive at http://www.gr

[gmx-users] bundling four water molecules

Dear all, I wonder how I can bundle 4 water molecules together as a single object? I heard some thing called *virtual bond* can do it in gromacs, but I could not find any documentation about it in the manual. I guess the virtual bond is not the virtual site in the manual. Thank you. Alex -- Groma

[gmx-users] Calculations of preferential interaction coefficient

Dear All, I want to calculate the preferential interaction coefficient and subsequently the Gibbs free energy of solvation for protein in water and in water-co-solvent mixture. 1. According to the equation specified in the literature, if I can generate a list of no. of solvent molecules (for each l

[gmx-users] Doubts in g_select and g_trjconv

With reference to my earlier message, I have also tried the g_trjorder command giving reference group as Backbone. When I give the command, g_trjorder -f 100ns_nc_72um2.xtc -s md.tpr -nshell nshell_urea.xvg -r 0.45 -da 0 I am getting reasonable no.of urea molecules like 6,8,9,etc. Same goes for

[gmx-users] Doubts regarding g_select

Dear All, I am confused between different commands and their outputs for g_select. I want to choose a cutoff of 0.45nm and want to calculate the no. of urea molecules within 0.45 as well as beyond 0.45nm of the peptide backbone. I have a total of 18 urea molecules in my system One of the commands

[gmx-users] mdp-settings for charmm36 and lipid apl values

Dear Gromacs Users, I have recently started performing membrane simulations in gromacs 5.01 version, I have started running simulations with pure POPE bilayer constructed from charmm-gui membrane builder with XY dimension 70 angs (84 lipids in each bilayer). The bilayer is solvated with 0.15

Re: [gmx-users] Virtual sites causing npt simulation instabilities

On 6/5/18 9:10 AM, Eisenhart, Andrew (eisenhaw) wrote: Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds

Re: [gmx-users] Box dimension

Perhaps a solution for those who don't like off-GROMACS topics, is to not get involved in such threads? ;) -- Viveca On Mon, Jun 4, 2018 at 9:07 AM, Alex wrote: > And again, your question has nothing to do with Gromacs. It has to do with > what you want to do, common sense, and basic arithmeti

Re: [gmx-users] Virtual sites causing npt simulation instabilities

Hello again, I have done a few things since I last updated this list. I generated a new system of only 1000 water instead of the original 2000, I used a more careful approach in my energy minimization, minimizing first with all bonds and angles constrained then again without those hash constra

Re: [gmx-users] spc.itp file and flexspc.itp

On 6/5/18 8:48 AM, Anjana Jayasinghe wrote: Dear Prof. Justin and Gromacs users, Thank you very much for the reply. I  noticed that FLEX_SPC is defined in the .top file of the bilayer simulations for CiEj systems ( in  patrickfuchs/CiEj_2016H66 ). They used a modified force field known as 20

Re: [gmx-users] spc.itp file and flexspc.itp

Dear Prof. Justin and Gromacs users,  Thank you very much for the reply. I  noticed that FLEX_SPC is defined in the .top file of the bilayer simulations for CiEj systems ( in  patrickfuchs/CiEj_2016H66 ). They used a modified force field known as 2016H66 with Gromacs 4.0.7. I am also trying to u

Re: [gmx-users] regarding rmsd calculation

On 6/5/18 3:05 AM, SHAHEE ISLAM wrote: hello sir, there are two proteins in a water box system.i am doing martini protein cg simulation and following this tutorial http://cgmartini.nl/index.php/tutorials-general-introduction/protein at the 7 no step i have done grompp -f dynamic.mdp -c equil

Re: [gmx-users] How to add distance and angle restraints in the topology file?

On 6/5/18 3:50 AM, Qing Liu wrote: Hello, everyone, I just used Gromacs-5.1.4 to run a MD with distance and angle restraints. These restraints are between a protein and a ligand. However, the ligand topology is included in the "ligand.itp", and its atom numbers begin from 1. This is

Re: [gmx-users] Extension on different machines (CPU/GPU

Hi Mark, Thank you for the quick answer. However, the problem is not only a problem of reproducibility of a single simulation. To make sure that I have converged results with proper sampling, I am performing each time 10 simulations of the same system with different positions of the solvent molecu

Re: [gmx-users] mdrun -rerun

Hi, Rerun post-processes the trajectory. If it could guess about frames that aren't there, then you wouldn't need to have run the simulation. ;-) Mark On Tue, Jun 5, 2018 at 10:43 AM venkat wrote: > Hi, > For my work, I did md simulations (200ns) by setting with > 0.5 ns xtc

[gmx-users] mdrun -rerun

Hi, For my work, I did md simulations (200ns) by setting with 0.5 ns xtc and 0.5 ns trr files (interval used to save the coordinates). But now I require 4000 frame for 200 ns MD simulations trajectory (25000 steps, 500 ps) is that possible to get from using "*-rerun*" option

Re: [gmx-users] Extension on different machines (CPU/GPU

Hi, You'll basically never get a reproducible trajectory http://www.gromacs.org/Documentation/Terminology/Reproducibility. If your conclusions would depend on the configurations in any single trajectory, you'll have a hard time demonstrating that those conclusions are valid reflection of reality.

[gmx-users] Extension on different machines (CPU/GPU

Dear all, I ran a 250ns simulation with Gromacs 5.1.2 on a machine with only CPUs. I then wanted to extend the simulation to 300ns, and copied the .tpr and the .cpt to another machine with GPUs (also running Gromacs 5.1.2). I observed strange results, so I decided to also extend the simulation (fr

Re: [gmx-users] keep the size of simulation box constant in one direction

http://manual.gromacs.org/online/mdp_opt.html#pc pcoupltype = semiisotropic and set zero compressibility in the z-direction. Alex On 6/5/2018 2:25 AM, 凌未风 wrote: Hi there, I am simulating a membrane using charmm force field, unfortunately I always found huge fluctuation of the box size. I

[gmx-users] keep the size of simulation box constant in one direction

Hi there, I am simulating a membrane using charmm force field, unfortunately I always found huge fluctuation of the box size. I am wondering whether it is possible to fix the box size in the z direction, and allow pressure coupling in xy directions? How could we set up this in the mdp files?

Re: [gmx-users] How to add distance and angle restraints in the topology file?

Hello, I guess you should add your ligand.itp to aminoacids.rtp, and then use pdb2gmx to generate a combined topology file. After that, you can use distance or angle restraints between the protein and the ligand. Maybe you can try to parmed from Amber to combine your protein and ligand topol

[gmx-users] How to add distance and angle restraints in the topology file?

Hello, everyone, I just used Gromacs-5.1.4 to run a MD with distance and angle restraints. These restraints are between a protein and a ligand. However, the ligand topology is included in the "ligand.itp", and its atom numbers begin from 1. This is same as the protein atom numbers. As a

[gmx-users] regarding free energy perturbation

Hello everyone: Is there anyone who can perturb a portion of a molecule or protein when you do FEP analysis ? May you help me to solve the problem ? Many Thanks! Best regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Us

Re: [gmx-users] regarding rmsd calculation

sorry to forget about the recentering of the .xtc file.after getting the dynamic.xtc file i just recenter the .xtc file before doing rmsd analysis. On 6/5/18, SHAHEE ISLAM wrote: > hello sir, > there are two proteins in a water box system.i am doing martini > protein cg simulation and following t

Re: [gmx-users] regarding rmsd calculation

hello sir, there are two proteins in a water box system.i am doing martini protein cg simulation and following this tutorial http://cgmartini.nl/index.php/tutorials-general-introduction/protein at the 7 no step i have done grompp -f dynamic.mdp -c equilibration.gro -p system.top -o dynamic.tpr md