[gmx-users] addition of an isopeptide bond and its simulation

Hi! I need to study the effect of post-translational modifications on the biophysical properties of my protein. This involves the addition of an isopeptide bond to the primary chain of the C-terminal tail. How may I add this isopeptide bond? And then which force field can I use to simulate it?

[gmx-users] Hbond residence time

Hi all! I have been looking into the autocorrelation function outputs of 'gmx hbond' in order to calculate the residence time for my water hbond to a specific heteroatom. It turns out that I couldn't find any detailed explanation about each 'type' outputted. In my case: Type Rate (1/ps)

[gmx-users] Most suitable intervals of temperature in REMD

Dear gmx users, Do you have a suggestions and discussions about most suitable temperature intervals for REMD simulations of the peptides? Best regards, Mijee -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] User Defined Potentials

Hi, I am Phd physics phd student at University of Delaware. I am using GROMACS for calculation of solvation energy of argon or methane in water. But Our water model has additional interaction terms other than already define in GROMACS. *Can we add our own interaction terms in GROMACS? If yes

Re: [gmx-users] HBond for F and S (Justin Lemkul)

Thanks, Justin! It worked just fine. I guess using a flag to include different atomtypes into the analyses would be a nice feature for next GROMACS versions. Cheers! -- Marcelo Depólo Polêto DSc. Cell and Molecular Biology - UFRGS (Brazil) Group of Structural Bioinformatics - Room 202 Center

[gmx-users] How to orientationally restrain a molecule?

I'm interested carrying out a long simulation of a thin, narrow protein. Clearly, the volume-minimizing way to do this would be to put it in a thin, narrow box of solvent. The issue with this is that it could rotate around and interact with itself. if the orientation of the protein changed

Re: [gmx-users] HBond for F and S

On 4/24/17 3:15 PM, Marcelo Depólo wrote: Hi, Can gmx hbond also calculates hbonds between non-canonical atoms like S or F as well? If so, how can I do it? Without changing the code, the only way to do it is to rename the atoms in the topology as some type of oxygen, create a new .tpr

[gmx-users] HBond for F and S

Hi, Can gmx hbond also calculates hbonds between non-canonical atoms like S or F as well? If so, how can I do it? Cheers! -- Marcelo -- 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

Re: [gmx-users] cant load trajectory, low memory

On 4/24/17 12:56 PM, abhisek Mondal wrote: Hello, I'm using the configurations generated by pulling run to re-box > resolvate ion addition > EM > npt_umbrella(10ns) and forward. So, please clarify me something. Am I following correct path ? Should I have given a npt equilibration step

Re: [gmx-users] cant load trajectory, low memory

Hello, I'm using the configurations generated by pulling run to re-box > resolvate > ion addition > EM > npt_umbrella(10ns) and forward. So, please clarify me something. Am I following correct path ? Should I have given a npt equilibration step prior to npt_umbrella step ? Thank you. On Mon,

Re: [gmx-users] Gcc

Dear Joao, U r right, it's my fault, but the thing is that i was tried lot of thing but not found anything perfect. That's by , i was waiting from weekend for one answer. Regards, Anshul On Mon, Apr 24, 2017 at 2:53 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > Dear Mark and by

Re: [gmx-users] Gcc

Dear Joao, U r right, it's my fault, but the thing is that i was tried lot of thing but not found anything perfect. That's by , i was waiting from weekend for one answer. On Mon, Apr 24, 2017 at 2:53 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > Dear Mark and by extension Anshul,

Re: [gmx-users] cant load trajectory, low memory

Hi, I already answered that. You're effectively starting again, so do that. Mark On Mon, Apr 24, 2017 at 12:28 PM abhisek Mondal wrote: > Ok, I got it this time. > But what kind of equilibration I'm to perform on these stripped structures. > Should I perform normal NPT

Re: [gmx-users] cant load trajectory, low memory

Ok, I got it this time. But what kind of equilibration I'm to perform on these stripped structures. Should I perform normal NPT equilibration as done before generating configurations ? or I'm to run gmx grompp -f npt_umbrella.mdp -c conf0.gro -p topol.top -n index.ndx -o npt0.tpr (using standard

Re: [gmx-users] cant load trajectory, low memory

If you are taking confout.gro as your starting input file, it will have all water and ions of the previous simulation. On Mon, Apr 24, 2017 at 3:35 PM, Tasneem Kausar wrote: > Create index group that have both protein and ACO. gmx make_ndx will serve > this task. >

Re: [gmx-users] cant load trajectory, low memory

Create index group that have both protein and ACO. gmx make_ndx will serve this task. Then create a pdb file file from gmx trjconv Or you can choose system as output and delete ions and solvent from any editor. On Mon, Apr 24, 2017 at 3:21 PM, abhisek Mondal wrote: >

Re: [gmx-users] cant load trajectory, low memory

Hi, You need to make an index group (e.g. gmx select or gmx make_ndx) that has the things you want (e.g. protein + ACO, or perhaps everything but water+ions). See also http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume. I'd guess your system has at least a factor of

Re: [gmx-users] cant load trajectory, low memory

Hello, Alright. I have tried this but I'm stuck in the following scenario. I'm using trjconv for getting pdb file of the protein-ligand complex (used for umbrella sampling). trjconv_mpi -f confout1.gro -o conf_1.pdb -n index.ndx -s npt.tpr This is giving me the following prompt: Select group for

Re: [gmx-users] Gcc

Dear Mark and by extension Anshul, I did make an assumption at the bottom of my previous email, and that was uncalled for (despite having good intentions, but that doesn't change anything). I apologize for that. That, however, does not overshadow the fact that I provided Anshul with all the

Re: [gmx-users] Gcc

Hi Joao, Anshul and all, Let's all please remember to keep the environment friendly and professional. That means not making assumptions about other people's intentions. Learning complex things like simulation science take time, and people often make mistakes when joining new communities,

Re: [gmx-users] Filling box with long linear molecules

Hi, Not really. The general problem of filling space in a tight packing is hard. Usable approaches include decreasing the VDW radius while inserting molecules, using gmx genconf to start from an initially crystalline configuration of suitable density that is then equilibrated for a long time,

[gmx-users] Filling box with long linear molecules

Dear GMX users, I am working with polymers (~20 carbon atoms) in an enclosed box. In order to fill this box with polymers, I currently use an iteration of multiple steps. Currently, the polymers are created via an external code, and the resulting polymers are linear strings of polymers, with

Re: [gmx-users] Gcc

Dear Anshul, I thought by movie you meant that you wanted to visually check the trajectory. ​For PyMOL, google search "pymol movie" produces about 31.000 results in 0,31 seconds. The first hit is exactly what you want: https://pymolwiki.org/index.php/MovieSchool My previous email will still be

Re: [gmx-users] Regarding finding orientation of angles of solvent with desired atom

Hello, I have simulated amino acid (eg., glycine) with water solvent mixture in gromacs.. my question is .. 1] How can i find out the solvent orientation (angle made) ie.,angle made by water (HOH) with respect to alpha carbon of amino acid (eg., glycine)...?? 2] I have tried with gmx sorient

[gmx-users] Regarding finding orientation of angles of solvent with desired atom

Hello, I have simulated amino acid (eg., glycine) with water solvent mixture in gromacs.. my question is .. 1] How can i find out the solvent orientation (angle made) ie.,angle made by water (HOH) with respect to alpha carbon of amino acid (eg., glycine)...?? 2] I have tried with gmx sorient

Re: [gmx-users] Gcc

Hi, Please search for information before asking. Google has plenty of good hits for "make md movie" for example. Mark On Mon, 24 Apr 2017 09:24 Anshul Lahariya wrote: > hello rahul, > can u tell me how to make movie?? > > > On Fri, Apr 21, 2017 at 3:12 PM, João

Re: [gmx-users] Gcc

hello rahul, can u tell me how to make movie?? On Fri, Apr 21, 2017 at 3:12 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > ​Plus, installing multiple version of the same software (e.g. gcc) is not > problematic at all *when done by someone that knows what he/she is doing*. >