Re: [gmx-users] regarding rmsd calculation of protein

Really thank you so much for your reply. can i select the two chain at a time.because both protein contain 120 amino acid respectively. then > ri 1-120 Found 262 atoms with resind.+1 in range 1-120 15 r_1-120 : 262 atoms > rename Chain_A Found 0 atoms with residue names ENAME

Re: [gmx-users] regarding rmsd calculation of protein

You should give like ri 1-120 On Thu, 24 May 2018, 11:14 am SHAHEE ISLAM, wrote: > yes its working. > now > >ri ( give numbers for residue number of each chain) > i have 120 amino acids of two protein each. > when i am giving > > ri 120 > > > 15 r_120 :

Re: [gmx-users] regarding rmsd calculation of protein

yes its working. now >ri ( give numbers for residue number of each chain) i have 120 amino acids of two protein each. when i am giving > ri 120 15 r_120 : 2 atoms should i give this in the way. On 5/24/18, Soham Sarkar wrote: > Put L(small) > It will

Re: [gmx-users] regarding rmsd calculation of protein

Put L(small) It will give the residue number On Thu, 24 May 2018, 11:00 am SHAHEE ISLAM, wrote: > after giving this command > make_ndx -f em.gro -o index.ndx > nr : group ! 'name' nr name 'splitch' nrEnter: list groups > 'a': atom& 'del' nr

Re: [gmx-users] regarding rmsd calculation of protein

after giving this command make_ndx -f em.gro -o index.ndx nr : group ! 'name' nr name 'splitch' nrEnter: list groups 'a': atom& 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr'splitat' nr'h': help 'r': residue 'res'

Re: [gmx-users] regarding rmsd calculation of protein

It is any .gro file of your system You can make index file after final md On Thu, 24 May 2018, 10:37 am SHAHEE ISLAM, wrote: > you have mention here em.gro,i think it is a gro file of > equilibration.can i make the index file after production run to > calculate rmsd. > >

Re: [gmx-users] regarding rmsd calculation of protein

you have mention here em.gro,i think it is a gro file of equilibration.can i make the index file after production run to calculate rmsd. On 5/23/18, SHAHEE ISLAM wrote: > thank you so much for your quick reply. > > On 5/23/18, Soham Sarkar wrote: >>

[gmx-users] Fwd: Molar heat capacity calculations

-- Forwarded message -- From: Sushant Sharma Date: 23 May 2018 at 11:27 Subject: Molar heat capacity calculations To: "gmx-us...@gromacs.org" I am currently calculating the molar heat capacity of neon. First, I minimized the system.

Re: [gmx-users] Simulating protein-lipid interactions

CHARMM36-m is the most recent release of the CHARMM forcefield, with improved protein dynamics . You can find the force field files here: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs That webpage also has a list of relevant publications for you to look over. Alternatively, the

Re: [gmx-users] Simulating protein-lipid interactions

Mixing force-fields is generally considered a bad idea. Though there are some papers where people do mix the force-fields, these are limited cases and typically require substantial validation against experimental data and additional tuning of the resulting mixed force-field. -Micholas

[gmx-users] Simulating protein-lipid interactions

Dear Gromacs users, I want to simulate the interaction of a protein and a lipid. For the protein simulation I have chosen the CHARMM27 force field, because is the one I had selected for the lipid simulation. Does the force field have to be the same for both molecules? How I select the best

Re: [gmx-users] regarding rmsd calculation of protein

thank you so much for your quick reply. On 5/23/18, Soham Sarkar wrote: > Do proper indexing of each chain >> make_ndx -f em.gro -o index.ndx >>l (shows total residue with number) >>ri ( give numbers for residue number of each chain) >>rename them as Chain_A and Chain_B >>v

Re: [gmx-users] regarding rmsd calculation of protein

Do proper indexing of each chain > make_ndx -f em.gro -o index.ndx >l (shows total residue with number) >ri ( give numbers for residue number of each chain) >rename them as Chain_A and Chain_B >v (shows the newly indexed file) >q (save) Now your index has two chain seperated On Wed, May 23, 2018

[gmx-users] regarding rmsd calculation of protein

hi, i have two protein in my gro file.when i am calculating rmsd by this command g_rms -s dynamic.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns this options are coming Group 0 ( System) has 12059 elements Group 1 (Protein) has 566 elements Group 2 ( Protein-H) has

[gmx-users] Molar heat capacity calculations

I am currently calculating the molar heat capacity of neon. First, I minimized the system. Then i performed NVT followed by NPT equlibrations. Then i perdormed a production run. I performed MSD calculations of the results and calculated Diffusion coefficent whic was within 1% error. However

[gmx-users] is there a suitable FF for perovskite?

Dear all, Do you think there is a suitable FF that can do simulation for perovskite(CH3NH3PbI3) in gromacs? Thanks, Tong -- 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] partial exclusion of interactions within 1-4

Hi, That's what we hope people use the tables of contents and text searches for ;-) Next year's reference manual content will come also on the web, so Google will search it, but the feature to beam exactly what you want directly into your brain is a few years away... :-D The reference manual has

[gmx-users] S-S bond

Hi, I want to functionalize ZnS nanotube with different molecules which all have sulfur in their structures, like cystein amino acid and ... . I want to study the interaction of this functionalized nanotube with different proteins. I use DFT for calculating the partial charges and bond length

Re: [gmx-users] partial exclusion of interactions within 1-4

This is the part I don't really understand, as I've never done this before. Let's assume we generated those pairs (it would actually be easy to obtain directly from bonds/angles/dihedrals). LJ is set throughout the system. Can one specify pairs with specific LJ params only for those pairs? In

Re: [gmx-users] partial exclusion of interactions within 1-4

Hi, I suggested that [pairs] with the LJ parameters specified as zero was a way to be non-simultaneous. That adds back the Coulomb you want. Mark On Wed, May 23, 2018 at 10:55 AM Alex wrote: > It is my understanding that either [pairs] or [exclusions] affect LJ and >

Re: [gmx-users] partial exclusion of interactions within 1-4

It is my understanding that either [pairs] or [exclusions] affect LJ and electrostatics simultaneously, please correct me if I'm wrong. Maybe this just isn't meant to be, being a highly artificial setup (nearest-neighbor electrostatics on, LJ off)... The idea for this comes from authors who

Re: [gmx-users] md simulation of a protein in mixture of water and DMSO

Hi, As always, one needs to seek a forcefield that already supports such a molecule, or someone who has parameterized an extension for one that does. Generally that starts with a literature search, or maybe the contribution section of the GROMACS website. And then to test the quality yourself.

[gmx-users] g_cluster error

Hello all, I have done two independent GROMACS run for same protein system. I would like to cluster and do further analyses. I used the following commands: 1. g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -f2 md_0_1_noPBC_simulation2.xtc -m rmsd-matrix.xpm Selected '4' for back bone atoms. This