Re: [gmx-users] unexpecter rmsd

Thank you Justin On Fri, Mar 27, 2020, 19:47 Justin Lemkul wrote: > > > On 3/27/20 11:10 AM, Emran Heshmati wrote: > > Thanks to Paul and jorden, I repost my question: > > I am working on a protein consisting 2 chains. After performing > > regular MD simulation >

[gmx-users] unexpecter rmsd

Thanks to Paul and jorden, I repost my question: I am working on a protein consisting 2 chains. After performing regular MD simulation and analysis the outputs, I got unexpecter rmsd, as seen in link below. What is the problem??

[gmx-users] Inexpected rmsd

I am working on a protein consisting 2 chains. After performing regular MD simulation and analysis the outputs, I got unexpecter rmsd, as shown in arttached graph. What is the problem? -- Gromacs Users mailing list * Please search the archive at

[gmx-users] gmx distance

Dear All I am in trouble with gmx distance command. I want to calculate the distance between two amino acids (residue 130 and residue 153) in a protein after gromacs standard simulation. After generating of r130.ndx and r153.ndx index files, I use this command: gmx distance -f md_0_1_noPBC.xtc -s

[gmx-users] (no subject)

Dear All I am in trouble with gmx distance command. I want to calculate the distance between two amino acids (residue 130 and residue 153) in a protein after gromacs standard simulation. After generating of r130.ndx and r153.ndx index files, I use this command: gmx distance -f md_0_1_noPBC.xtc -s

[gmx-users] Protein dipole moments

What are the physical meaning of <|M|^2> and <|M|>^2 in the outputs of gmx dipoles command ?? Any help is welcome. -- 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] residue number in secondary structure plot

Than you Justin. I used CHARMM force field. On Sat, Sep 9, 2017 at 10:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/9/17 1:58 PM, Emran Heshmati wrote: > >> Dear Gromacs users >> I performed a md simulation on apeptide fragment consist of 16 aa . wh

[gmx-users] residue number in secondary structure plot

Dear Gromacs users I performed a md simulation on apeptide fragment consist of 16 aa . when I analysed its secondary structure content using "gmx do_dssp " command, there was only 15 aa in y-axis in resultig *.eps file format. can anyone explain this controversy. -- Gromacs Users mailing list *

Re: [gmx-users] difference in potential energy

tic and potential energies. our question is related to the interpretation of this finding!! Regards Emran On Sun, Jun 25, 2017 at 2:45 AM, Emran Heshmati <compbi...@gmail.com> wrote: > Dear Gromacs users > I performed alanine scaning mutagenesis using gromacs on a peptide > fragmen

[gmx-users] difference in kinetic energy

Dear Gromacs users I performed alanine scaning mutagenesis using gromacs on a peptide fragment consisting 16 aa. In one of the mutations, the kinetic energy of the system was significantly different. How can I interpret this result? any comment is welcome regards -- Gromacs Users mailing list *

[gmx-users] difference in potential energy

Dear Gromacs users I performed alanine scaning mutagenesis using gromacs on a peptide fragment consisting 16 aa. In one of the mutations, the kinetic energy of the system was significantly different. How can I interpret this result? any comment is welcome regards Emran -- Gromacs Users mailing

[gmx-users] positive potential energy

Hi all I run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing

Re: [gmx-users] (no subject)

total charge of your molecule depends on ionizable groups on your molecule and the pH.   Best Regards Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to From: Shivangi Agarwal <shivangi.agar

Re: [gmx-users] (no subject)

molecules, for use with CHARMM or GROMACS | | | 3- https://atb.uq.edu.au/   Best Regards Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to From: Shivangi Agarwal <shivangi.agarwal...@gmail.

Re: [gmx-users] Vmd error

Dear Rahulyou can visualize your final *.xtc output in another tool/software first, to ensure your simulation steps.   Best Regards Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to From: RAHUL SURESH

[gmx-users] Positive potential energy

system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred?  Best Regards Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- Gromacs Users mailing list * Please search

[gmx-users] Positive potential energy

system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred?  Best Regards Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- Gromacs Users mailing list * Please search

[gmx-users] Positive potential energy

system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred?  Best Regards Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- Gromacs Users mailing list * Please search

[gmx-users] nano structure simulation

Dear Gromacs usersI want to  simulate the effects of a nano structure (such as graphene oxide) on the structure of a protein but I have problems in constructing nano structure topology file. Do anyone have an explained tutorial?  Best Regards Emran Heshmati Ph. D.Biophysicist,Computational  Bio

[gmx-users] TFE

the massand radius of the atom type. Please check the outputfiles if necessary. Reading solvent configurationALL ATOM STRUCTURE FOR MOLECULE UNKsolvent configuration contains 9 atoms in 1 residues what is wrong? help me please.  Best Regards Emran Heshmati Ph. D.Biophysicist,Computational

[gmx-users] Charge of the system

. After adding these parameters to protein topologyfile (as proposed by Lemkul) , the net charge of the system waschanged from 0 to -4. Is it needed to neutralize the system again oranything els?    Best Regards Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist P Save a tree... please