Re: [gmx-users] New in the mailing list

Hi, Use the same version of GROMACS for converting the tpr as you used for running the simulation. Old code can't know about new modules, etc. Mark On Thu, Feb 22, 2018, 14:37 Giordano Perini wrote: > Hello everyone, > I've just joined this mailing list in order

[gmx-users] New in the mailing list

Hello everyone, I've just joined this mailing list in order to understand how to solve a problem while extending a simulation. I am trying to generate a new tpr file via command line: gmx convert-tpr -s [old].tpr -extend [timeneeded] -o new.tpr BUT, when compiling, it tells me: reading tpx

[gmx-users] problems with the output of pullx

Hi, I am using gromacs to get the PMF of a peptide of about 20 amino acids, moving inside of a bilayer membrane. After pulling the peptide inside the membrane now I am using pull-coord1-type = umbrella and pull-coord1-geometry = distance to sample configurations in each window for the

[gmx-users] calculating force for a restrained structure

Dear Justin and all GROMACS users, I'm simulating a nano tube which is placed in a lipid system. the nano tube is completely restrained to halt rotation or COM movement. Now, I intend to calculate the force applied from lipid layer to nanotube. the question is how can i eliminate the effect of

[gmx-users] Example of arithmetic expression in gmx select?

Hi all, I'm trying to do selections that require addition, which is supposed to be supported according to 'gmx help selections'. I get syntax error however when doing from within 'gmx select': a=1+1 resid a What is the right syntax for achieving a=2...? Thanks, Viveca -- Gromacs Users mailing

[gmx-users] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?

Dear Gromacs, The scount.xvg file was obtained after running echo 1 | gmx do_dssp -f md_0_1_noPBC.xtc -s md_0_1.tpr -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -tu ns The secondary structures listed are:

Re: [gmx-users] query about coul-SR

Thanks for your reply Alex. ‌ On 23 February 2018 at 02:01, Alex wrote: > No, this is the particle-particle cutoff portion in the particle-particle > + particle-mesh scheme. Unless the size of your entire protein is smaller > than rcoulomb. > > Alex > > > On 2/22/2018

[gmx-users] query about coul-SR

Dear Users, In the output of gmx energy, coul-SR means short range Coulomb interactions. So if I have coul-SR for a protein, does it give the total self-interaction energy (Coulomb) of the protein? Any help is much appreciated. Thanks & regards, *Saumyak Mukherjee* Senior Research Fellow,

Re: [gmx-users] query about coul-SR

No, this is the particle-particle cutoff portion in the particle-particle + particle-mesh scheme. Unless the size of your entire protein is smaller than rcoulomb. Alex On 2/22/2018 1:07 PM, Saumyak Mukherjee wrote: Dear Users, In the output of gmx energy, coul-SR means short range Coulomb

[gmx-users] selection of the type of box in molecular dynamics in GROMACS

Hi everyone, I want to know that on what basis we have to select the specific type of a box for a particular protein during molecular dynamics in GROMACS ? Thank you in advance. -- Thanks & Regards, VIKRAM DALAL Research Scholar -- Gromacs Users mailing list * Please search the

[gmx-users] The PMF curve is asymmetric (However many results of membrane penetration are symmetric)

Hi all: I tried to use MD simulation to pull a drug across the POPC membrane and to calculate PMF. I obtained the PMF curve following the guide (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/) I found the PMF curve increases as the penetration process

Re: [gmx-users] PROBLEM IN COORDINATES

thanks. problem resolved. On 21 Feb 2018 08:13, "Justin Lemkul" wrote: > > > On 2/20/18 9:50 PM, neelam wafa wrote: > >> Dear gmx users >> >> I am still stuck at this point. >> error obtained is this >> Fatal error: >> number of coordinates in coordinate file (solv.gro, 32803)