[gmx-users] ERROR 1: atom C4 (Res ORP-1) has mass 0

Dear all, I am simulating a Protein-Drug complex. I am following Justin's tutorial. I have used *PRODRG *for generating topology. *Gaussian *has given me the ESP charges. I have edited the charges in the itp file using the *Gaussian*'s ESP charges*. *Then I am getting this strange error. *ERROR 1

Re: [gmx-users] GPU warnings

Hi Szilárd, I was able to run code compiled with icc 13 on Fedora 17, but as I don't > have Intel Compiler v13 on this machine I can't check it now. > > Please check if it works for you with gcc 4.7.2 (which is the default) and > let me know if you succeed. The performance difference between icc a

Re: [gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5

Look at the top of the output of any GROMACS program. Mark On Sun, Nov 25, 2012 at 10:06 AM, Acoot Brett wrote: > Dear All, > > Is any gromacs command which can tell us or distinguish whether what > installed is gromacs 4.5.4 or 4.5.5? > > Cheers, > > Acoot > > > --- On Sat, 24/11/12, David van

[gmx-users] Is any command to distinguish gromacs 4.5.4 and 4.5.5

Dear All, Is any gromacs command which can tell us or distinguish whether what installed is gromacs 4.5.4 or 4.5.5? Cheers, Acoot --- On Sat, 24/11/12, David van der Spoel wrote: > From: David van der Spoel > Subject: Re: [gmx-users] Different average H bonds with different g_hbond > rele

[gmx-users] Principal Component Analysis (PCA)

hi all, Can we plot RMSF versus atom numbers using eigenvectors of a different simulation and trajectory of another simulation. I know we can plot RMSF versus atom numbers using the eigenvectors and trajectory of a same simulation using g_anaeig Thanks in advance -- View this message in contex