Re: [gmx-users] How to do Normal Modes Analysis with Gromacs4.5.5?

Dear David, Thank you very much!! Your suggestion works!! After removing water and ion from my structure, I did normal mode analysis successfully!! I appreciate your help. Shen 在 2012年3月17日 下午11:45，Justin A. Lemkul 写道： > > > qiancheng shen wrote: > >> Dear David, >>

[gmx-users] HBonds between molecules

Dear Gromacs users, I ran a simulation with 13 Hypericin molecules in water for 10 ns and 7 of them formed an aggregate.Is there any way to find out between what molecules and atoms Hbonds were formed? Thanks in advance Hovakim Grabski Russian-Armenian(Slavonic) University -- gmx-users mailing

Re: [gmx-users] HBonds between molecules

Hovakim Grabski wrote: Dear Gromacs users, I ran a simulation with 13 Hypericin molecules in water for 10 ns and 7 of them formed an aggregate.Is there any way to find out between what molecules and atoms Hbonds were formed? Yes, see the various options that g_hbond provides, particularly -

[gmx-users] Problem Installing Gromacs

Newbie here. I'm trying to install Gromacs and I'm following the instructions at the following link: http://www.gromacs.org/Downloads/Installation_Instructions The problem is when I type ./configure --enable-float It gives me 'No such file or directory' I even tried ./configure --enable-fl

Re: [gmx-users] Problem Installing Gromacs

Suhaila Haji Mohd Hussin wrote: Newbie here. I'm trying to install Gromacs and I'm following the instructions at the following link: http://www.gromacs.org/Downloads/Installation_Instructions The problem is when I type ./configure --enable-float It gives me 'No such file or directory'

RE: [gmx-users] Problem Installing Gromacs

> Date: Sun, 18 Mar 2012 12:35:26 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Problem Installing Gromacs > > > > Suhaila Haji Mohd Hussin wrote: > > Newbie here. > > > > I'm trying to install Gromacs and I'm following the instructions at the > > foll

[gmx-users] electrostatics in liquid/vapor interface

Dear All -- I have a system of the liquid/vapor interface kind. The droplet of liquid with a radius of about 10nm is surrounded by a volume of vacuum of ~1000nm^3. What is the best method among those currently in GROMACS4 to treat electrostatics in this case? Dr. Vitaly V. Chaban, 430 Hutchison

[gmx-users] Problem installing Gromacs: What next?

Hello. I already installed fftw3. After unpacking it, I install via the following: ./configure make make install But after that the instructions are not clear to me. Like, it's not telling where do I download Gromacs tar? Or do I need to type some command from fftw so that Gromacs sho

[gmx-users] FW: Problem installing Gromacs: What next?

OK. I downloaded Gromacs 4.5.5. Unpacked it then type ./configure configure: error: Cannot find fftw3f library But I already install fftw3 properly. What is happening? Cheers, Suhaila. From: bell_beaut...@hotmail.com To: gmx-users@gromacs.org Subject: Problem installing Gromacs: What next? D

Re: [gmx-users] Problem installing Gromacs: What next?

Suhaila Haji Mohd Hussin wrote: Hello. I already installed fftw3. After unpacking it, I install via the following: ./configure make make install But after that the instructions are not clear to me. Like, it's not telling where do I download Gromacs tar? Or do I need to type some

Re: [gmx-users] FW: Problem installing Gromacs: What next?

Suhaila Haji Mohd Hussin wrote: OK. I downloaded Gromacs 4.5.5. Unpacked it then type ./configure configure: error: Cannot find fftw3f library But I already install fftw3 properly. What is happening? The commands below will install double-precision fftw, but Gromacs is single precision

Re: [gmx-users] FW: Problem installing Gromacs: What next?

Please be sure to keep the discussion on the mailing list and not my personal email. You may need to specify the location of the fftw installation using LDFLAGS and CPPFLAGS for the libraries and headers, respectively. See example usage at: http://www.gromacs.org/Documentation/Installation_

[gmx-users] number of coordinates in coordinate file does not match topology

Dear All,   I am practicing the on-line tutorial http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/.   In the step "mdrun -v -deffnm 1LW9-EM-solvated" of "Energy minimization of the solvated system", it says " Converged to machine precision  , but not to the requested precision Fmax < 1". Bef

Re: [gmx-users] number of coordinates in coordinate file does not match topology

Acoot Brett wrote: Dear All, I am practicing the on-line tutorial http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/. In the step "mdrun -v -deffnm 1LW9-EM-solvated" of "Energy minimization of the solvated system", it says " Converged to machine precision , but not to the requested pr

RE: [gmx-users] Energy minimization of crystal structure with water

Hi Mark, Thanks - I completely forgot about that! Cheers, Huiwen From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham Sent: Sunday, March 18, 2012 2:03 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization of crysta

Fw: [gmx-users] number of coordinates in coordinate file does not match topology

Dear All,   The problem really occurs in the ion addition step.   In order to keep 0.1 M ion concentration, 20 Na+ and 20 C1- were added. In order to keep 0 charge, 8 Cl- were added.   From the .gro file, 48 water (72 H and 48 O) were deleted in order to add the 38 charges, which makes there was

Re: Fw: [gmx-users] number of coordinates in coordinate file does not match topology

Hi Acoot, Read the tutorial. It's explained there... Mind that that tutorial was written for an earlier version of Gromacs and some things have changed. The names of ions, for instance. Cheers, Tsjerk On Mar 19, 2012 6:40 AM, "Acoot Brett" wrote: Dear All, The problem really occurs in the io