[gmx-users] Gromacs 4.6.3 Installation Issues,

hi, i'm having difficulties installing gromacs by creating static links to the libraries for fftw3. i am currently running: cygwin1.7.24-1 cmake2.8.11.2-1 fftw33.3.3-1 this is the input that i'm attempting to utilize and flags errors (and some combination there of): cmake FFTW3F_INCLUDE_DIR=C:

[gmx-users] 'Command not found' after installation

Hello all, I have been trying to get GROMACS (4.6.3) to work on my Mac (10.8.1). I downloaded the latest Intel C++ compilers and built Gromacs successfully (at least it appeared to be successful since I saw no error messages). I appended this line to my ~/.profile file: source /usr/local/gromacs

Re: [gmx-users] 'Command not found' after installation

Try "g_luck". That's what has worked for me. On 08/24/2013 12:37 PM, Nimmy McNimmerson wrote: > Hello all, > I have been trying to get GROMACS (4.6.3) to work on my Mac (10.8.1). I > downloaded the latest Intel C++ compilers and built Gromacs successfully (at > least it appeared to be successful

[gmx-users] VDW Cut-off vs Switch with CHARMM force field

Hi! I am running explicit solvent simulations with the CHARMM force field implemented in gromacs 4.6.3. For VDW I have been using: rlist= 1.0 vdw-type = Cut-off rvdw = 1.0 in conjunction with PME and rcoulomb=1 for electrostatics. I wonder whether it would be more accurate to use ins

Re: [gmx-users] 'Command not found' after installation

"Barnett, James W." wrote: >Unfortunately this is now beyond what I know with a Mac. It sounds like a >library is missing that GROMACS needs, or GROMACS can't find it, which is >probably a simple fix. > >Perhaps someone more familiar with Mac will be able to weigh in. > >jbarn...@tulane.edu |

Re: [gmx-users] VDW Cut-off vs Switch with CHARMM force field

CHARMM is generally used with vdw switching between 1.0 and 1.2 nm - I presume it must be more accurate that way. There are a number of discussions on this already. Justin recommended using rlistlong 1.4 as well I think. You might want to use a short range cutoff (rcoulomb) of 1.2 for PME as wel

Re: [gmx-users] VDW Cut-off vs Switch with CHARMM force field

Here is a relevant previous discussion http://lists.gromacs.org/pipermail/gmx-users/2013-May/081425.html Best wishes James On 25 Aug 2013, at 00:28, James Krieger wrote: > CHARMM is generally used with vdw switching between 1.0 and 1.2 nm - I > presume it must be more accurate that way. There

Re: [gmx-users] VDW Cut-off vs Switch with CHARMM force field

Thanks James! I was also wondering whether there is a significant penalty in performance if I use rlist=1.2 instead of rlist=1.0 There has already been a discussion in the NAMD mailing list about the VDW cutoff issue: http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/7551.html It is

Re: [gmx-users] VDW Cut-off vs Switch with CHARMM force field

On 8/24/13 8:19 PM, Gianluca Interlandi wrote: Thanks James! I was also wondering whether there is a significant penalty in performance if I use rlist=1.2 instead of rlist=1.0 I doubt one would consider it "significant," but of course any time you decrease rlist, you potentially speed up t

[gmx-users] Help with Error Message

So I started following some tutorials online since I didn't get a response last time. the tutorial I'm using is: http://nmr.chem.uu.nl/%7Etsjerk/course/molmod/ I followed that tutorial to the second page and got stuck at the step where it asks you to input: pdb2gmx -f protein.pdb -o protein.gro -p

Re: [gmx-users] Help with Error Message

It sounds like you dont have the .pdb file in your working directory. Perhaps you need to learn a bit about unix filesystems On Sat, Aug 24, 2013 at 6:18 PM, The One And Only wrote: > So I started following some tutorials online since I didn't get a response > last time. the tutorial I'm using i

Re: [gmx-users] Help with Error Message

that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis within a week so I'm pretty desperate right now in te

Re: [gmx-users] Help with Error Message

On 8/24/13 9:26 PM, The One And Only wrote: that's something i know nothing about; I just graduated from high school and I have no background or experience in open source projects or programs like pymol/gromacs. My professor wants me to be able to produce a setup, simulation, and analysis withi

Re: [gmx-users] Help with Error Message

so how do i solve the protein.pdb issue? On Sat, Aug 24, 2013 at 6:37 PM, Justin Lemkul wrote: > > > On 8/24/13 9:26 PM, The One And Only wrote: > >> that's something i know nothing about; I just graduated from high school >> and I have no background or experience in open source projects or pro

Re: [gmx-users] Help with Error Message

Never mind, I'm dumb. I just realized that protein.pdb means i have to specify which protein i want like "1qlz.pdb" and not actually type "protein.pdb" BUT THANKS GUYS!! On Sat, Aug 24, 2013 at 6:40 PM, The One And Only wrote: > so how do i solve the protein.pdb issue? > > > On Sat, Aug 24, 2013

[gmx-users] Ok now what?

I've been able to set up everything correctly according to the tutorial I found on the website. I got the following error when I typed: grompp -v -f minim.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o 1qlz-EM-solvated.tpr Ignoring obsolete mdp entry 'title' Ignoring obsolete mdp entry 'cpp' Back Off! I

RE: [gmx-users] Ok now what?

-Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of The One And Only Sent: Sunday, 25 August 2013 12:20 PM To: forum Subject: [gmx-users] Ok now what? I've been able to set up everything correctly according to the tutorial I found

Re: [gmx-users] VDW Cut-off vs Switch with CHARMM force field

vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 I'm confused about the difference between rlist and rlistlong. I am planning to also setup an implicit solvent simulation with GBSA and CHARMM-FF. Would this make sense? rlist= 1.4 c

[gmx-users] rvdw, rlist and rcoulomb for Amber03

Hi Justin, In a recent post (http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944) you commented that: "Unless you can demonstrate that your changes in cutoffs do not produce artifacts or lead to other inaccuracies using robust test s

[gmx-users] #coordinates do not match

I've tried the same process twice to two different proteins, but still got the same error that the #coordinates in the topology file did not match the #coordinates of the file I'm trying to use (1xyw-solvated.pdb). Below is the process I went through: *pdb2gmx -f 1xyw.pdb -o 1xyw.gro -p 1xyw.top -

Re: [gmx-users] #coordinates do not match

Hi, In *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral -pname NA -nname CL* , you have not used -p 1xys.top Consequently, I don't think the ions are written into your .top . Please check and see if grompp works. On Sun, Aug 25, 2013 at 9:34 AM, The One And Only wrote: > I've

Re: [gmx-users] #coordinates do not match

How do you decrease the number of solvent molecules in a topology file? I think this will solve my problem. On Sat, Aug 24, 2013 at 9:08 PM, rajat desikan wrote: > Hi, > In *genion -s 1xyw-water.tpr -o 1xyw-solvated.pdb -conc 0.15 -neutral > -pname NA -nname CL* , you have not used -p 1xys.top

Re: [gmx-users] 'Command not found' after installation

Hi, Apparently this is an issue with my intel compiler; the dynamic linker isn't finding the libiomp5.dylib library. However, I don't know how to fix this (the google results haven't worked.) Please help, Thanks, John From: "Barnett, James W." To:  Sent: