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:
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
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
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 -
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
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
-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
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
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
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
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
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
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
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
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
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
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
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
"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 |
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
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
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
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:
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