Sarah Witzke wrote:
Dear gmx-users,
I have done simulations of one small molecule that diffuses into a DMPC
membrane. This small molecule contains an alcohol group and is therefore
capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol
region).
I have read the manual (se
Dear gmx-users,
I have done simulations of one small molecule that diffuses into a DMPC
membrane. This small molecule contains an alcohol group and is therefore
capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol
region).
I have read the manual (section 8.12 and g_hb
ms wrote:
Hi,
I would like to understand a basic question about the usage of tabulated
potential for non-bonded interaction. If I use an arbitrary function and
I write a table for it, is the functional shape then applied to *all* my
atoms, or can I specify which ones use the tabulated potential
Chih-Ying Lin wrote:
HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I
simulate the protein and ligand system and then calculate the MSD of the
ligand. Then, i drew the plot of the time evolution of the MSD. But the
the MSD decreases as time for some period. I see not
HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I
simulate the protein and ligand system and then calculate the MSD of the
ligand. Then, i drew the plot of the time evolution of the MSD. But the the
MSD decreases as time for some period. I see nothing about my codings. Would
yo
Hi,
I would like to understand a basic question about the usage of tabulated
potential for non-bonded interaction. If I use an arbitrary function and
I write a table for it, is the functional shape then applied to *all* my
atoms, or can I specify which ones use the tabulated potential -and how?
T
Hi,
The problem that I fixed last week occured after the use of g_covar -mwa
with a fit selection that is not the first N atoms of the system.
Berk
> Date: Tue, 17 Nov 2009 18:03:37 +0100
> Subject: Re: [gmx-users] segmentation fault in g_anaeig
> From: tsje...@gmail.com
> To: gmx-users@gromacs
Hi Nilu,
Can you paste the exact commands you entered, and indicate the
selections you made? Oh, and can you check the archives to whether
this is the same problem that was reported a few weeks ago?
Cheers,
Tsjerk
On Tue, Nov 17, 2009 at 5:53 PM, Nilu Chakrabarti
wrote:
> I am used to do PC an
I am used to do PC analysis with g_covar followed by g_anaeig.
But recently, I am getting segmentation fault with g_anaeig.
The g_covar gives eigenval.xvg, eigenvec.trr and average.pdb.
In the next step I use those 3 files to generate -
(1) a projection of each individual vectors on the traj using
Nilesh Dhumal wrote:
Tsjerk,
When I open di.pdb (output file) in VMD. I see all CL are repalced by C.
I can't go to next step. What information do you want more. I checked the
format of pdb file again. Its looks dioxin.pdb is ok. After running
pdb2gmx, the di.pdb output file don't have any CL
Tsjerk,
When I open di.pdb (output file) in VMD. I see all CL are repalced by C.
I can't go to next step. What information do you want more. I checked the
format of pdb file again. Its looks dioxin.pdb is ok. After running
pdb2gmx, the di.pdb output file don't have any CL atom. Hopes you get me
n
Oops, there's an .rtp entry. Shame on me :$
Maybe a good idea though to post the output of pdb2gmx.
Cheers,
Tsjerk
On Tue, Nov 17, 2009 at 3:44 PM, Tsjerk Wassenaar wrote:
> Justin,
>
>> What is the problem? It looks like you got everything to work, but the .pdb
>> file you've posted is misfor
Justin,
> What is the problem? It looks like you got everything to work, but the .pdb
> file you've posted is misformatted on the CL lines:
>
> ATOM 14 C14 PCD 1 -2.372 -1.395 0.000 1.00 0.00
> C
> ATOM 15 CL1 PCD 1 5.070 1.618 -0.001 1.00 0.00
> CL
>
> Not
Orca is free for example. Apparently, there's an implementation for Gromacs.
Please send flowers and chocolate directely to Villa Bosch, where I am
working. You find the adress on the internet ;)
Quoting Farzad Molani :
Hi Ilona,
I saw the web adress. unfortunetly we don't have gaussia
Nilesh Dhumal wrote:
here is all information. I attached 2 attachment to my privious mail. It
looks 2nd didn't come. Sorry. Here I am giving details.
I am using opls force field . I added "PCD" as residue name in
aminoacid.dat file.
pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter
i have atta
here is all information. I attached 2 attachment to my privious mail. It
looks 2nd didn't come. Sorry. Here I am giving details.
I am using opls force field . I added "PCD" as residue name in
aminoacid.dat file.
pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter
i have attached input:dioxin.pdb, ou
karan syal wrote:
Dear All,
I am looking for urea topology* (smith et al) *for gromos 96 force
field. I tried searching through user contributions in gromacs site but
couldnt find it. Is it possible for anyone who has already used it to
mail me their toplogy file?
If the parameters are
Hi Ilona,
I saw the web adress. unfortunetly we don't have gaussian and gamess uk. I want
to calculate QM region by ab inition or DFT methods. which quantum mechanic
package do I use?
Farzad Molani,
Ph.D Student,
Department of Theoretical Chemistry and Biochemistry,
K. N. Toosi University of Te
Hi,
I would also like to be sure that everything works as I have intended it.
So I guess the following input should work:
pull = umbrella
pull_geometry= direction
pull_dim = N N Y
pull_start = no
pull_ngroups = 1
pull_group
http://www.kntu.ac.ir
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Message: 7
Date: Tue, 17 Nov 2009 09:37:28 +
From: "Kukol, A
Dear All,
I am looking for urea topology* (smith et al) *for gromos 96 force field. I
tried searching through user contributions in gromacs site but couldnt find
it. Is it possible for anyone who has already used it to mail me their
toplogy file?
--
gmx-users mailing listgmx-users@gromacs.org
GROMACS can do QM/MM.
Andreas
---
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Farzad Molani
Sent: 17 November 2009 08:57
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] access code for qmmm
Hello,
Have you ever done
Hello,
Have you ever done QM/MM? please introduce a free and good package for academic
user.
Thanks in advance
Farzad Molani,
Ph.D Student,
Department of Theoretical Chemistry and Biochemistry,
K. N. Toosi University of Technology,
Tehran, Iran.
Tel.: 009821 2306 4280
Fax: 009821 2285 3650
Web:
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