Dear Gromacs Users!
I'm simulating membrane receptor embedded in the explicit membrane
using charmm36 ff.
My simulation setup consist of
; Compound#mols
Protein 1
iso 1
POPC 228
SOL 11713
NA 66
CL 70
I've done
Thank Justin and Tsjerk so much for your help !
I will try smaller time step. And i hope it work :-)
Regards,
KT
On Mon, Jan 28, 2013 at 10:19 AM, Tsjerk Wassenaar wrote:
> Well, 20-30 fs is fine with Martini. But you may have to take care
> initially, and start with a smaller time step.
>
> Ch
Dear EB
Thank you very much.
Now, it works and looks OK to me.
Regards
Kenji
- Original Message -
>> From: Emanuel Birru
>> To: 'Discussion list for GROMACS users'
>> Date: 2013-01-28 14:04:37
>> Subject: RE: [gmx-users] making .top file of new LJ in Water
>>
>> Hi Kenji,
>>
>> I
Hi Kenji,
I guess if you change/swap the order of molecules in top file it will work. The
order of molecules in your gro file should match up with your top file. If you
give us more info it would be good :) I am just guessing :(
[ molecules ]
SOL 1088
LJN 1
Swap them like this
Cheers,
Dear gmx users
I would like to start MD simulation for GAS Hydrate,
consisting of TIP4P and LJ representing N2.
I have made .top file by hand as following.
When I use grompp_d for making .tpr file,
I got the following error.
However, LJ name in .gro file is same as in .top file, which is "NX"
Dear Gromacs experts,
I am running gromacs for the first time, and this is my em.mdp file.
define = -DFLEXIBLE
constraints = none
integrator = steep
dt = 0.01 ; ps !
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier
Well, 20-30 fs is fine with Martini. But you may have to take care
initially, and start with a smaller time step.
Cheers,
Tsjerk
On Mon, Jan 28, 2013 at 3:11 AM, Justin Lemkul wrote:
>
>
> On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:
>
>> @Justin,
>> Fmax=8.0226669e+00
>>
>
> OK, that looks goo
On 1/27/13 9:56 PM, Xu Dong Huang wrote:
If I don't specify -extend (time) , will it automatically use the time step
defined in the .tpr i'm using?
Runs can be extended with -extend, -until, or with -nsteps. If you don't apply
any of those, then yes, the number of steps in the .tpr file i
If I don't specify -extend (time) , will it automatically use the time step
defined in the .tpr i'm using?
Or should I just define the time anyway ?
Thanks
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 27, 2013, at 9:54 PM, Xu
Thank you. I was just reading that as well, but didn't realize it could also be
used to extend. I thought it was just runs that terminated early.
Thanks
Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering
xudo...@eden.rutgers.edu
On Jan 27, 2013, at 9:51 PM, Justin
On 1/27/13 9:49 PM, Xu Dong Huang wrote:
Dear advanced users,
I'm trying determine the procedure for extending NPT run (i.e I realized the
NPT run I did wasn't long enough, so I wish to run it for another million
steps. ) what should I do to set up the run again continuing with the previous
Dear advanced users,
I'm trying determine the procedure for extending NPT run (i.e I realized the
NPT run I did wasn't long enough, so I wish to run it for another million
steps. ) what should I do to set up the run again continuing with the previous
data?
Thanks,
Xu Dong Huang
Chemical & B
On 1/27/13 12:15 PM, Kieu Thu Nguyen wrote:
@Justin,
Fmax=8.0226669e+00
OK, that looks good.
the system includes protein, lipid, water, ion Cl-
em.mdp file is
integrator = steep
tinit= 0.0
dt = 0.02
nsteps = 5
n
@Justin,
Fmax=8.0226669e+00
the system includes protein, lipid, water, ion Cl-
em.mdp file is
integrator = steep
tinit= 0.0
dt = 0.02
nsteps = 5
nstcomm = 1
nstxout = 5000
nstvout
It is 15 ns of NPT equilibration and I have not got a proper npt output yet to
go to the MDrun. Because when I run the -mdrun command, I get fatal error as
water molecule can not be settled.
I guess that the system might need more equilibration.
These are the settings of my npt.mdp file. The
On 1/27/13 3:39 AM, Sathish Kumar wrote:
-- Forwarded message --
From: Sathish Kumar
Date: Sun, Jan 27, 2013 at 2:02 PM
Subject: REgarding for the disulphide bond
To: gmx-users@gromacs.org
Sir,
I am sathish kumar working as junior research fellow.I have taken
pdb fi
Using ICC 13.0, I got a same result.
--
View this message in context:
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Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.or
-- Forwarded message --
From: Sathish Kumar
Date: Sun, Jan 27, 2013 at 2:02 PM
Subject: REgarding for the disulphide bond
To: gmx-users@gromacs.org
Sir,
I am sathish kumar working as junior research fellow.I have taken
pdb file from protein data bank.I need to break the
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