Hi,
I am trying to use two types of force fields for my system which has protein
and fullerene. i want to use OPLS for protein and ffG53a6 for fullerene(as i
don't have opls readily available for this). When i use two itp files in
#include section grompp does not allow me to do that with the
Hi Gromacs users,
I am trying to run a fullerene simulaton in TIP4P water model, i am using
the c70_G53a6.itp http://tfy.tkk.fi/soft/downloads/files/c70_G53a6.itp
file downloaded from http://tfy.tkk.fi/soft/downloads/. i have added TIP4P
water model using genbox command, later when i am trying
, but
i suspect some thing is going wrong with atom types in .atp file.
any suggestions?
Thanks
Srinivs.
On Fri, Jul 22, 2011 at 5:11 PM, Justin A. Lemkul jalem...@vt.edu wrote:
jampani srinivas wrote:
Hi Gromacs users,
I am trying to run a fullerene simulaton in TIP4P water model, i am
Oh sorry, i used spc.itp now and it works.
Thanks.
Srinivas.
On Fri, Jul 22, 2011 at 5:48 PM, Justin A. Lemkul jalem...@vt.edu wrote:
jampani srinivas wrote:
Hi Justin,
Thanks for your reply, i have no particular choice i was using it for my
other work and just started with it.
Now i
Hi
Try with -dd 2 x 2 x 2 option with 8 nodes and check the performance. I too
got the same problems, i could overcome with symmetrical -dd option.
Srinivas.
On Fri, May 7, 2010 at 8:57 AM, irene farabella
i.farabe...@mail.cryst.bbk.ac.uk wrote:
Hello!
I am new to Gromacs and especially at
Dear Berk,
Yes the system is stable and the small velocity appears only at step 0 as
you said.
This looks fine now, Thanks a lot for you continuous support
Thanks very much.
Srinivas.
On Mon, Apr 26, 2010 at 7:43 AM, Berk Hess g...@hotmail.com wrote:
Hi,
So the system seems to be stable
Dear Berk,
First of all thanks very much for your kind patience and help. As a new user
i am facing some problems and not clear about many options and how to use
them. I was reading several messages of yours from mailing list which are
very close to my problem.
After reading several of them from
Dear Berk,
I have run it for 5ns, as you said for first 1ns i have not seen much drift
in the energy there after energy is slowly increasing in each step. Should i
run it again and send you the edr file? can you please let me know on which
version of gromacs you have run this file?
Thanks very
Dear Berk,
I am sorry for poor communication, Herewith i am giving my md.mdp file. I
this file as you could see i am using two temp coupling groups Tmp1 is
protein and a 2nm spherical layer of water around it, and the second one
Tmp2 which has only water. Now i want to fix the Tmp2 and apply 0 K
Srinivas.
On Fri, Apr 9, 2010 at 1:26 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 9/04/2010 1:25 PM, jampani srinivas wrote:
Dear Justin,
I am sorry for the poor description of the problem, OK let me explain
you clearly here.
I have taken a decapeptide and solvated it with box size
.
On Wed, Apr 7, 2010 at 4:47 PM, ms deviceran...@gmail.com wrote:
jampani srinivas ha scritto:
Dear Berk,
I am sorry if i am confusing you with my poor description of problem,
actually I have submitted simulation with two temperature coupling groups
(i
think you already know that from
Thanks
Srinivas.
On Thu, Apr 8, 2010 at 7:52 PM, Justin A. Lemkul jalem...@vt.edu wrote:
jampani srinivas wrote:
Hi
Thanks for your response, I am allowing the two groups (frozen and
non-frozen) groups interact each other, i guess i am getting the energy of
total system from
please help me to solve this problem?
Thanks very much for your kind help.
Srinivas.
On Wed, Mar 17, 2010 at 8:25 PM, jampani srinivas jampa...@gmail.comwrote:
Dear Berk,
Sorry for the delayed reply, We have compiled the gromacs with readir.c
that you have sent me, now it is working fine
Dear All,
I am running MD simulation with TIP4P water and OPLS force field in NVT and
NVE. I have noticed a continuous energy increase in both NVE and NVT
simulations when i freeze a selected portion of my system. Recently i had
problem with temperature coupling, Berk has sent me a file which has
Dear Zuzana,
Recently i have done similar selection, I have got this error only when i
miss some atoms or when i have some atoms in both groups. I would suggest
you to check your groups carefully or you can make indexes for these
selections in VMD and check whether you are missing some atoms from
Dear Berk,
Sorry for the delayed reply, We have compiled the gromacs with readir.c
that you have sent me, now it is working fine.
Thank you very much for your kind help.
Srinivas.
On Wed, Mar 3, 2010 at 1:56 PM, jampani srinivas jampa...@gmail.comwrote:
Dear Berk,
Thanks for your
, 2010 at 5:37 PM, jampani srinivas jampa...@gmail.comwrote:
Dear Berk,
I have checked my inputs and tcl scripts that i have used for
the selection, i could see that my selection doesn't have any problem.
I submitted it again still i am getting the same log file with nrdf 0 for
non-freezing
Dear Berk,
Thanks for your previous responses, Can you please let me know if you have
any solution for the size of freezing groups? I am still not able to do if i
have larger freezing groups.
Thanks again for your kind help.
srinivas.
On Fri, Feb 26, 2010 at 5:37 PM, jampani srinivas jampa
Dear Berk,
Thanks for your response, As you mentioned i have separated t-coupling group
for frozen and non-frozen groups, still the result is same.
Herewith i am giving my md.mdp file, Can you suggest me if i am missing any
options in my md.mdp file?
Thanks again
Srinivas.
md.mdp file
HI
Thanks, My log file shows me nrdf: 0
###
grpopts:
nrdf: 0
ref_t:0
tau_t: 0
###
Thanks
Srinivas.
On Fri, Feb 26, 2010 at 10:25 AM, Berk Hess g...@hotmail.com wrote:
Hi,
Then I have no clue what might be wrong.
Hi Berk,
I am extremely sorry, here is the correct log file
grpopts:
nrdf: 0 0
ref_t: 300 0
tau_t: 0.1 0.1
Thanks
Srinivas.
On Fri, Feb 26, 2010 at 11:01 AM, Berk Hess g...@hotmail.com wrote:
Dear Berk,
It looks to me some thing is wrong when i change the radius from 35 to 25,
herewith i am giving grpopts for both systems
+
grpopts: (system with 35 A)
nrdf: 33141.4 0
ref_t: 300 0
tau_t: 0.1 0.1
Dear Berk,
They are same, freeze and Tmp2 are exactly the same groups. I just put them
like that for my convenience, just to avoid confusion in my second email i
made it uniform.
Thanks
Srinivas.
On Fri, Feb 26, 2010 at 11:59 AM, Berk Hess g...@hotmail.com wrote:
That is what I suspected, by
Dear Berk,
I am using VERSION 4.0.5. As you said if there is no problem i should get it
correctly, i don't know where it is going wrong. I have written a small
script in tcl to use in vmd to get my selections. i will check the script
and the selection again. I will let you know my results again.
, and help me if you have solution for this problem.
Thanks and Regards
Srinivas.
On Fri, Feb 26, 2010 at 12:39 PM, jampani srinivas jampa...@gmail.comwrote:
Dear Berk,
I am using VERSION 4.0.5. As you said if there is no problem i should get
it correctly, i don't know where it is going wrong
Dear all,
I am sorry for poorly describing my problem about the freezing group size.
Here I am giving my question very briefly, can anybody help me please?
I would like to know the relation between the size of freezing group and the
temperature coupling. when I separate the temperature coupling
Dear Gromacs Users,
I would like to compare the diffusion coefficient of water in different
confined spheres with the bulk solvent, I have taken a solvent box of size
7nm, and I have created a sphere with radius 25 Å as lowest and 35 Å as
highest spheres. I have not used the pressure coupling for
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