On Mon, Oct 5, 2015 at 7:03 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 10/5/15 2:01 PM, Rasoul Nasiri wrote:
>
>> On Mon, Oct 5, 2015 at 6:52 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>>
>>
>>>
>>> On 10/5/15 1:50 PM, Pall
This non-zero value becomes quite significant if you are dealing with
highly flexible molecules -
Internal molecular dynamics effects are different in the gas and liquid
phases.
Rasoul
On Mon, Oct 5, 2015 at 3:53 PM, Pallavi Banerjee <
pallavis...@students.iiserpune.ac.in> wrote:
> Hello
On Mon, Sep 22, 2014 at 7:33 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/22/14 10:45 AM, Александр Селютин wrote:
Thanks to everyone
I have idea that I can stop simulation, change topology(move end of
molecule, add new atoms) and start again. It should be repeated every 2
ps.
But it
On Mon, Jul 14, 2014 at 12:51 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/13/14, 8:41 PM, Rasoul Nasiri wrote:
On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/13/14, 7:11 PM, Rasoul Nasiri wrote:
On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul jalem
On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/12/14, 7:25 AM, Rasoul Nasiri wrote:
On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Note that two constrained atoms correspond to one constraint.
C12H26
26 constrained atoms due
On Mon, Jul 14, 2014 at 1:02 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/13/14, 7:11 PM, Rasoul Nasiri wrote:
On Sun, Jul 13, 2014 at 2:27 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/12/14, 7:25 AM, Rasoul Nasiri wrote:
On Sat, Jul 12, 2014 at 12:17 PM, Tsjerk Wassenaar tsje
On Sat, Jul 12, 2014 at 8:03 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Please just tell me how values of obtained T by g_traj can be corrected
when I use trajectory and tpr files of constrain MD simulations (OPLS) as
an input?
T(corrected) = T(g_traj)*natoms/(natoms-nconstraints)
constrained atoms
in cell.
Cheers,
T.
Rasoul
On Jul 12, 2014 12:01 PM, Rasoul Nasiri nasiri1...@gmail.com wrote:
On Sat, Jul 12, 2014 at 8:03 AM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Please just tell me how values of obtained T by g_traj can be corrected
when I use trajectory
On Fri, Jul 11, 2014 at 10:27 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/10/14, 9:30 PM, Rasoul Nasiri wrote:
On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/10/14, 7:09 PM, Rasoul Nasiri wrote:
Because
1- Estimation of T for different sub-systems say
Hi,
Can anybody tell me why these two tools give different temperature values
based on same trajectory and input files?
1- g_energy_d -f md_shor.edr -s topol_shor.tpr -o T.xvg
0.00 508.066786
1.00 496.066137
2.00 501.665712
3.00 498.809896
4.00
Is there any other (not g_energy) tools in GROMACS to estimate T properly?
Rasoul
On Thu, Jul 10, 2014 at 5:51 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/10/14, 12:49 PM, Rasoul Nasiri wrote:
Hi,
Can anybody tell me why these two tools give different temperature values
based on same
On Fri, Jul 11, 2014 at 12:58 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/10/14, 7:09 PM, Rasoul Nasiri wrote:
Because
1- Estimation of T for different sub-systems say phases of gas, interface
and liquid.
Can be obtained with g_energy?
No, not unless they are assigned as separate tc
Why do you think positive values are doubtful?
What matters are energy differences between different snapshots
The absolute energy is meaningless in the FF framework.
Rasoul
On Tue, May 13, 2014 at 3:59 PM, Bryan Roessler roess...@uab.edu wrote:
Did you hit your nsteps limit? 2 probably
See following paper for modelling of initial steps of glycation process
protein:
http://www.tandfonline.com/doi/abs/10.1080/07391102.2010.10507354#preview
For study of advanced glycation end processes, there is nothing to do with
emperical FF,
you need to use QC approches;
see following papers
On Mon, Dec 23, 2013 at 9:40 AM, Rasoul Nasiri nasiri1...@gmail.com
wrote:
Many thanks Tsjerk,
Let me ask another question. As you know in most cases of analysis, one
needs to have tpr file along with the trajectory.
How can I construct it? The potential that I'm using in my MD
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