On Wed, Apr 3, 2013 at 4:56 AM, Elisabeth wrote:
> Hi Vitaly,
>
> I realize that when one extends the Z direction the resulting interface is
> liquid-vacuum, but I see that even at T below boiling point some molecules
> still leave the interface and enter the empty zone and are added to the
> oth
Sorry, meant to post this on the bb.
Gesendet: Dienstag, 02. April 2013 um 11:50 Uhr
Von: "lloyd riggs"
An: vvcha...@gmail.com
Betreff: Aw: Re: [gmx-users] Re: density profile
How would you set up a gas/gas interface, say modeled after a large gas planet or upper atmospher
There is a wonderful data page devoted to methane in wikipedia...
It follows from this webpage that you will get a perfect density profile if
you decrease your T down to 150K...
On Mon, Apr 1, 2013 at 8:37 PM, Dr. Vitaly Chaban wrote:
>
>
>
> On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth wrote:
>
On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth wrote:
> You are right. I compressed my alkane system under NPT at 400 K at 100
> bar. The normal boiling point is below 425 K. So it seems there in no way
> one can obtain profiles obove boiling point of liquid given than with the
> current NVT recipe mo
On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth wrote:
> Hi Vitaly,
>
> The problem was with cpt file since it re sets the last line of gro. I
> removed the -f flag and now the Z direction is extended. However, I see
> that molecules tend to fill up the upper zone (free space) rapidly. I am
> wondering
Hi Vitaly,
The problem was with cpt file since it re sets the last line of gro. I
removed the -f flag and now the Z direction is extended. However, I see
that molecules tend to fill up the upper zone (free space) rapidly. I am
wondering how I can obtain the density profile if I am going to get ano
Justin -
I am sure mdrun reads coordinates from -cpi state.cpt
Vitaly
On Mon, Apr 1, 2013 at 7:44 PM, Justin Lemkul wrote:
>
>
>
> On Mon, Apr 1, 2013 at 1:29 PM, Dr. Vitaly Chaban wrote:
>
>> It is something very new for me.
>>
>> If structure, etc are not read from CPT files, why do
It is something very new for me.
If structure, etc are not read from CPT files, why does one need them for...
On Mon, Apr 1, 2013 at 7:21 PM, Justin Lemkul wrote:
>
>
>
> On Mon, Apr 1, 2013 at 1:14 PM, Dr. Vitaly Chaban wrote:
>
>> I think if you use checkpoint files, the program does not rea
On Mon, Apr 1, 2013 at 1:14 PM, Dr. Vitaly Chaban wrote:
> I think if you use checkpoint files, the program does not read either MDP,
> or GRO, or TOP, or anything except CPT.
>
>
>
I would have to check the code to be sure, but that is certainly not true
in the case of the .mdp file. That is alw
I think if you use checkpoint files, the program does not read either MDP,
or GRO, or TOP, or anything except CPT.
Dr. Vitaly Chaban
On Mon, Apr 1, 2013 at 7:10 PM, Elisabeth wrote:
> Hi vitaly,
>
> The initial structure is indeed extended but the final output.gro is not.
> I think its beca
Hi vitaly,
The initial structure is indeed extended but the final output.gro is not. I
think its because I am using the cpt file from the previous NPT runs as
input for the new runs? Do I have to remove the -t flag?
On 1 April 2013 12:47, Dr. Vitaly Chaban wrote:
> Hi Elisabeth -
>
> The only
Hi Elisabeth -
The only explanation is that you actually DID NOT extend the box in Z
direction. Look at the last line of confout.gro.
g_density -d Z gives you a [local] density versus Z coordinate.
Dr. Vitaly Chaban
On Mon, Apr 1, 2013 at 5:33 PM, Elisabeth wrote:
> Hi Vitaly,
>
> I did N
Hi Elisabeth -
On Sun, Mar 31, 2013 at 8:28 PM, Elisabeth wrote:
> Thanks Vitaly. I am wondering what is the use of semiisotropic with 0
> compressibility in Z then? I was hoping to run NPT to secure a fixed
> pressure.
>
Please, read about Gibbs phase rule... This is your case.
Anisotropic
Thanks Vitaly. I am wondering what is the use of semiisotropic with 0
compressibility in Z then? I was hoping to run NPT to secure a fixed
pressure.
I also wanted to know if surface tension can be also calculated under NVT
(if NPT fails for this puporse)
Thanks!
On 31 March 2013 14:01, Dr. Vital
> Thanks Justin for your reply. To avoid compressing down the cell I thought
> using semiisotropic option with 0 compressibility in Z would be
> appropriate.
>
>
You must use NVT only. Otherwise, the cell will compress in XY directions
to compensate its inability to compress in Z direction.
>
Dear Ali:
I am not sure what ecenter is, it looks like it might be the position to which
the user wants to set the center?
In any event, it doesn't mater for this modification.
I did not write the center_x() function, it is a standard part of gmx_trjconv.c
What I did was to copy center_x() to
tekle...@ualberta.ca wrote:
Dear Gromacs Users,
I run an MD simulation of a pure solvent and found out that the density
of the solvent deviated a little bit from the actual experimental data.
MD density is 880g/ml and the experimental data is 866g/ml. Is this
reasonable for toluene solvent
tekle...@ualberta.ca wrote:
Thank you Justine
I have another question. I run my simulation for 5ns and when i just
check the density of my solvent, the density did not look right. I used
the N-H and P-R for the thermostat and barostat. Both shows the correct
temperature and pressure (300K a
Thank you Justine
I have another question. I run my simulation for 5ns and when i just
check the density of my solvent, the density did not look right. I
used the N-H and P-R for the thermostat and barostat. Both shows the
correct temperature and pressure (300K and 1bar). when I use the
g
What do you mean the value for methane? As in the charges? This is my
topology file and I am using OPLS-AA for methane.
Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Namenrexcl
Methane3
[ atoms ]
; nr type resnr residue atom cgnr
>
> I am trying to get an rdf graph actually, and my values are very close
> to one, but not exactly one, and I was wondering if there is some
> normalization issue with g_rdf? These are my values for rdf:
>
> 0 0
> 0.002 0
> 0.004 0
> 0.006 0
>
Hi,
This force field was designed to be used with constraints.
First try running with constraints set to all-bonds and without -DFLEXIBLE and
check
the densities again.
Berk
> Date: Mon, 1 Feb 2010 16:58:44 +0100
> From: ana...@fundp.ac.be
> To: gmx-users@gromacs.org
> Subject: [g
I have changed tau_t=0.2 for 1.0 but the density is not restored. I have tried
with the parameters from Villa and Mark (J Comput Chem, 2002, 23, 548)
, tau_t=0.2 and tau_p=2.0 and still get the same density. The self-diffusion
coefficient is indeed half of that with md with sd and tau_t=0.2 (0.7
xianghong qi wrote:
Yes, you are right. I didn't apply pressure coupling and my simulation
is under NVT.
I just want to get the density of water vs time . Thanks so much .
You need to apply NPT conditions to get density information.
-Justin
-Xianghong Qi
On Wed, Nov 5, 2008 at 4:32 PM,
de 2008 10:18 p.m.
> *Para:* Discussion list for GROMACS users
> *Asunto:* [gmx-users] Re: density vs time?
>
>
>
> Hello, all:
>
> I checked the mailing list. Looks like g_energy can calculate density vs
> time, but
> my g_energy doesn't have options like density, vol
Yes, you are right. I didn't apply pressure coupling and my simulation is
under NVT.
I just want to get the density of water vs time . Thanks so much .
-Xianghong Qi
On Wed, Nov 5, 2008 at 4:32 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> Justin A. Lem
Are you working at constant volume? It would be useful to see your mdp file
Angel.
De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] En
nombre de xianghong qi
Enviado el: miércoles, 05 de noviembre de 2008 10:18 p.m.
Para: Discussion list for GROMACS users
Asunto: [gmx-users] Re: density
Justin A. Lemkul wrote:
Justin A. Lemkul wrote:
xianghong qi wrote:
Thanks, Justin:
I use 4.0. Mine is here:
---
1 LJ-(SR) 2 Disper.-corr.3 Coulomb-(SR) 4
Coul.-recip. 5 Potential6 Kineti
Justin A. Lemkul wrote:
xianghong qi wrote:
Thanks, Justin:
I use 4.0. Mine is here:
---
1 LJ-(SR) 2 Disper.-corr.3 Coulomb-(SR) 4
Coul.-recip. 5 Potential6 Kinetic-En. 7
Total-Energy
xianghong qi wrote:
Thanks, Justin:
I use 4.0. Mine is here:
---
1 LJ-(SR) 2 Disper.-corr.3 Coulomb-(SR) 4
Coul.-recip.
5 Potential6 Kinetic-En. 7 Total-Energy 8
Temperature
9
Thanks, Justin:
I use 4.0. Mine is here:
---
1 LJ-(SR) 2 Disper.-corr.3 Coulomb-(SR) 4
Coul.-recip.
5 Potential6 Kinetic-En. 7 Total-Energy 8
Temperature
9 Pressure-(bar) 10 Vir-XX
xianghong qi wrote:
Hello, all:
I checked the mailing list. Looks like g_energy can calculate density vs
time, but
my g_energy doesn't have options like density, volume? I am wondering
how I can
get my density vs time graph? Any suggestion is appreciated. Thanks.
Look more closely. Bot
Hello, all:
I checked the mailing list. Looks like g_energy can calculate density vs
time, but
my g_energy doesn't have options like density, volume? I am wondering how I
can
get my density vs time graph? Any suggestion is appreciated. Thanks.
-Xianghong Qi
--
Some people make the world mor
huan wrote:
Dear Justin and all gmx users,
I double checked the density graph (obtained by using g_energy, option 18)
which is a energy at y-axis and time at the x-axis. but how can i get a density
vs time graph?
g_energy defaults to kJ/mol as its unit, but in the case of density it
calculation and assuming 18 g for the molar mass of water
Peter Nagy
From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED]
Sent: Thu 12/13/2007 5:04 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: Density Deferences between spc216 and tip4p
Dear Jochen
[EMAIL PROTECTED] wrote:
Dear Jochen,
Sorry to bother you. I did not calculate the densities it is the program
output!. Is this a bug?.
Sorry to say that, but I don't have the feeling that it's my job to find
the error in your calcuation...
Regards
Chandu
Message: 8
Date: Thu, 13 Dec 2
Chandu,
It's clear you didn't do the calculations. Please do them yourself and see
what answer you get for the density of 32885 water molecules in a box with
volume 10^3 nm^3. Note also that there may be implicit assumptions
underlying the value of the density provided by genbox, but it's the numb
Dear Jochen,
Sorry to bother you. I did not calculate the densities it is the program
output!. Is this a bug?.
Regards
Chandu
> Message: 8
> Date: Thu, 13 Dec 2007 10:28:02 +0100
> From: Jochen Hub <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] Density Deferences between spc216 and tip4p
> w
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