Re: [gmx-users] Re: density profile
On Wed, Apr 3, 2013 at 4:56 AM, Elisabeth katesed...@gmail.com 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 other side due to PBC. as a result the density profile does not exactly go down to zero but tends to zero anyways. I was wondering if this is considered a liquid-vapor interface? YES or it is still liquid-vacuum? thanks! On 1 April 2013 14:43, Dr. Vitaly Chaban vvcha...@gmail.com wrote: 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 vvcha...@gmail.comwrote: On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth katesed...@gmail.com 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 molecules tend to fill up the free zone no matter how much pressure was applied in the previous NPT runs? You cannot get a profile just because you have NO LIQUID and NO INTERFACE upon these conditions. Gas fills all the available space, there is no such thing as gas/gas interface. And yeah... Forget about NPT and learn the Gibbs phase rule. Dr. Vitaly Chaban On 1 April 2013 14:22, Dr. Vitaly Chaban vvcha...@gmail.com wrote: On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth katesed...@gmail.comwrote: 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 another uniformly distributed box after this NVT run? Here we come to the question what your system is composed of... Based on the density profile, this is not a (conventional) liquid... Polymer, non-Newtonian liquid ... or what? If molecules tend to fill vacuum, it can only mean that the matter you are simulating is above critical point. What is your T and what are the particles in your box? Dr. Vitaly Chaban I am expecting to see how density changes with Z at the solvent -vacuum interface Please advise me on this,, Thanks! On 1 April 2013 13:14, Dr. Vitaly Chaban vvcha...@gmail.com wrote: 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 katesed...@gmail.comwrote: 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 vvcha...@gmail.comwrote: 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 katesed...@gmail.comwrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Fw: Aw: Re: [gmx-users] Re: density profile
Sorry, meant to post this on the bb. Gesendet:Dienstag, 02. April 2013 um 11:50 Uhr Von:lloyd riggs lloyd.ri...@gmx.ch 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 atmosphere, without effects from garvity and pressures in the 10K plus ATM? In such a system the gases behave almost like liquids, but most effects are from extreems of conditions. Actaul interfaces though I assume would include large amounts of mixing right at the atomic level interface, but I have no clue how far this would extend. If you remove rotational effects, I am willing to bet you can model a gas/gas interface at the atomic level with extreem conditions, which might be an aset in some fileds/areas of research. Minus gravitational effects though, I do not know if they could work properly. You can however set up a ligid gas interface by introducing box systems with differences in force at a plain across the midpoint equal to gas/liquid interfaces, or gradients of force, etc...but in all cases I assume a minimal amount of programming might be necessary. Opinions/answers anyone? Stephan Watkins Gesendet:Montag, 01. April 2013 um 20:43 Uhr Von:Dr. Vitaly Chaban vvcha...@gmail.com An:Elisabeth katesed...@gmail.com, gmx-users@gromacs.org Betreff:Re: [gmx-users] Re: density profile 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 vvcha...@gmail.comwrote: On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth katesed...@gmail.com 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 molecules tend to fill up the free zone no matter how much pressure was applied in the previous NPT runs? You cannot get a profile just because you have NO LIQUID and NO INTERFACE upon these conditions. Gas fills all the available space, there is no such thing as gas/gas interface. And yeah... Forget about NPT and learn the Gibbs phase rule. Dr. Vitaly Chaban On 1 April 2013 14:22, Dr. Vitaly Chaban vvcha...@gmail.com wrote: On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth katesed...@gmail.com 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 how I can obtain the density profile if I am going to get another uniformly distributed box after this NVT run? Here we come to the question what your system is composed of... Based on the density profile, this is not a (conventional) liquid... Polymer, non-Newtonian liquid ... or what? If molecules tend to fill vacuum, it can only mean that the matter you are simulating is above critical point. What is your T and what are the particles in your box? Dr. Vitaly Chaban I am expecting to see how density changes with Z at the solvent -vacuum interface Please advise me on this,, Thanks! On 1 April 2013 13:14, Dr. Vitaly Chaban vvcha...@gmail.com wrote: 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 katesed...@gmail.comwrote: 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 vvcha...@gmail.com wrote: 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 katesed...@gmail.comwrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http
Re: [gmx-users] Re: density profile
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 katesed...@gmail.com wrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
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 vvcha...@gmail.com wrote: 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 katesed...@gmail.com wrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
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 katesed...@gmail.com wrote: 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 vvcha...@gmail.com wrote: 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 katesed...@gmail.com wrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
On Mon, Apr 1, 2013 at 1:14 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: 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 always read. I want to say that the coordinate file is required as well, though that would be an easy test using grompp. It should be easy to track the box vectors from the .edr file to see what the initial value was, to see if it came from the .cpt or .gro file. Likely from the .cpt file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
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 jalem...@vt.edu wrote: On Mon, Apr 1, 2013 at 1:14 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: 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 always read. I want to say that the coordinate file is required as well, though that would be an easy test using grompp. It should be easy to track the box vectors from the .edr file to see what the initial value was, to see if it came from the .cpt or .gro file. Likely from the .cpt file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
Justin - I am sure mdrun reads coordinates from -cpi state.cpt Vitaly On Mon, Apr 1, 2013 at 7:44 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 1, 2013 at 1:29 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: It is something very new for me. If structure, etc are not read from CPT files, why does one need them for... I just tested and verified that -c is required, even in the presence of -t passing a .cpt file. I suspect that the rationale is that the .cpt file is used for state variables, velocities, etc (i.e. an upgrade over the very old mechanism of passing a .trr to -t and .edr to -e). It would certainly make sense if the coordinates from the .cpt were read, but I don't know if doing so present a substantial improvement over using a coordinate file to -c. -Justin On Mon, Apr 1, 2013 at 7:21 PM, Justin Lemkul jalem...@vt.edu wrote: On Mon, Apr 1, 2013 at 1:14 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: 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 always read. I want to say that the coordinate file is required as well, though that would be an easy test using grompp. It should be easy to track the box vectors from the .edr file to see what the initial value was, to see if it came from the .cpt or .gro file. Likely from the .cpt file. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
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 another uniformly distributed box after this NVT run? I am expecting to see how density changes with Z at the solvent -vacuum interface Please advise me on this,, Thanks! On 1 April 2013 13:14, Dr. Vitaly Chaban vvcha...@gmail.com wrote: 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 katesed...@gmail.com wrote: 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 vvcha...@gmail.com wrote: 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 katesed...@gmail.com wrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth katesed...@gmail.com 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 how I can obtain the density profile if I am going to get another uniformly distributed box after this NVT run? Here we come to the question what your system is composed of... Based on the density profile, this is not a (conventional) liquid... Polymer, non-Newtonian liquid ... or what? If molecules tend to fill vacuum, it can only mean that the matter you are simulating is above critical point. What is your T and what are the particles in your box? Dr. Vitaly Chaban I am expecting to see how density changes with Z at the solvent -vacuum interface Please advise me on this,, Thanks! On 1 April 2013 13:14, Dr. Vitaly Chaban vvcha...@gmail.com wrote: 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 katesed...@gmail.com wrote: 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 vvcha...@gmail.com wrote: 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 katesed...@gmail.com wrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth katesed...@gmail.com 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 molecules tend to fill up the free zone no matter how much pressure was applied in the previous NPT runs? You cannot get a profile just because you have NO LIQUID and NO INTERFACE upon these conditions. Gas fills all the available space, there is no such thing as gas/gas interface. And yeah... Forget about NPT and learn the Gibbs phase rule. Dr. Vitaly Chaban On 1 April 2013 14:22, Dr. Vitaly Chaban vvcha...@gmail.com wrote: On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth katesed...@gmail.com 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 how I can obtain the density profile if I am going to get another uniformly distributed box after this NVT run? Here we come to the question what your system is composed of... Based on the density profile, this is not a (conventional) liquid... Polymer, non-Newtonian liquid ... or what? If molecules tend to fill vacuum, it can only mean that the matter you are simulating is above critical point. What is your T and what are the particles in your box? Dr. Vitaly Chaban I am expecting to see how density changes with Z at the solvent -vacuum interface Please advise me on this,, Thanks! On 1 April 2013 13:14, Dr. Vitaly Chaban vvcha...@gmail.com wrote: 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 katesed...@gmail.com wrote: 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 vvcha...@gmail.com wrote: 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 katesed...@gmail.comwrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
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 vvcha...@gmail.comwrote: On Mon, Apr 1, 2013 at 8:29 PM, Elisabeth katesed...@gmail.com 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 molecules tend to fill up the free zone no matter how much pressure was applied in the previous NPT runs? You cannot get a profile just because you have NO LIQUID and NO INTERFACE upon these conditions. Gas fills all the available space, there is no such thing as gas/gas interface. And yeah... Forget about NPT and learn the Gibbs phase rule. Dr. Vitaly Chaban On 1 April 2013 14:22, Dr. Vitaly Chaban vvcha...@gmail.com wrote: On Mon, Apr 1, 2013 at 8:16 PM, Elisabeth katesed...@gmail.com 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 how I can obtain the density profile if I am going to get another uniformly distributed box after this NVT run? Here we come to the question what your system is composed of... Based on the density profile, this is not a (conventional) liquid... Polymer, non-Newtonian liquid ... or what? If molecules tend to fill vacuum, it can only mean that the matter you are simulating is above critical point. What is your T and what are the particles in your box? Dr. Vitaly Chaban I am expecting to see how density changes with Z at the solvent -vacuum interface Please advise me on this,, Thanks! On 1 April 2013 13:14, Dr. Vitaly Chaban vvcha...@gmail.com wrote: 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 katesed...@gmail.comwrote: 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 vvcha...@gmail.com wrote: 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 katesed...@gmail.comwrote: Hi Vitaly, I did NVT simulations and tried to obtain density profile at interface along Z using g_density -f .trr -s .tpr -d Z but I what I see is the density profile in the box not the interface. Box size is 3 nm and Before NVT runsI extended Z to 6 nm. Please see the attached profile. Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: density profile
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. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I extended the box in Z to more than twice the initial box size and issued the following: grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v My questions are: 1) Can I get the proper solvent-air interface to obtain density profile by extending the Z direction (last line of the gro file obtained from NPT at each pressure)? Is that what yo mean by then build a new unit cell and run under NVT ? If you want solvent/air interface, you should add $air. If you want solvent/vacuum interface, it is enough to extend the box. If you want liquid/vapor interface, you need to re-equilibrate the system in NVT with a space for vapor available in the box. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
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. Vitaly Chaban vvcha...@gmail.com wrote: 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. Here are the steps: 1- First I did a 10 ns NPT to equilibrate the box and used the last frame gro and cpt file as input for the next step 2- I extended the box in Z to more than twice the initial box size and issued the following: grompp -f md.mdp -c extendedZ.gro -t .cpt -p .top -o extendedZ.tpr mpirun -np 4 mdrun_mpi -deffnm .extendedZ -s -o -c -g -e -x -v My questions are: 1) Can I get the proper solvent-air interface to obtain density profile by extending the Z direction (last line of the gro file obtained from NPT at each pressure)? Is that what yo mean by then build a new unit cell and run under NVT ? If you want solvent/air interface, you should add $air. If you want solvent/vacuum interface, it is enough to extend the box. If you want liquid/vapor interface, you need to re-equilibrate the system in NVT with a space for vapor available in the box. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: density profile
Hi Elisabeth - On Sun, Mar 31, 2013 at 8:28 PM, Elisabeth katesed...@gmail.com 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 P-coupling is for certain tasks with anisotropic systems, i.e. where you have a large non-spherical object, such as nanotube or graphene. It is not for liquid/non-liquid interfaces. I also wanted to know if surface tension can be also calculated under NVT (if NPT fails for this puporse) I believe surface tension should be calculate ONLY from fixed-volume simulations. By definition of the property, isn't it? Thanks! Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
