Re: [gmx-users] NPT-REMD

Pressure should fluctuate significantly. The estimator for the pressure that is generally used is very noisy. The question is, do the pressure averages over, say, 500 ps or 1 ns look about right? On Sun, Aug 25, 2013 at 5:07 PM, Mark Abraham wrote: > On Sun, Aug 25, 2013 at 6:22 PM, rahul seth >

Re: [gmx-users] NPT-REMD

On Sun, Aug 25, 2013 at 6:22 PM, rahul seth wrote: > Hi All, > > I have been trying to perform NPT-REMD with a Protein Substrate and water. > I am trying to use md+nose-hoover thermostat and parrinello-rahman > barostat. However, I am not quite sure about the tau-t and the tau-p that I > should be

[gmx-users] NPT-REMD

Hi All, I have been trying to perform NPT-REMD with a Protein Substrate and water. I am trying to use md+nose-hoover thermostat and parrinello-rahman barostat. However, I am not quite sure about the tau-t and the tau-p that I should be using here. I paste a part of my mdp file below: define

Re: [gmx-users] NPT, freezegroups and Position Restraints.

Thanks a lot. I could set up and perform the simulations using position restraints and md+nose-hoover thermostat as suggested by Justin. The combination seems to yield the correct canonical ensembles. Equilibration with Berendsen barostat (with integrator=sd and refcoord-scaling = com) does not se

Re: [gmx-users] NPT, freezegroups and Position Restraints.

On Thu, Aug 22, 2013 at 12:51 AM, HANNIBAL LECTER wrote: > Thanks. I am not interested in the real physics of the freezegroups as I am > assuming the fluctuations are negligible in the timescale of the > fluctuations of the non-freeze groups. That may be true in the case where the non-interesting

Re: [gmx-users] NPT, freezegroups and Position Restraints.

Thanks. I am not interested in the real physics of the freezegroups as I am assuming the fluctuations are negligible in the timescale of the fluctuations of the non-freeze groups. I thought that the langevin thermostat is quite effective in this case just to ensure that there is no net heat flow fr

Re: [gmx-users] NPT, freezegroups and Position Restraints.

On Wed, Aug 21, 2013 at 10:22 PM, HANNIBAL LECTER wrote: > I am not sure what is the problem with using NPT, constraints and > freezegroups. Unless there is some fundamental issue (which I cannot think > of) one should in principle be able to run NPT with the CNT system by > freezing the CNT group

Re: [gmx-users] NPT, freezegroups and Position Restraints.

On 8/21/13 4:22 PM, HANNIBAL LECTER wrote: I am not sure what is the problem with using NPT, constraints and freezegroups. Unless there is some fundamental issue (which I cannot think of) one should in principle be able to run NPT with the CNT system by freezing the CNT group. I am using sd wit

Re: [gmx-users] NPT, freezegroups and Position Restraints.

I am not sure what is the problem with using NPT, constraints and freezegroups. Unless there is some fundamental issue (which I cannot think of) one should in principle be able to run NPT with the CNT system by freezing the CNT group. I am using sd with LINCS to constraint the bonds. However, if md

Re: [gmx-users] NPT, freezegroups and Position Restraints.

Interestingly, removing position restraints does not have much of an impact. On Mon, Aug 19, 2013 at 1:40 PM, Justin Lemkul wrote: > > > On 8/19/13 11:58 AM, HANNIBAL LECTER wrote: > >> I usually use 1.0 for my systems and I get the correct values for the >> temperatures. If I couple it as a sy

Re: [gmx-users] NPT, freezegroups and Position Restraints.

On 8/19/13 11:58 AM, HANNIBAL LECTER wrote: I usually use 1.0 for my systems and I get the correct values for the temperatures. If I couple it as a system, the low T-CNT yields a different value than the target 300K. What about changing the integrator to md? What happens if you remove restr

Re: [gmx-users] NPT, freezegroups and Position Restraints.

I usually use 1.0 for my systems and I get the correct values for the temperatures. If I couple it as a system, the low T-CNT yields a different value than the target 300K. On Mon, Aug 19, 2013 at 11:48 AM, Justin Lemkul wrote: > > > On 8/19/13 11:42 AM, HANNIBAL LECTER wrote: > >> Thanks Justi

Re: [gmx-users] NPT, freezegroups and Position Restraints.

On 8/19/13 11:42 AM, HANNIBAL LECTER wrote: Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The refcoord-scaling option doesn't matter with frozen groups. Anything that is froze

Re: [gmx-users] NPT, freezegroups and Position Restraints.

I am performing NPT here but this artifact is independent of whether one is using NPT or NVT. On Mon, Aug 19, 2013 at 11:42 AM, HANNIBAL LECTER < hanniballecte...@gmail.com> wrote: > Thanks Justin. > > I am not sure how it is fundamentally incompatible. Especially with > refcoord-scaling = com.

Re: [gmx-users] NPT, freezegroups and Position Restraints.

Thanks Justin. I am not sure how it is fundamentally incompatible. Especially with refcoord-scaling = com. Can you please provide with some more input on that? The outputs are from g_energy. Here is the .mdp file. define = -DPOSRES_CNT constraints = all-bonds pbc

Re: [gmx-users] NPT, freezegroups and Position Restraints.

On 8/19/13 11:32 AM, HANNIBAL LECTER wrote: Hi, I have been performing NPT simulations with CNT, Protein and water. However, when I freeze the CNT, the system crashes with segmentation fault. That is to be expected. Frozen atoms and pressure coupling are fundamentally incompatible. If

[gmx-users] NPT, freezegroups and Position Restraints.

Hi, I have been performing NPT simulations with CNT, Protein and water. However, when I freeze the CNT, the system crashes with segmentation fault. If I use position restraints, the temperature of the system is lower than what it is expected to be. I am using sd coupling. If I couple the protein

Re: [gmx-users] npt equilbration + density

:* Re: [gmx-users] npt equilbration + density On 2/8/13 10:49 AM, Bahar Mehrpuyan wrote: > Dear gmx users > > > My system is a single amino acid in water. I use two stage equilibration : NVT (300 k) and NPT (300k , 1 barr) with position restrain. > > NPT simulation were d

Re: [gmx-users] npt equilbration + density

) From: Justin Lemkul To: Bahar Mehrpuyan ; Discussion list for GROMACS users Sent: Friday, February 8, 2013 7:56 PM Subject: Re: [gmx-users] npt equilbration + density On 2/8/13 10:49 AM, Bahar Mehrpuyan wrote: > Dear gmx users > > > My system is a single amino acid in wate

Re: [gmx-users] npt equilbration + density

On 2/8/13 10:49 AM, Bahar Mehrpuyan wrote: Dear gmx users My system is a single amino acid in water. I use two stage equilibration : NVT (300 k) and NPT (300k , 1 barr) with position restrain. NPT simulation were done for 2.4 ns and 1.14 barr was obtained for pressure. but density is 974.

[gmx-users] npt equilbration + density

Dear gmx users My system is a single amino acid in water. I use two stage equilibration :  NVT (300 k) and NPT (300k , 1 barr) with position restrain. NPT simulation were done for 2.4 ns and 1.14 barr was obtained for pressure. but density is 974.031 . is this reasonable? should i change the

Re: [gmx-users] npt error

On 2/4/13 5:19 AM, Rajalakshmi.C wrote: hi all, i am trying to simulate a polymer in 5.2 nm box using the gromacs45a3 forcefield. the system is highly concentrated with 3400 water molecules. i did energy minimization for 10ps and NVT, NPT simulations for 100 ps during NPT simulation i got the

[gmx-users] npt error

hi all, i am trying to simulate a polymer in 5.2 nm box using the gromacs45a3 forcefield. the system is highly concentrated with 3400 water molecules. i did energy minimization for 10ps and NVT, NPT simulations for 100 ps during NPT simulation i got the error message as "inner product between old

Re: [gmx-users] npt equilibrium

I got it. Thanks for your reply. Sincerely, Shima From: Peter Lai To: Shima Arasteh ; Discussion list for GROMACS users Sent: Monday, January 7, 2013 7:02 PM Subject: Re: [gmx-users] npt equilibrium Shima Arasteh wrote: Dear Peter, > >Would you

Re: [gmx-users] npt equilibrium

Shima Arasteh wrote: >Dear Peter, > >Would you please let me know how much time approximately the system of >protein/popc took to be npt-equilibrated sufficiently, in accordance >with the simulation you have reported in "Beyond modeling " paper. > >In fact, I put the protein in popc and then

[gmx-users] npt equilibrium

Dear Peter, Would you please let me know how much time approximately the system of protein/popc took to be npt-equilibrated sufficiently, in accordance with the simulation you have reported in "Beyond modeling " paper. In fact, I put the protein in popc and then ran NPT-equilibrium on i

[gmx-users] npt equilibrium

Dear Peter, Would you please let me know how much time approximately the system of protein/popc took to be npt-equilibrated sufficiently, in accordance with the simulation you have reported in "Beyond modeling " paper. In fact, I put the protein in popc and then ran NPT-equilibrium on it f

Re: [gmx-users] NPT and NVT eqquilibruim - membrane simulation

 Thank you Justin. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Saturday, October 6, 2012 1:26 PM Subject: Re: [gmx-users] NPT and NVT eqquilibruim - membrane simulation On 10/6/12 3:15 AM, Shima

Re: [gmx-users] NPT and NVT eqquilibruim - membrane simulation

On 10/6/12 3:15 AM, Shima Arasteh wrote: In my own, I want to simulate POPC-water and then insert a protein in it. Then run a new simulation for my new system. I got the starting structure from Prof.Klauda website. Then dear Peter provides this link to get some useful files: http://uab.hy

Re: [gmx-users] NPT and NVT eqquilibruim - membrane simulation

ristopher Neale To: "gmx-users@gromacs.org" Cc: Sent: Saturday, October 6, 2012 10:24 AM Subject: [gmx-users] NPT and NVT eqquilibruim - membrane simulation The answer depends on what you are doing and where you got your starting structure. Please provide more information. Generally,

[gmx-users] NPT and NVT eqquilibruim - membrane simulation

The answer depends on what you are doing and where you got your starting structure. Please provide more information. Generally, if you are in doubt, then do NVT prior to NPT. Nevertheless, going straight to NPT is often ok. -- original message -- I'd like to know if it is necessary to run NVT

[gmx-users] NPT and NVT eqquilibruim - membrane simulation

Hi all, I'd like to know if it is necessary to run NVT and NPT equilibrium on a membrane-water system? Would only the NPT be sufficient? How can I understand it? Thanks in advance. Sincerely, Shima  -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] NPT equilibration in KALP15-DPPC

On 8/28/12 12:33 PM, Shima Arasteh wrote: OK, but what about the index file after removing water molecules, updating .gro and .top file? Should it be generated again? Yes. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Bioch

Re: [gmx-users] NPT equilibration in KALP15-DPPC

PM Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC On 8/27/12 10:27 AM, Shima Arasteh wrote: > I removed the water molecules located between carbon chains of lipids. Then > updated the top file. Should the atom numbers of "nvt.gro"  be changed? This > is not clear

Re: [gmx-users] NPT equilibration in KALP15-DPPC

should be accordingly decreased by 6. -Justin Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Monday, August 27, 2012 2:33 PM Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC On 8/27/12 2:30 AM, Shima Ara

Re: [gmx-users] NPT equilibration in KALP15-DPPC

t it gives me an error about one of the atoms in index file! Or I am supposed to run mdrun without a new grompp?   Sincerely, Shima - Original Message - From: Justin Lemkul To: Discussion list for GROMACS users Cc: Sent: Monday, August 27, 2012 2:33 PM Subject: Re: [gmx-

Re: [gmx-users] NPT equilibration in KALP15-DPPC

incerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Sunday, August 26, 2012 5:29 PM Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC On 8/26/12 8:54 AM, Shima Arasteh wrote: Hi, For NPT equilibration of

Re: [gmx-users] NPT equilibration in KALP15-DPPC

vance. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Sunday, August 26, 2012 5:29 PM Subject: Re: [gmx-users] NPT equilibration in KALP15-DPPC On 8/26/12 8:54 AM, Shima Arasteh wrote: > > > Hi, > > F

Re: [gmx-users] NPT equilibration in KALP15-DPPC

On 8/26/12 8:54 AM, Shima Arasteh wrote: Hi, For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when I run the grompp command, I get 4 notes. Is it necessary to pay attention to the notes ? Are they notable? Notes are generally notable, yes ;) Never ignore anything

[gmx-users] NPT equilibration in KALP15-DPPC

 Hi, For NPT equilibration of KALP15 in DPPC following the Justin's tutorial, when I run the grompp command, I get 4 notes. Is it necessary to pay attention to the notes ? Are they notable? NOTE 1 [file npt.mdp]:   You are using a cut-off for VdW interactions with NVE, for good energy   cons

Re: [gmx-users] NPT Equilibration error

On 8/22/12 8:26 AM, Ankita naithani wrote: Hi, I am trying to run NPT equilibration on two separate systems both with ligands present in the structure. However, I got two different errors for both of these and these are below: Fatal error: A charge group moved too far between two domain deco

[gmx-users] NPT Equilibration error

Hi, I am trying to run NPT equilibration on two separate systems both with ligands present in the structure. However, I got two different errors for both of these and these are below: Fatal error: A charge group moved too far between two domain decomposition steps. Fatal error: 8 particles comm

Re: [gmx-users] NPT simulation for mutation study

On 2012-04-16 17:23, Shyno Mathew wrote: Dear Gromcas users, I am doing some mutation study, NPT simulations. Initially I was using a generic .mdp file I got from my advisor and I was able to run the systems for ~50ns with out any issues. But then I spend time reading about gromacs and created a

[gmx-users] NPT simulation for mutation study

Dear Gromcas users, I am doing some mutation study, NPT simulations. Initially I was using a generic .mdp file I got from my advisor and I was able to run the systems for ~50ns with out any issues. But then I spend time reading about gromacs and created a .mdp file. However, with my .mdp file the r

Re: [gmx-users] NPT simulation with parinello-rahman pressure coupling

Shyno Mathew wrote: Dear gromacs users, I am having some difficulty in setting up an NPT simulation, following are the issues 1. With Parinello-Rahman coupling, I am getting the error: Fatal error: The X-size of the box (4.224258) times the triclinic skew factor (1.00) is smaller than t

[gmx-users] NPT simulation with parinello-rahman pressure coupling

Dear gromacs users, I am having some difficulty in setting up an NPT simulation, following are the issues 1. With Parinello-Rahman coupling, I am getting the error: Fatal error: The X-size of the box (4.224258) times the triclinic skew factor (1.00) is smaller than the number of DD cells (5) t

Re: [gmx-users] NPT - umbrella sampling

Steven Neumann wrote: On Thu, Feb 23, 2012 at 12:00 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: Dear Justin and Gmx Users, I extracted 42 frames from my trajctory of pulling ligand away from my protein (no position restarined).

Re: [gmx-users] NPT - umbrella sampling

On Thu, Feb 23, 2012 at 12:00 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Dear Justin and Gmx Users, >> I extracted 42 frames from my trajctory of pulling ligand away from my >> protein (no position restarined). I would like to run NPT before running >> umbrella sampling simulat

Re: [gmx-users] NPT - umbrella sampling

Steven Neumann wrote: Dear Justin and Gmx Users, I extracted 42 frames from my trajctory of pulling ligand away from my protein (no position restarined). I would like to run NPT before running umbrella sampling simulations. As far I see Justin in his tutorial NPT and umbrella sampling mdp

[gmx-users] NPT - umbrella sampling

Dear Justin and Gmx Users, I extracted 42 frames from my trajctory of pulling ligand away from my protein (no position restarined). I would like to run NPT before running umbrella sampling simulations. As far I see Justin in his tutorial NPT and umbrella sampling mdp files looks the same which mea

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

By the way I also wounder to know how I could keep my system after equilibration. E.g I've equilibrated CCl4+water system and obtain stabile system on desired timescale. Than I've used genbox to merge my pre-oriented peptide with the pre-equilibrated system. genbox -cp peptide_newbox.gro -cs CC

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

On 17/02/2012 5:33 PM, James Starlight wrote: Mark, The pure Ccl4 cube was expanded in X dimension during npt phase. So assuming you simulated long enough to have reasonable convergence, your model is not stable at the initial volume with whatever that reference pressure was. By the way

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Mark, The pure Ccl4 cube was expanded in X dimension during npt phase. By the way I've been able to prevent it by increasing the ref_p of X up to 5 ussing semiisotropic pcoupltype By when I've inserted peptide on the npt of that system my Ccl4 box was expanded on Z rapidly. Might this way to

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

On 17/02/2012 4:46 PM, James Starlight wrote: So my problem still is 1) During npt without peptide my Ccl4 system expan rapidly in X-dimension. That produce error on 2nd ns of equilibration One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz h

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

he moment, forget about all the stuff where you were >> struggling to insert more CCl4 into a box with CCl4 (probably creating a >> far-from-equilibrium starting configuration). Don't try to learn to run on >> stilts while shaving. Learn to shave, then to walk on stilts, then to run, >&g

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

shaving. Learn to shave, then to walk on stilts, then to run, > then start combining them. > > Mark > > > > James > > -- Forwarded message -- > From: Mark Abraham > Date: 2012/2/15 > Subject: Re: [gmx-users] Npt equilibration of the membrane-

Re: Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

starting configuration). Don't try to learn to run on stilts while shaving. Learn to shave, then to walk on stilts, then to run, then start combining them. Mark James -- Forwarded message -- From: *Mark Abraham* <mailto:mark.abra...@anu.edu.au>> Date: 2012/2/15

Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

wich I've found in the KALP tutorial because I have not found the same npt example file in the Biphastic tutorial :) Could you advise me another p_coup algorithm for my Ccl4 system? James -- Forwarded message -- From: Mark Abraham Date: 2012/2/15 Subject: Re: [gmx-users] Npt

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

On 15/02/2012 4:45 PM, James Starlight wrote: Mark, due to hight density the volume of my system have been slightly increased and during NPT phase I've obtained error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Mark, due to hight density the volume of my system have been slightly increased and during NPT phase I've obtained error Fatal error: One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off. I'm using 0.9 for elect

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

On 14/02/2012 11:01 PM, James Starlight wrote: This also was solved by the some extra minimisation steps. I've forced with another problem :D During npt equilibration my system have slightly expanded so my desired volume and density were perturbed. I've noticed the below options in npt wich

[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

I assume that you energy minimisd the system, but still have atomic clashes? One thing which helped me in a similar case, was a short simulation at low temperature with a really small timestep (about 3-5 magnitudes smaller than the normal timestep). With this the atoms which clashes move away

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

This also was solved by the some extra minimisation steps. I've forced with another problem :D During npt equilibration my system have slightly expanded so my desired volume and density were perturbed. I've noticed the below options in npt wich could help me ref_p= 1 1 compressibility

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

It seems that I've fixed that problem by reduce vdv radii for Cl during defining of my box Eventually I've obtained box with the desired density than I've delete vdvradii.dat for my wor dir by when I've launched equilibration I've oibtained Fatal error: Too many LINCS warnings (1598) If you kno

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Mark, I've checked only density value with 500 molecules Ccl4 I have density that is twisely less that I need ( in accordance to the literature ). Also I've checked my box visually and found that the box is not properly tightly packed so I dont know why genbox didnt add some extra mollecules :(

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

On 14/02/2012 4:57 PM, James Starlight wrote: Justin, Firstly I've created the box of desired size with only 500 molecules ( I need 1000) Than I've tried to add extra 200 molecules by means of Genbox genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro but no molecules have been

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Justin, Firstly I've created the box of desired size with only 500 molecules ( I need 1000) Than I've tried to add extra 200 molecules by means of Genbox genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro but no molecules have been added Added 0 molecules (out of 200 requested) of

[gmx-users] Npt equilibration of the membrane-mimicking, CCl4 layer

Hi, i second Justins seond idea (creating a small box of equilibrated CCl4 and then fill the simulation box via the -cs option). Depending if you have other molecules in your system, make the simulation box a little bit bigger, because you will get some holes. In the subsequent NPT simulation t

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

James Starlight wrote: Justin, 2012/2/6 Justin A. Lemkul mailto:jalem...@vt.edu>> Some simple calculations using the desired density and the box dimensions (to get the volume) will tell you exactly how many molecules you need. If you only "suppose" you've got a reasonable n

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Justin, 2012/2/6 Justin A. Lemkul > > Some simple calculations using the desired density and the box dimensions > (to get the volume) will tell you exactly how many molecules you need. If > you only "suppose" you've got a reasonable number, there are better ways to > be sure ;) > > In accordan

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

James Starlight wrote: Justin, I've built my system in accordance to the first way from your Biphgastic system tutorial. I've defined system with slight biger ( on 1 nm in each dimension) dimensions that I needed and place maximym CCl4 molecules in that box by genbox -ci ccl4.gro -nmol

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Justin, I've built my system in accordance to the first way from your Biphgastic system tutorial. I've defined system with slight biger ( on 1 nm in each dimension) dimensions that I needed and place maximym CCl4 molecules in that box by genbox -ci ccl4.gro -nmol 900 -box 9.6 7.5 4 -o new_box.

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

James Starlight wrote: Justin, Larger cutoffs would not only make the problem worse (read the error message carefully and consider the minimum image convention), but it would also potentially break the validity of the force field model. The vdW cutoff for Gromos96 should be 1

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Justin, Larger cutoffs would not only make the problem worse (read the error > message carefully and consider the minimum image convention), but it would > also potentially break the validity of the force field model. The vdW > cutoff for Gromos96 should be 1.4 nm, not 0.9 nm, in any case. Thi

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

James Starlight wrote: Dear Gromacs Users! I have problems during npt equilibration of my solvent box with the CCl4 solvent (I'm preparing this hydrophobic layer for further membrane-mimicking system). As the result I want to obtain density value ~ 1.5 for such box but between 2 and 3 n

[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Dear Gromacs Users! I have problems during npt equilibration of my solvent box with the CCl4 solvent (I'm preparing this hydrophobic layer for further membrane-mimicking system). As the result I want to obtain density value ~ 1.5 for such box but between 2 and 3 ns ( where the desity was 1.3) o

[gmx-users] NPT error

Hi: I am following the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html the NVT step goes well, but the NPT always doesn't work. it said: Program mdrun_mpi_bg, VERSION 4.5.5 Source code file: ../../../src/mdlib/domdec.c, line: 2633 Fa

[gmx-users] NPT error

Hi: I am following the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html the nvt step goes well, but the NPT always doesn't work. it said: Program mdrun_mpi_bg, VERSION 4.5.5 Source code file: ../../../src/mdlib/domdec.c, line: 2633 Fat

[gmx-users] NPT or NVT for calculating averaged experimental parameters

Hi there, Is there any consensus on whether to use NVT or NPT runs for calculating averaged NMR parameters in water at room temperature? I have seen some papers which use NPT, others use NVT. Thanks you, Igor -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

Re: [gmx-users] NPT - density off

On 21/08/2011 2:08 PM, Elisabeth wrote: On 20 August 2011 21:20, Mark Abraham > wrote: On 20/08/2011 8:02 AM, Elisabeth wrote: Dear experts, I am intending to calculate the equilibrium density of a pure hydrocarbon at different pressures , at

Re: [gmx-users] NPT - density off

On 20 August 2011 21:20, Mark Abraham wrote: > On 20/08/2011 8:02 AM, Elisabeth wrote: > > Dear experts, > > I am intending to calculate the equilibrium density of a pure hydrocarbon > at different pressures , at 425 K. The normal boiling point of the liquid is > around 350 K. For pressures belo

Re: [gmx-users] NPT - density off

On 20/08/2011 8:02 AM, Elisabeth wrote: Dear experts, I am intending to calculate the equilibrium density of a pure hydrocarbon at different pressures , at 425 K. The normal boiling point of the liquid is around 350 K. For pressures below 100 bar densities I am getting from NPT is in accurate

Re: [gmx-users] NPT - density off

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, August 22, 2011. For all questions about CloudBroker and the CloudBroker Platfor

[gmx-users] NPT - density off

Dear experts, I am intending to calculate the equilibrium density of a pure hydrocarbon at different pressures , at 425 K. The normal boiling point of the liquid is around 350 K. For pressures below 100 bar densities I am getting from NPT is in accurate. I start form a structure which is compresse

Re: [gmx-users] NPT for compressing

Elisabeth wrote: On 21 May 2011 19:02, Justin A. Lemkul > wrote: Elisabeth wrote: On 20 May 2011 23:04, Mark Abraham mailto:mark.abra...@anu.edu.au> >> wrote: On 21

Re: [gmx-users] NPT for compressing

On 21 May 2011 19:02, Justin A. Lemkul wrote: > > > Elisabeth wrote: > > >> >> >> >> On 20 May 2011 23:04, Mark Abraham > mark.abra...@anu.edu.au>> wrote: >> >>On 21/05/2011 10:45 AM, Elisabeth wrote: >> >>>Dear experts, >>> >>>I have a box of pure hexane with density of around 50 SI

Re: [gmx-users] NPT for compressing

Elisabeth wrote: On 20 May 2011 23:04, Mark Abraham > wrote: On 21/05/2011 10:45 AM, Elisabeth wrote: Dear experts, I have a box of pure hexane with density of around 50 SI (size 7nm). With the settings below I get error: vol 0.65 i

Re: [gmx-users] NPT for compressing

On 20 May 2011 23:04, Mark Abraham wrote: > On 21/05/2011 10:45 AM, Elisabeth wrote: > > Dear experts, > > I have a box of pure hexane with density of around 50 SI (size 7nm). With > the settings below I get error: > > vol 0.65 imb F 3% step 42100, will finish Fri May 20 18:54:05 2011 > Warni

Re: [gmx-users] NPT for compressing

On 21/05/2011 10:45 AM, Elisabeth wrote: Dear experts, I have a box of pure hexane with density of around 50 SI (size 7nm). With the settings below I get error: vol 0.65 imb F 3% step 42100, will finish Fri May 20 18:54:05 2011 Warning: 1-4 interaction between 1246 and 1249 at distance 3.5

[gmx-users] NPT for compressing

Dear experts, I have a box of pure hexane with density of around 50 SI (size 7nm). With the settings below I get error: vol 0.65 imb F 3% step 42100, will finish Fri May 20 18:54:05 2011 Warning: 1-4 interaction between 1246 and 1249 at distance 3.580 which is larger than the 1-4 table size 2.

Re: [gmx-users] NPT and NVT ensembles

ahmet yıldırım wrote: Dear Justin, In the first tutorial You said "After we arrive at the correct temperature (based on kinetic energies), we will apply pressure to the system until it reaches the proper density." That is, you apply each NVT and NPT ensembles when you did the position restr

[gmx-users] NPT and NVT ensembles

Dear Justin, In the first tutorial You said "After we arrive at the correct temperature (based on kinetic energies), we will apply pressure to the system until it reaches the proper density." That is, you apply each NVT and NPT ensembles when you did the position restraints. Would not it only be s

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

On 15/04/2011 10:29 AM, Moeed wrote: So Sorry I did not mean to be rough :) . Thanks for your comments...:) No no, no problem. By "rough", I meant being rough on the simulation system, with conditions too strenuous :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

So Sorry I did not mean to be rough :) . Thanks for your comments...:) -- 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)subs

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

On 15/04/2011 5:55 AM, Moeed wrote: On 14 April 2011 02:11, Mark Abraham > wrote: On 14/04/2011 3:40 PM, Moeed wrote: On 13 April 2011 18:45, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote: On 14/04/2011 10:22 AM, Moeed wrote:

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

Moeed wrote: On 14 April 2011 02:11, Mark Abraham > wrote: On 14/04/2011 3:40 PM, Moeed wrote: On 13 April 2011 18:45, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote: On 14/04/2011 10:22 AM, Moeed wrote: Hello, I hav

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

On 14 April 2011 02:11, Mark Abraham wrote: > On 14/04/2011 3:40 PM, Moeed wrote: > > > > On 13 April 2011 18:45, Mark Abraham wrote: > >> On 14/04/2011 10:22 AM, Moeed wrote: >> >> Hello, >> >> I have run 2 ns simulations on a hydrocarbon system (initial density of ~ >> 2 SI and box size is 1

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

On 14/04/2011 3:40 PM, Moeed wrote: On 13 April 2011 18:45, Mark Abraham > wrote: On 14/04/2011 10:22 AM, Moeed wrote: Hello, I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2 SI and box size is 15 nm), one with versi

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

On 13 April 2011 18:45, Mark Abraham wrote: > On 14/04/2011 10:22 AM, Moeed wrote: > > Hello, > > I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2 > SI and box size is 15 nm), one with version 4.0.7 and the other trial using > 4.5.3. Both runs are almost equilibrated t

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

On 14/04/2011 10:22 AM, Moeed wrote: Hello, I have run 2 ns simulations on a hydrocarbon system (initial density of ~ 2 SI and box size is 15 nm), one with version 4.0.7 and the other trial using 4.5.3. Both runs are almost equilibrated to 70 bar pressure but one is giving density of above 60

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