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

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

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.

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

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

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

 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.hyperfine.info/~pcl/files/popc36/ Regarding to

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

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

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

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

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

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

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

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

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

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

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

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

Re: [gmx-users] NPT equilibration

shivangi nangia wrote: Hello, I am having problems in carrying out a NPT equilibration of my system at 500 K. System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid anion. NVT equilibration gives expected results. When I load the npt.gro file in VMD, its seems as if th

Re: [gmx-users] NPT

mohsen ramezanpour wrote: On 1/3/11, Justin A. Lemkul wrote: mohsen ramezanpour wrote: Dear All In doing umbrella sampling ,when I want to generate NPT every thing is going well but one error is occuring in the first. please let me know how can I solve this problem. Is it usefull to extend

Re: [gmx-users] NPT

On 1/3/11, Justin A. Lemkul wrote: > > > mohsen ramezanpour wrote: >> Dear All >> In doing umbrella sampling ,when I want to generate NPT every thing is >> going well but one error is occuring in the first. >> please let me know how can I solve this problem. >> Is it usefull to extend the degree

Re: [gmx-users] NPT

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, January 10, 2011. For all questions about CloudBroker, please contact the compan

Re: [gmx-users] NPT

mohsen ramezanpour wrote: Dear All In doing umbrella sampling ,when I want to generate NPT every thing is going well but one error is occuring in the first. please let me know how can I solve this problem. Is it usefull to extend the degree which is defined in .mdp file? No. The constraints

Re: [gmx-users] NPT for compressing the system

Moeed wrote: Hello, Thanks for your reply. As for the simulation box, I did not change anything and I am still saying that I am having a cubic box of size 30nm. When I view the molecule in ngmx I see the cubic box.. no problem with that. What I was referring to was the option on menu bar wh

Re: [gmx-users] NPT for compressing the system

On 14/07/2010 1:09 PM, Moeed wrote: Hello, Thank you for suggestions. Yes simulation crashes. I am not able see the whole run (1000ps). For all pressures I tired the final simulation box is 2.2*2.2*2.2 nm but simulation crashes before 1000ps. The longest simulation is for 120 bar (727ps). and

Re: [gmx-users] NPT for compressing the system

Moeed wrote: Hello, Thank you for suggestions. Yes simulation crashes. I am not able see the whole run (1000ps). For all pressures I tired the final simulation box is 2.2*2.2*2.2 nm but simulation crashes before 1000ps. The longest simulation is for 120 bar (727ps). and I think that is why

Re: [gmx-users] NPT for compression

On 14/07/2010 6:40 AM, Moeed wrote: Hello, I followed the hints. I did several NPT runs and I found out pressure above 100 eg 120 bar gives final boxsize close to volume of box I want. But I dont know why pressure given by g_energy is totally different. 1- I looked at values in xvg file and

Re: [gmx-users] NPT for compression

Moeed wrote: Hello, I followed the hints. I did several NPT runs and I found out pressure above 100 eg 120 bar gives final boxsize close to volume of box I want. But I dont know why pressure given by g_energy is totally different. If you're compressing the system, it likely has not had t

Re: [gmx-users] NPT system density

Hi, For one thing; to keep density constant (as in fixed) you want NVT, not NPT. NPT could, depending on your starting state, allow for initial drift in the system size. Cheers, Erik Marklund Moeed skrev: Hello, I have 125 hexane molecules in a box of 0.25nm3. The desnity I calculate fro

Re: [gmx-users] NPT restarts without .edr, can the simulations be used anyway?

Matteus Lindgren wrote: Hi all I am new to gromacs and despite my efforts in reading tutorials, the manual and this mailing list I managed to make errors when restarting (continuing) some NPT MD simulations. I have continued my simulation runs with grompp but with an mdp-file lacking t