Re: [gmx-users] Reg: NPT Equilibration of water

On 31/10/2010 8:17 PM, Tsjerk Wassenaar wrote: Hey, There's quite a number of people that should be rereading their statistics... :p First of all, there are instantaneous measurements, averages and fluctuations. If the statistics (mean/fluctuation) are 7 +/- 500, then that doesn't mean that the

Re: [gmx-users] Reg: NPT Equilibration of water

Hey, There's quite a number of people that should be rereading their statistics... :p First of all, there are instantaneous measurements, averages and fluctuations. If the statistics (mean/fluctuation) are 7 +/- 500, then that doesn't mean that the average of 7 is an estimate that may be off by 5

Re: [gmx-users] Reg: NPT Equilibration of water

On 29/10/2010 7:50 PM, vinothkumar mohanakrishnan wrote: Hi Mark How come 7 +/- 500 bar is approximately 1 bar. Can you explain it more clearly? It will be of more useful to me to understand the concept. It's a pretty basic one in scientific measurement. See http://en.wikipedia.org/wiki/Erro

Re: [gmx-users] Reg: NPT Equilibration of water

vinothkumar mohanakrishnan wrote: Hi Justin Thank you. One more question regarding the Compressibility value usage. can i use the Compressibility value of water (4.5e-5) for the NPT equilibration of organic liquids (say DCE)? Is it resonable? It was said in the gromacs mailing archive that

Re: [gmx-users] Reg: NPT Equilibration of water

Hi Justin Thank you. One more question regarding the Compressibility value usage. can i use the Compressibility value of water (4.5e-5) for the NPT equilibration of organic liquids (say DCE)? Is it resonable? It was said in the gromacs mailing archive that for all liquids one can use the Compress

Re: [gmx-users] Reg: NPT Equilibration of water

vinothkumar mohanakrishnan wrote: Hi Justin Thank you for your comments. Yes i want to concatenate two systems such that their cross sections are same ( X and Y axis length are same for both the boxes) allowing only the Z axis to change. The above procedure was employed in the literature an

Re: [gmx-users] Reg: NPT Equilibration of water

Hi Justin Thank you for your comments. Yes i want to concatenate two systems such that their cross sections are same ( X and Y axis length are same for both the boxes) allowing only the Z axis to change. The above procedure was employed in the literature and latter they combined two boxes. what i

Re: [gmx-users] Reg: NPT Equilibration of water

vinothkumar mohanakrishnan wrote: Hi Mark How come 7 +/- 500 bar is approximately 1 bar. Can you explain it more clearly? It will be of more useful to me to understand the concept. Suppose you do two simulations. In one, the result is 7+/-500 and in the other, the result is 1+/-500. Ev

Re: [gmx-users] Reg: NPT Equilibration of water

Hi Mark How come 7 +/- 500 bar is approximately 1 bar. Can you explain it more clearly? It will be of more useful to me to understand the concept. One more thing, density (from g_energy command) of water is found to low (expected 1000) after NPT is equilibration. why? given below is my average de

Re: [gmx-users] Reg: NPT Equilibration of water

On 29/10/2010 6:39 PM, vinothkumar mohanakrishnan wrote: I am using the semiisotropic pressure scaling because i want the box size to remain the same as that of the original box size in X and Y axis and want to change it only on the Z axis. I am doing this because at a latter stage i want to cr

Re: [gmx-users] Reg: NPT Equilibration of water

I am using the semiisotropic pressure scaling because i want the box size to remain the same as that of the original box size in X and Y axis and want to change it only on the Z axis. I am doing this because at a latter stage i want to create an interface with organic solvent where i need the cross

Re: [gmx-users] Reg: NPT Equilibration of water

On 2010-10-29 09.08, vinothkumar mohanakrishnan wrote: Hi Mark I read the link before posting the question. even though the fluctation is between 500-600 (as said in the link) bar the average pressure is around 7.4 bar. my concern is the average pressure?. Because at a latter stage i am going t

Re: [gmx-users] Reg: NPT Equilibration of water

Hi Mark I read the link before posting the question. even though the fluctation is between 500-600 (as said in the link) bar the average pressure is around 7.4 bar. my concern is the average pressure?. Because at a latter stage i am going to combine this water box with another organic solvent and

Re: [gmx-users] Reg: NPT Equilibration of water

On 29/10/2010 5:48 PM, vinothkumar mohanakrishnan wrote: Hi Gromacians I want to do equilibration of water (spc model) first in the NVT ensemble and then in the NPT ensemble to maintain a temperature of 300K and a pressure of 1 bar respectively. The NVT equilibration works fine and the averag

[gmx-users] Reg: NPT Equilibration of water

Hi Gromacians I want to do equilibration of water (spc model) first in the NVT ensemble and then in the NPT ensemble to maintain a temperature of 300K and a pressure of 1 bar respectively. The NVT equilibration works fine and the average temperature turns out to be 299.229 K. Energy