[gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

Hi again guys, Few more questions: 1. I would like to calculate compressibility of the protein+water system, but separating it into bulk water, hydration water and protein. So I need to pick these and compute volumes separately. When picking hydration water molecules, two tools are mentioned on

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

Frankie Montenegro wrote: Hi again guys, Few more questions: 1. I would like to calculate compressibility of the protein+water system, but separating it into bulk water, hydration water and protein. So I need to pick these and compute volumes separately. When picking hydration water

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

Frankie Montenegro wrote: Hi again guys, Few more questions: 1. I would like to calculate compressibility of the protein+water system, but separating it into bulk water, hydration water and protein. So I need to pick these and compute volumes separately. When picking hydration water

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

On 9/11/07, David van der Spoel [EMAIL PROTECTED] wrote: Frankie Montenegro wrote: That sounds difficult because computing volume is difficult. We should write a better program for this, but the problem lies in definition: where does one water molecule stop and the next begin? Thanks. I

[gmx-users] stopcom and acc_grps

Hi all， When I use acc_grps (e.g.: SOL), I think I should not use com motion removal on that group, even the whole system. Am I right? Thanks ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

Frankie Montenegro wrote: On 9/11/07, David van der Spoel [EMAIL PROTECTED] wrote: Frankie Montenegro wrote: That sounds difficult because computing volume is difficult. We should write a better program for this, but the problem lies in definition: where does one water molecule stop and the

Re: [gmx-users] stopcom and acc_grps

Zhou Bo wrote: Hi all， When I use acc_grps (e.g.: SOL), I think I should not use com motion removal on that group, even the whole system. Am I right? yes. Thanks

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

On 9/11/07, Mark Abraham [EMAIL PROTECTED] wrote: Frankie Montenegro wrote: Hi again guys, Few more questions: 1. I would like to calculate compressibility of the protein+water system, but separating it into bulk water, hydration water and protein. So I need to pick these and

[gmx-users] Protein coming out of the box

Hi all I'm simulating a helical protein in a water box, neutralized with Na and Cl to a 0.2M comcentration. I had to pick the smallest box I could (in editconf, rectangular, with -d 0.1, and -princ to align the box with the helix). But in the MD trajectory I see the protein coming out of the

Re: [gmx-users] Protein coming out of the box

[EMAIL PROTECTED] wrote: Hi all I'm simulating a helical protein in a water box, neutralized with Na and Cl to a 0.2M comcentration. I had to pick the smallest box I could (in editconf, rectangular, with -d 0.1, and -princ to align the box with the helix). But in the MD trajectory I see the

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

I am not sure what I'm missing here. I just ran an example from /tutor/water and got even worse number for specific heat, around 12.5 J/mol.K. Sure, it was with Berendsen T-coupling, no shifted VdW, but one would still expect better number. Anyone? Thanks, Frankie

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

Frankie Montenegro wrote: I am not sure what I'm missing here. I just ran an example from /tutor/water and got even worse number for specific heat, around 12.5 J/mol.K. Sure, it was with Berendsen T-coupling, no shifted VdW, but one would still expect better number. Anyone? Berendsen t

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

OK but I thought your number comes from equipartition theorem, not fluctuations. I think I remember correctly someone posting the code on the list a while ago. Besides, I am also running 3000 SPC waters with Nose-Hoover. After 250ps, the number is identical to the one from the example: 12.5

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

Frankie Montenegro wrote: OK but I thought your number comes from equipartition theorem, not fluctuations. I think I remember correctly someone posting the code on the list a while ago. Besides, I am also running 3000 SPC waters with Nose-Hoover. After 250ps, the number is identical to the one

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

Correction: the number is -706.4J/mol.K (negative) . Are you sure 6 is correct for ndf? I am running ffgmx force field and all bonds constrained spc water. F. On 9/12/07, Frankie Montenegro [EMAIL PROTECTED] wrote: David, I didn't realize what the nmol option does, thanks for the tip. But

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

Frankie Montenegro wrote: Correction: the number is -706.4J/mol.K (negative) . Are you sure 6 is correct for ndf? I am running ffgmx force field and all bonds constrained spc water. constrained SPC water has 6 dof (3x3 - 3 constraints). Is the temperature constant? Maybe you do not need the

Re: [gmx-users] Help! A dummy atom definition problem!

The problem actually is, that you mixed up a dummy atom with a virtual site, I guess. Virtual sites are not allowed to have a mass, as the error message claims. Also, a proper hydrogen should have a mass. If you want a hydrogen to appear, you have to place a particle in A-state which has no

Re: [gmx-users] 1. better tool: g_hbond or trjorder 2. g_energy: specific heat and compressibility

I got a fairly good number using fluctuations formula: cv=3.91J/K.g. I can't seem to figure out what am I doing wrong with g_energy. If someone could run /tutor/water/spc216 and get Cv it would be greatly appreciated. BTW, I do get interesting numbers for that system when I run g_energy -nmol 216

Re: [gmx-users] Help! A dummy atom definition problem!

Hi Maik, I really did mix up a dummy atom with a virtual site. Any difference? Thank you very much for your help. Regards, Qin On 9/12/07, Maik Goette [EMAIL PROTECTED] wrote: The problem actually is, that you mixed up a dummy atom with a virtual site, I guess. Virtual sites

[gmx-users] Solaris x86 instalation problem

Hi, I'm instaling gromacs in a Sun x86 machine with Solaris 10. Configure seams to be ok but when compiling an error ocourrs. Could any one help me? Thanks the configure and compiling output: -bash-3.00$ ./configure checking build system type... i386-pc-solaris2.10 checking host system type...

Re: [gmx-users] Help! A dummy atom definition problem!

Wang Qin wrote: Hi Maik, I really did mix up a dummy atom with a virtual site. Any difference? Thank you very much for your help. we changed the name from dummy to virtual site a few years back. We didn't want to be associated with MD for dummies. Regards, Qin On 9/12/07,

[gmx-users] Distance Restraints Violations

Hi, all: Im using g_disre in gmx3.3.1 to calculate violations of distance restraints in a simulation and I saw the message: Fatal error: tpr inconsistency. ndr = 0, label = 1 The gmxdump of tpr shows functype[459]=DISRES, label= 1, type=1, low= 1.8007e-01, up1=