Re: [gmx-users] Continue run in Gromacs-4 with check point file

xuji wrote: > Hi all: > > > > I wrote an e-mail many days ago about continuing run in Gromacs-4.0 with > check point file. But I can't solve this problem yet. > I run a simulation with > mpiexec -machinefile ./mf_24 -np 24 mdrun -v -append -cpt 5 -cpi > dppc_md_prev.cpt -cp

[gmx-users] Continue run in Gromacs-4 with check point file

Hi all: I wrote an e-mail many days ago about continuing run in Gromacs-4.0 with check point file. But I can't solve this problem yet. I run a simulation with mpiexec -machinefile ./mf_24 -np 24 mdrun -v -append -cpt 5 -cpi dppc_md_prev.cpt -cpo dppc_md.cpt -s dppc_md.tpr -o

Re: [gmx-users] Questions About Gromacs

Xi Ouyang wrote: Hi, there are 3 questions I want to ask. 1. I run the md from the pdb file successfully and get a .trr trajectory file. But when I load the .trr file in VMD, there is just 1 frame. I have 1000 steps and want to have every step as a frame. How can I do this? Consult section

[gmx-users] hydrophobicity

Hello Users I have a question about defining an atom to be either hydrophobic or hydrophilic. The gromacs manual shows that the maximum charge of the hydrophobic atom is 0.2. Does anyone know where this number is coming from? Any good reasons or references? Thank you in advance Sunjoo ___

[gmx-users] Nomenclature Inconsistency between *.rtp and *nb.itp in ffG53a5 and ffG53a6 (CH2r vs CH2R)

Hello, I noticed that there is an inconsistency between the files ffG53a6nb.itp and ffG53a6.rtp, and between the corresponding files in the ffG53a5 FF. The atom type that is used for some CH2 atoms inside rings (e.g. CB CG CD in Proline) is defined as CH2r type in the fG53a6nb.itp file (line 20):

RE: [gmx-users] Questions About Gromacs

> Date: Thu, 19 Mar 2009 11:51:51 +0800 > From: xouy...@uvm.edu > To: gmx-users@gromacs.org > Subject: [gmx-users] Questions About Gromacs > > Hi, there are 3 questions I want to ask. > > 1. I run the md from the pdb file successfully and get a .trr trajectory > file. But when I load the .trr

[gmx-users] Questions About Gromacs

Hi, there are 3 questions I want to ask. 1. I run the md from the pdb file successfully and get a .trr trajectory file. But when I load the .trr file in VMD, there is just 1 frame. I have 1000 steps and want to have every step as a frame. How can I do this? 2. Since I do signal processing, I

Re: [gmx-users] inertia

Antonia V. wrote: Hello, I want to calculate the moments of inertia of a system of liquid crystals. Using the tool g_gyrate I get 5 values. The three last values are called I1, I2 and I3. I suppose that they are Ixx, Iyy and Izz respectively. Is that correct? What about the second column w

[gmx-users] inertia

Hello, I want to calculate the moments of inertia of a system of liquid crystals. Using the tool g_gyrate I get 5 values. The three last values are called I1, I2 and I3. I suppose that they are Ixx, Iyy and Izz respectively. Is that correct? What about the second column which is called Itot. Wh

Re: [gmx-users] how to get the the force plot after pulling, dynamic simulation using GMX-3.3

- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090319/2f249dff/attachment-0001.html > > -- > ___ gmx-users mailing listgmx-users@gromacs.org ht

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

Pawan Kumar wrote: Hello Justin Sir, Greetings from Pawan Thanks for your valuable suggestion and reply. After inserting the protein in the bilayer using genbox I have minimized the whole system without using any position restraints (i.e. define = -DFLEXIBLE in em.mdp file). I used vanderwaa

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

Hello Justin Sir, Greetings from Pawan Thanks for your valuable suggestion and reply. After inserting the protein in the bilayer using genbox I have minimized the whole system without using any position restraints (i.e. define = -DFLEXIBLE in em.mdp file). I used vanderwaal's distance parameter (

Re: [gmx-users] Re: gmx-users Digest, Vol 59, Issue 136

Pawan Kumar wrote: Hello Justin Sir, Thanks for your reply. I changed the dt value as per the suggestion. But after 200 steps the same kind of warnings came like "pressure scaling more than 1%" and "1-4 interactions" and then it stopped after writing few pdb files. Then I decreased the dt v

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

Hello Justin Sir, Thanks for your reply. I changed the dt value as per the suggestion. But after 200 steps the same kind of warnings came like "pressure scaling more than 1%" and "1-4 interactions" and then it stopped after writing few pdb files. Then I decreased the dt value still lesser (0.

[gmx-users] Re: gmx-users Digest, Vol 59, Issue 136

Hello Justin Sir, Thanks for your reply. I changed the dt value as per the suggestion. But after 200 steps the same kind of warnings came like "pressure scaling more than 1%" and "1-4 interactions" and then it stopped after writing few pdb files. Then I decreased the dt value still lesser (0.

RE: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems

Hi, You will have to come up yourself with a reasonable guess. If you have a hard crystal, I guess it would be close to the diagonal values. Note that with PR coupling tau_p has to be large enough, something like 10 ps. (note that in Gromacs 4.0 a bug has been corrected which scaled tau_p by

RE: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems

Hello,I do have a crystal system. You refer to an initial guess. So if I understand correctly, it is a trial and error, if I do not have any data, this is what I can make out of. The part of the shear stress you are reffering I think that it is from experimental values? Now you say that : compre

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

= 173529 Thanking you, Yours sincerely, Pawan -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090319/00417c68/attachment-0001.html -- Message: 2

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

ef_t = 300300 > ; Energy monitoring > energygrps= ProteinNon-Protein > ; Pressure coupling is not on > Pcoupl = berendsen > tau_p = 5.0 5.0 > compressibility = 4.5e-5 4.5e-5 > ref_p = 1.0 1.0 >

[gmx-users] Re: Softcores: sc-power = 1 or 2 ? again (Berk and Justin)

Hello Berk and Justin. Thanks for the help. In fact I was not using hardcore for electrostatic interactions and also had a silly error in my topology. I fix everything and now is working perfectly, without the giant peak near lambda = 0. Bests ___ Eudes Eterno Fi

RE: [gmx-users] compressibility tensor components, pressure coupling anisotropic PR, triclinic systems

Hi, If you have a liquid system (no off-diagonal elasticity), you should not use full anistropic pressure coupling. If you have a solid system (for instance a crystal), you will have an elastic shear stress response and you can determine and use off-diagonal compressibility values. You need

Re: [gmx-users] Doubt regarding membrane protein in POPC bilayer

It is a bit difficult to guess what is exactly happening. Your starting structure seem to be the problem, but your topology could also be partly responsible. One easy thing to do is the decrease your time step to 0.0001 which would decrease the chances that your system explodes. Also tr