Re: [gmx-users] About the biotin parameter.....

2012-11-27 Thread rama david
Hi justin, Thank you for your suggestion. I read the ATB paper but the paper does not mention any thing related to the biotin. When I mail them, they replied .. To clarify the validation: There are different levels of validation criteria used in the ATB. The one which is available on the ATB we

[gmx-users] Re: About Temperature coupling and Energy Transfer....

2012-11-27 Thread cyberjhon
Dear Justin Thanks for your answer. I know what you mean, but the problem is that this is not a possible physical (real) behaviour. If the temperature is not controlled as you said, the energy should continue growing not stop, but in these case after 50ps it reaches some kind of equilibrium a

Re: [gmx-users] g_bar and second law violations

2012-11-27 Thread Justin Lemkul
On 11/27/12 11:43 AM, Sanku M wrote: Hi, I am trying to compute the free energy change using g_bar: I am using two-stage decoupling process as in Justin Lemkul's tutorial. But , I get following warning in all cases regarding violation of second law of thermodynamics. Can someone explain wh

[gmx-users] Gromacs 4.6 segmentation fault with mdrun

2012-11-27 Thread Makoto Yoneya
Dear GROMACS users: On "Gromacs 4.6 segmentation fault with mdrun", I'd also met the same segmentation fault problem with gromacs-4.6. on my linux box with GTX-580. For my case, change the compilor solved this problem. Raf Ponsaerts wrote he used > gcc 4.4.5 (Debian 4.4.5-8), Linux kernel 3.1.1

Re: [gmx-users] itp atomtypes section

2012-11-27 Thread James Cannon
Dear Tsjerk, Thanks for clarifying that for me. I appreciate it. Best regards, James On Tue, Nov 27, 2012 at 5:25 PM, Tsjerk Wassenaar wrote: > Hi James, > > The 6 and 1 are the number of electrons the atomtype has, which is used for > QM/MM stuff. Gromacs can tell whether or not it is given

Re: [gmx-users] how to run charmm2gromacs-pvm.py correctly?

2012-11-27 Thread David van der Spoel
On 2012-11-27 17:58, Albert wrote: Hello: I am trying to convert the output from CGenFF website into Gromacs .itp format by command: python charmm2gromacs-pvm.py charmm.rst you need an extra file. IIRC the cgenff method gives you two files. but it said: Traceback (most recent call last)

[gmx-users] Fwd: Validation of topology ....

2012-11-27 Thread rama david
Dear Gromacs friends, I want to simulate a system containing the biotin. I get the topology from ATB. I want to validate these toplogy for my use . So please could some one told me the way how I can do it ?? I never had any such experience. Is these is any tutorial regarding to these. T

[gmx-users] how to run charmm2gromacs-pvm.py correctly?

2012-11-27 Thread Albert
Hello: I am trying to convert the output from CGenFF website into Gromacs .itp format by command: python charmm2gromacs-pvm.py charmm.rst but it said: Traceback (most recent call last): File "charmm2gromacs-pvm.py", line 33, in parFile = open(sys.argv[2], 'r') IndexError: list index

[gmx-users] g_bar and second law violations

2012-11-27 Thread Sanku M
Hi,   I am trying to compute the free energy change using g_bar: I am using two-stage decoupling process as in Justin Lemkul's tutorial. But , I get following warning in all cases regarding violation of second law of thermodynamics. Can someone explain what is this error about and which lambda I

Re: [gmx-users] g_select error

2012-11-27 Thread Albert
On 11/27/2012 03:33 PM, Justin Lemkul wrote: Well, like I warned, I wasn't 100% sure of the syntax, so it was no guarantee that I was right. Reading into the documentation and examples a bit, it seems that "resname SOL and name OW" should be enclosed within double quotes, within the single-quo

Re: [gmx-users] g_select error

2012-11-27 Thread Justin Lemkul
On 11/27/12 9:18 AM, Albert wrote: hello Justin: thanks for kind tips. I've tried both methods: g_select -f md.xtc -s npt3.pdb -os size.xvg -sf selection.dat g_select -f md.xtc -s npt3.pdb -os size.xvg -select 'resname SOL and name OW within 0.6 of resid 114' but they all failed with

Re: [gmx-users] g_select error

2012-11-27 Thread Albert
hello Justin: thanks for kind tips. I've tried both methods: g_select -f md.xtc -s npt3.pdb -os size.xvg -sf selection.dat g_select -f md.xtc -s npt3.pdb -os size.xvg -select 'resname SOL and name OW within 0.6 of resid 114' but they all failed with messages: log---

Re: [gmx-users] error during minimization

2012-11-27 Thread Justin Lemkul
On 11/27/12 4:31 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization (after shrinking), getting error like this. Fatal error: Invalid line in system_shrink26.gro for atom 8703: 6.4140 6.44350 6.59650.why this er

Re: [gmx-users] error during minimization

2012-11-27 Thread Venkat Reddy
Probably..there is a problem in spacing at the bottom of your gro file. The line mentioning the vectors should be like this eg:, 5012OBC49 47 1.088 1.094 2.775 0.0 0.0 0.0 On Tue, Nov 27, 2012 at 3:01 PM, Shine A wrote: > Sir, > >I am studying the dynamics o

[gmx-users] error during minimization

2012-11-27 Thread Shine A
Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. But during minimization (after shrinking), getting error like this. Fatal error: Invalid line in system_shrink26.gro for atom 8703: 6.4140 6.44350 6.59650.why this error?plz give me a solution to overcome it. -

Re: [gmx-users] itp atomtypes section

2012-11-27 Thread Tsjerk Wassenaar
Hi James, The 6 and 1 are the number of electrons the atomtype has, which is used for QM/MM stuff. Gromacs can tell whether or not it is given by checking the format of the line. If the 5th column is a letter, then the number isn't there, if the 6th column is a letter, it must be there. Hope it h