Re: [gmx-users] remd- Function not implemented

On 3/11/2011 6:15 PM, 杜波 wrote: Dear teacher, when i do remd , the power is off . Then i use the commd to=21 lamboot mpirun_lam -np $to mdrun_mpi_4.5 -multi $to -replex 100 -nice 0 -cpi state.cpt -s pmma.tpr -o md -c after_md -v to continue to run the progarm. But there is a Fatal error!!

Re: [gmx-users] segmentation fault from power6 kernel

Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Fabio The most likely issue is some normal blowing up scenario leading to a table-lookup-overrun segfault in the 3xx series kernels. I don't know why the

[gmx-users] Energy Minimisation

*Dear all, I am trying to minimize the energy of the single molecule using gromacs. I tried with the following mdp ; VARIOUS PREPROCESSING OPTIONS FOR ENERGY MINIMIZATION OF ISOLATED MOLECULE include = define = ; RUN CONTROL PARAMETERS integrator

Re: [gmx-users] source of opls Mg2+ parameters?

Hi Chris, If I remember correctly the magnesium ion parameters are the Aquvist parameters (http://pubs.acs.org/doi/abs/10.1021/j100384a009). Cheers Tom chris.ne...@utoronto.ca wrote: Dear users: does anybody know where the OPLS magnesium parameters are from? As far as I can tell, they

[gmx-users] Small molecule - CHARMM

Dear Gmx Users, I have produced itp file using SwissParam - for CHARMM ff. As far as I know using this topology is not a good idea and the charges of my atoms should be parametrized. My question is how to do this? Will you suggest any reading? Regards, Steven -- gmx-users mailing list

Re: [gmx-users] Simulation of membrane protein

Mark, Firstly I've downloaded Berger's dppc.itp and dppc.gro ( I've already have had gromos lipid ff) than I made pdb file for just 1 molecule of the dppc lipid consisted of 50 atoms and generate for that new molecule lipid_posres.itp via pdb2gmx than I've included lipid_posre.itp to the

Re: [gmx-users] Small molecule - CHARMM

I'm not a regular contributor, but I thought I'd comment since I just went through this exercise. I found the tutorial from the VMD group to be the easiest to follow. http://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/05-qm-tutorial/part1.html This tutorial uses GAMESS, which

RE: [gmx-users] Simulation of membrane protein

1) Ensure that lipid_posres.itp was included in the topology by using grompp -pp processed.top 2) Check the content of lipid_posres.itp (often the P-atoms are restraint only and not the tails), you may post an extract of that file to the mailing list. Andreas From:

Re: [gmx-users] Energy Minimisation

Ravi Kumar Venkatraman wrote: *Dear all, I am trying to minimize the energy of the single molecule using gromacs. I tried with the following mdp ; VARIOUS PREPROCESSING OPTIONS FOR ENERGY MINIMIZATION OF ISOLATED MOLECULE include = define = ;

[gmx-users] umbrella sampling restart

Hello, Can we restart the umbrella sampling simulation after some 10 or 15ns simulation using the cpt and gro files generated from the previous step. I am not sure whether it will take force generated from the previous step. Regards, Vijay. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] umbrella sampling restart

Vijayaraj wrote: Hello, Can we restart the umbrella sampling simulation after some 10 or 15ns simulation using the cpt and gro files generated from the previous step. I am not sure whether it will take force generated from the previous step. Yes, you can use a .cpt file to restart any

Re: [gmx-users] Simulation of membrane protein

On 3/11/2011 9:32 PM, James Starlight wrote: Mark, Firstly I've downloaded Berger's dppc.itp and dppc.gro ( I've already have had gromos lipid ff) than I made pdb file for just 1 molecule of the dppc lipid consisted of 50 atoms and generate for that new molecule lipid_posres.itp via

Re: [gmx-users] segmentation fault from power6 kernel

On 3/11/2011 7:59 PM, Fabio Affinito wrote: Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Sounds like a bug. Please file a report here http://redmine.gromacs.org http://redmine.gromacs.org/ including your

[gmx-users] source of opls Mg2+ parameters?

Thank you Tom! Aqvist_A12 = sqrt(gromacs_C12*10^12/4.184) Aqvist_A6 = sqrt(gromacs_C6*10^6/4.184) (equation verified based on the SPC water oxygen parameters, also listed in Aqvist). This reference (Aqvist, J (1990) J. Phys. Chem., 94 (21), pp 8021?8024) should probably be noted somewhere

[gmx-users] Gromacs query for vaccum medium

Let me know how to simulate a membrane protein in vaccum medium by using gromacs commands.What are the basic differences in commands as well as parameters used in liquid and vaccum medium? Please guide me. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Gromacs query for vaccum medium

On 4/11/2011 4:58 AM, Anushree Tripathi wrote: Let me know how to simulate a membrane protein in vaccum medium by using gromacs commands.What are the basic differences in commands as well as parameters used in liquid and vaccum medium? Please guide me. I suggest you do all the GROMACS

[gmx-users] www.gromacs.org down?

Hi gmx-users, It has been days that I cannot log into www.*gromacs*.org, does anyone know anything happed to it? Or is there any alternative website that we can see the documentation on www.*gromacs*.org/Documentation/ Thanks very much! Xiaojia -- gmx-users mailing list

Re: [gmx-users] www.gromacs.org down?

mu xiaojia wrote: Hi gmx-users, It has been days that I cannot log into www.*gromacs*.org, does anyone know anything happed to it? The site has been up and down for a few days. I have contacted Rossen about it to see if he can fix it. Or is there any alternative website that we can

Re: [gmx-users] segmentation fault from power6 kernel

Hi Mark, today I tested the 4.5.5 version. It seems here there's not that problem. Anyway, I will take some days to make more tests. Thank you, Fabio - Messaggio originale - Da: Mark Abraham mark.abra...@anu.edu.au A: Discussion list for GROMACS users gmx-users@gromacs.org Inviato:

[gmx-users] Steered MD in reverse direction?

Hi,   I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex. But, to check the

Re: [gmx-users] Steered MD in reverse direction?

Sanku M wrote: Hi, I am performing steered Molecular dynamics simulation to pull a molecule out of a complex. I am using gromacs 4.5.4 to perform the constant rate pulling..I have done the steered MD simulation in a particular direction i.e hav pulled the molecule out of complex. But, to

Re: [gmx-users] Steered MD in reverse direction?

Thanks for the suggestion.  Also, I was wondering how one can get the time profile of the irreversible work from the gromacs pull-code out put . From constant pulling-rate SMD, we get time profile of force pullf.xvg and pullx.xvg. I wonder does multiplying the the value from pullx.xvg and value