[gmx-users] Re: Warning and Notes in Grompp for minimization

Dear Justin Thank you very much for your reply >>Regarding Warning 1; Yes, I have introduced the new parameter for C C bond and it is what I want. >>Regarding Note 1; Actually, the charges for each atom in topology file are what I included myself in Cisplatin parameters based on the literature. Ma

Re: [gmx-users] the mdp parameters for localpressure calculation using gromacs-4.0.2_localpressure

Hi, Kong Xian, It is better to use SHAKE instead of LINCS since LINCS does not directly yield pairwise forces, as shown in the paper: Erik Lindahl and Olle Edholm. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. JOURNAL OF CH

[gmx-users] increasing cut-off and PME grid spacing

Hi Justin, I understand now. The vector of box changed from 5.8 to 44 after the short MD for equilibrium. I don't know what happened during equilibrium. But that is belong to the other question now. Thank you very much for your reply. Sincerely yours, Hsin-LIn > Hsin-Lin Chiang wrote: > > Hi, Ju

Re: [gmx-users] NPT - density off

On 21/08/2011 2:08 PM, Elisabeth wrote: On 20 August 2011 21:20, Mark Abraham > wrote: On 20/08/2011 8:02 AM, Elisabeth wrote: Dear experts, I am intending to calculate the equilibrium density of a pure hydrocarbon at different pressures , at

Re: [gmx-users] increasing cut-off and PME grid spacing

Hsin-Lin Chiang wrote: Hi, Justin Sorry for the unclear message. My box vector in .gro file are 44.22834 44.22834 44.22834 and the number of atoms is 20171 You've set an unreasonably large box, as I expected. The box should be set in nm, not Angstrom. 20171 atoms is a fairly small syst

[gmx-users] increasing cut-off and PME grid spacing

Hi, Justin Sorry for the unclear message. My box vector in .gro file are 44.22834  44.22834  44.22834 and the number of atoms is 20171 The output of grompp is shown below, I don't know if it is enough and I'm sorry I don't know how should I do after you reply. Could you please give me more messa

Re: [gmx-users] NPT - density off

On 20 August 2011 21:20, Mark Abraham wrote: > On 20/08/2011 8:02 AM, Elisabeth wrote: > > Dear experts, > > I am intending to calculate the equilibrium density of a pure hydrocarbon > at different pressures , at 425 K. The normal boiling point of the liquid is > around 350 K. For pressures belo

Re: [gmx-users] NPT - density off

On 20/08/2011 8:02 AM, Elisabeth wrote: Dear experts, I am intending to calculate the equilibrium density of a pure hydrocarbon at different pressures , at 425 K. The normal boiling point of the liquid is around 350 K. For pressures below 100 bar densities I am getting from NPT is in accurate

[gmx-users] wibke.sudholt spam needs to stop

That's 9 times in the last 20 days that a single user has hit the list with an auto-reply that seems a lot like an advertisement. Can somebody please ban this user? The most recent example: http://lists.gromacs.org/pipermail/gmx-users/2011-August/063991.html -- gmx-users mailing listgmx-

Re: [gmx-users] problem with g_density -center

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, August 22, 2011. For all questions about CloudBroker and the CloudBroker Platfor

[gmx-users] problem with g_density -center

g_density is not compatible with constant pressure simulations. You must modify it to construct the bins outward from the bilayer center when doing NPT: http://lists.gromacs.org/pipermail/gmx-users/2010-November/055651.html Further, trjconv -center is misleading. I actually lost a lot of tim

Re: [gmx-users] problem with g_density -center

Sanku M wrote: Hi, I am trying to calculate the density profile of head group of bilayer normal to z direction using gromacs 4.0.7. I was trying to center the density profile about dx/2.dy/2,0 . But, I am finding problem with using center option. I find using -center option does not shif

[gmx-users] problem with g_density -center

Hi,   I am trying to calculate the density profile of  head group of bilayer normal to z direction using gromacs 4.0.7. I was trying to center the density profile about dx/2.dy/2,0 . But, I am finding problem with using center option. I find using -center option does not shift the bilayer to 0.

Re: [gmx-users] Warning and Notes in Grompp for minimization

meisam valizadeh kiamahalleh wrote: Dear gmx-users Good day to you I have a system including carbon nanotube (1260atoms) and 18 Cisplatin molecules (198atoms) =1458atoms. I have created the topology file of the system and now I would like to run minimization on this system. The content of my

Re: [gmx-users] increasing cut-off and PME grid spacing

Hsin-Lin Chiang wrote: If the simulation is even stable, it will be horribly inaccurate. 12 nm cutoffs are unheard of and 2-nm grid spacing is about 20 times too large. Without seeing the original .mdp file that gave the high PME load, and without a further description about how large the s

[gmx-users] Warning and Notes in Grompp for minimization

Dear gmx-users Good day to you I have a system including carbon nanotube (1260atoms) and 18 Cisplatin molecules (198atoms) =1458atoms. I have created the topology file of the system and now I would like to run minimization on this system. The content of my mdp file is as below; define

[gmx-users] increasing cut-off and PME grid spacing

>If the simulation is even stable, it will be horribly inaccurate. 12 nm >cutoffs >are unheard of and 2-nm grid spacing is about 20 times too large. > >Without seeing the original .mdp file that gave the high PME load, and without >a >further description about how large the system is (number of

[gmx-users] increasing cut-off and PME grid spacing

Sorry for the confusing symbol. I tried to change it in this new mail. Hi, I want to run mdrun -nt 12 on our cluster. When I execute, grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p ../initial/insulin.top -n ../initial/index.ndx I got the message, Estimate for the relativ

Re: [gmx-users] increasing cut-off and PME grid spacing

Hsin-Lin Chiang wrote: **Hi, I want to run mdrun -nt 12 on our cluster. When I execute, grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p ../initial/insulin.top -n ../initial/index.ndx I got the message, Estimate for the relative computational load of the PME mesh part:

[gmx-users] increasing cut-off and PME grid spacing

Hi, I want to run mdrun -nt 12 on our cluster. When I execute, grompp -f test.mdp -o test.tpr -c ../3eq/eq.gro -t ../3eq/eq.trr -p ../initial/insulin.top -n ../initial/index.ndx I got the message, Estimate for the relative computational load of the PME mesh part: 1.00 NOTE 1 [file test.mdp]: