Re: [gmx-users] Regarding Equilibration

Ravi Kumar Venkatraman wrote: Dear all, Could you please tell me what kind of error limit is accepted for running NVT and NPT equilibration in terms of Temperature, Pressure and Density. You should obtain the values you set as ref_t and ref_p if you've done equilibration pro

[gmx-users] (no subject)

Hello, I want to simulate system with 128 ionic liquids (128 cation+128 anion). I have made a pdb file with a single ionic liquids ion pairs. How can I genrate 128 ion pairs using single ion pair .pdb file. I am using Gromacs 4.0.7 version. Thanks Nilesh vac.pdf Description: Adobe

[gmx-users] strange vdw energy from rerun with GBSA model.

Dear Gromacs users: I recently tried some MM/PBSA stuff using the rerun function of mdrun and GBSA model. All water molecules are stripped off the trajectory file. However, when I examine the different energy term, it is disturbing that short range vdw energy of some snapshot are very high (> 100

Re: [gmx-users] (no subject)

Nilesh Dhumal wrote: Hello, I want to simulate system with 128 ionic liquids (128 cation+128 anion). I have made a pdb file with a single ionic liquids ion pairs. How can I genrate 128 ion pairs using single ion pair .pdb file. You can use genconf -nbox to generate a grid of replicates,

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

On 11/08/2011 12:29 AM, Da-Wei Li wrote: Dear Gromacs users: I recently tried some MM/PBSA stuff using the rerun function of mdrun and GBSA model. All water molecules are stripped off the trajectory file. However, when I examine the different energy term, it is disturbing that short range vd

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

Dear Mark That is my thought too.To test this possibility, I created a mdp file without PBC and use trjconv -pbc nojump to make whole protein. From visualization in UCSF Chimera, the trajectory looks fine. But I still have some snapshot that have very high vdw energy. best dawei On Wed, Aug 10,

Re: [gmx-users] Gromacs compilation

On 10/08/2011 4:58 AM, Anthony Cruz Balberdi wrote: Dear User: I compiled GROMACS with OPEN64 without problems, Now I want to compile it using the ACML libraries to compare the performance mdrun will be identical. Several tools would improve. How I can compile gromacs using the ACML librar

[gmx-users] Re: RTILs

> > I want to simulate system with 128 ionic liquids (128 cation+128 anion). > > I have made a pdb file with a single ionic liquids ion pairs. > > How can I genrate 128 ion pairs using single ion pair .pdb file. GENCONF -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester,

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

On 11/08/2011 1:18 AM, Da-Wei Li wrote: Dear Mark That is my thought too.To test this possibility, I created a mdp file without PBC and use trjconv -pbc nojump to make whole protein. >From visualization in UCSF Chimera, the trajectory looks fine. But I still have some snapshot that have very

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

Dear all, we are trying to simulate molecule in specified depth in octanol to calculate logP. for this purpose we have used box with slab of octanol, molecule in specified distance in z-axis and this mdp: integrator = md dt = 0.002 tinit = 0 nsteps = 5125000

Re: [gmx-users] strange vdw energy from rerun with GBSA model.

Dear Mark Could you please help me out? I can send you the trajectory (1000 snapshot in pdb format), mdp, topol file. I use Gromacs-4.5.3. I checked the pdb file in UCSF Chimera and didn't find any crash. I have about 10 snapshot that has high vdw energy. best, dawei On Wed, Aug 10, 2011 at

Re: [gmx-users] Constraints not working in pull code (sometimes, sometimes not)

Krapnik wrote: Dear all, we are trying to simulate molecule in specified depth in octanol to calculate logP. for this purpose we have used box with slab of octanol, molecule in specified distance in z-axis and this mdp: integrator = md dt = 0.002 tinit = 0 ns

[gmx-users] Constraints not working in pull code (sometimes, sometimes not)

I agree that Justin is probably correct, although constraints should technically work just fine with a highly dynamic reference group. Any problems should show up as the system blowing up, but not in correctly setting the position. I think that the problems can arise, however, when you have

[gmx-users] append files in Gromacs 3.3

Hello, I have some old calculations (Umbrella Sampling) carried with Gromacs 3.3.3 and I need to extend them. I have tried to use the option "append" like in Gromacs 4.0, using: mdrun -v -np 8 -s Cl-2.4750_b.tpr -pi Cl-2.4750.ppa -po pullout.ppa -pn Cl-2.4750.ndx -pd -deffnm Cl-2.4750 -append

Re: [gmx-users] append files in Gromacs 3.3

Rebeca García Fandiño wrote: Hello, I have some old calculations (Umbrella Sampling) carried with Gromacs 3.3.3 and I need to extend them. I have tried to use the option "append" like in Gromacs 4.0, using: mdrun -v -np 8 -s Cl-2.4750_b.tpr -pi Cl-2.4750.ppa -po pullout.ppa -pn Cl-2.4750.nd

RE: [gmx-users] append files in Gromacs 3.3

Thanks a lot for your quick answer! Best wishes, Rebeca. > Date: Wed, 10 Aug 2011 14:34:42 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] append files in Gromacs 3.3 > > > > Rebeca García Fandiño wrote: > > Hello, > > I have some old calculations (Umbrella

[gmx-users] running at higher temperatures

Hi, When running simulations at a constant higher temperatures (such as simulating a thermophile) would changing "ref_t" and "gen_temp" to the appropriate kelvin is enough? Thanks and Regards, Raghu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-us

[gmx-users] Trouble installing mdrun-gpu from gromacs 4.5.4 package

Hello,After undergoing a fresh installation of Gromacs 4.5.4, I still can't seem to get the mdrun-gpu program to compile and install. In order to get the original package to install I had to use the standard automake method (cmake kept getting stuck at the 'make' phase).I have managed to get an old

RE: [gmx-users] running at higher temperatures

Yes, that will be enough. Andreas From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Ragothaman Yennamalli [ragotha...@gmail.com] Sent: 10 August 2011 20:35 To: Discussion list for GROMACS users Subject: [gmx-users] running a

[gmx-users] Viscosity calculations

Dear Gromacs Users, I am trying to learn viscosity calculations using non-equilibrium method in Gromacs 4.5.4. I have gone through Hess paper and several posts on viscosity calculation. I have setup a system of pure water (32000 molecules) and run till 10 ns using NPT and setting cos-acceleration=

Re: [gmx-users] Recommended parameters for NVE simulation of SPCE water

> 1.  NOTE 1 above suggests that I use vdwtype = Shift.  When I do this, do > you recommend that I apply long range dispersion corrections for both energy > and pressure, using DispCorr = EnerPres, or for only energy, using DispCorr > = Ener?  Typically, for various (non-NVE) calculations, I have b

[gmx-users] Kinetic energy of a single molecule

Hi there, I'm trying to find the kinetic energy for a single molecule in the system. I generated one individual group for the molecule in index.ndx file, and also put energygrps = ** (** is the name of the group represented the single molecule) in the .mdp file. But g_energy only allowed me to

Re: [gmx-users] Kinetic energy of a single molecule

Size Zheng wrote: Hi there, I'm trying to find the kinetic energy for a single molecule in the system. I generated one individual group for the molecule in index.ndx file, and also put energygrps = ** (** is the name of the group represented the single molecule) in the .mdp file. But g_ener

[gmx-users] To modify PRODRG-generated .itp file?

Hi all, In addition to modifying atomic charges to the .itp file generated by PRODRG, I also want to change the vdw C12 and C6 parameters of selected 1-4 LJ interactions and modify some 1-5 LJ interactions (or any non-bonded LJ interactions) with the vdw C12 and C6 parameters I prefer. So should

Re: [gmx-users] To modify PRODRG-generated .itp file?

Yun Shi wrote: Hi all, In addition to modifying atomic charges to the .itp file generated by PRODRG, I also want to change the vdw C12 and C6 parameters of selected 1-4 LJ interactions and modify some 1-5 LJ interactions (or any non-bonded LJ interactions) with the vdw C12 and C6 parameters

[gmx-users] Selenomethionine in pdb file

Hello Friends, I would like to do simulation of a protein containing 'selenomethionine' [MSE] in coordinate file, during the first step of pdb2gmx this residue is not recognizing by any of the force field and getting fatal error 'Residue 'MSE' not found in residue topology database'. Please help

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