Re: [gmx-users] error with genion

Note you have two different file names there, topol.top and topolo.top Should copy and paste commands and output to avoid typos, which may be the case here. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381

[gmx-users] Are there some environment variables not valid anymore?

Hi, I find this in the installation instruction part GMX 5.0： Helping CMake find the right libraries/headers/programs http://www.gromacs.org/Documentation/Installation_Instructions#TOC If libraries are installed in non-default locations their location can be specified using the

[gmx-users] Charmm to gromacs

Hi All, I took the following from Mark's script to convert non-bonded parameters of ZN manually: printf(% 5s %f 0.0 A %.4g %.4g\n, $atom, $element_mass, 2*$four_epsilon * $sigma**6, $four_epsilon * $sigma**12); I am getting: -0.0002245 -1.205e-08 instead of: 0.194215920555 1.046

[gmx-users] Positive potential energy during Energy minimization step

I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. After Adding Ion genion -s ions.tpr -o pro_POPC_sol_ions.gro -p topol.top -pname NA -np 1 -nname CL I preform energy minimization step. In energy

[gmx-users] can we use AMBER12 FF?

Hello: I am just wondering can we use Amber12 FF in Gromacs now? thank you very much Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] ligand binding

On 8/7/14, 8:47 AM, Meenakshi Rajput wrote: Thank you Justin. Please tell me if emtol should be 1000 or 100 for albumin There are no hard and fast rules when running normal MD simulations. protein complex? As for emtol=1000, complex(mentioned in the tutorial) is converged in some steps and

Re: [gmx-users] Eigenvalues not saved from gmx covar in GROMACS 5

On 8/7/14, 2:00 PM, Steven Morgan wrote: I have installed v5 of GROMACS and am doing simulations on a peptide VPGVG repeated five times. I am trying to calculate entropy and the eigenvalues of the covariance matrix to get eigenfrequencies. When I issue the command gmx covar -f full.trr -s

Re: [gmx-users] New residue in FF does not bond to others.

The problem is in atom naming. You have used MN1 and MC3 for the equivalent of amino acid N and C atoms, respectively. pdb2gmx chokes here, because Phe-65 tries to make a bond to the +N atom, which it does not find until it runs into Ser-69. Likewise with the C atom in CH6. If you rename

Re: [gmx-users] Charmm to gromacs

On 8/8/14, 3:11 AM, Abu Naser wrote: Hi All, I took the following from Mark's script to convert non-bonded parameters of ZN manually: printf(% 5s %f 0.0 A %.4g %.4g\n, $atom, $element_mass, 2*$four_epsilon * $sigma**6, $four_epsilon * $sigma**12); I am getting: -0.0002245

Re: [gmx-users] Positive potential energy during Energy minimization step

On 8/8/14, 7:25 AM, neha bharti wrote: I am trying to perform MD for protein ligand protein complex in popc lipid with charmm36 force field and also follow Justin A. Lemkul tutorial. After Adding Ion genion -s ions.tpr -o pro_POPC_sol_ions.gro -p topol.top -pname NA -np 1 -nname CL I

Re: [gmx-users] Are there some environment variables not valid anymore?

On 8/8/14, 1:22 AM, Theodore Si wrote: Hi, I find this in the installation instruction part GMX 5.0： Helping CMake find the right libraries/headers/programs http://www.gromacs.org/Documentation/Installation_Instructions#TOC If libraries are installed in non-default locations

Re: [gmx-users] New residue in FF does not bond to others.

2014-08-08 15:48 GMT+01:00 Justin Lemkul jalem...@vt.edu: The problem is in atom naming. You have used MN1 and MC3 for the equivalent of amino acid N and C atoms, respectively. pdb2gmx chokes here, because Phe-65 tries to make a bond to the +N atom, which it does not find until it runs into

Re: [gmx-users] New residue in FF does not bond to others.

Very well. Thank you for your assistance :). 2014-08-08 21:00 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 8/8/14, 1:58 PM, Dawid das wrote: Thank you but now I have different type of question. If I use -nocmap option for pdb2gmx what impact on the result of my simulation? Then you

Re: [gmx-users] Eigenvalues not saved from gmx covar in GROMACS 5

Hi Steven, The eigenvalue is the variance of the projection over time. So in stead of waiting for the bug fix, you can also calculate the projections and get the eigenvalues from those. Hope it helps, Tsjerk On Aug 7, 2014 10:32 PM, Steven Morgan smor...@brooklyn.cuny.edu wrote: I have

[gmx-users] Lysozyme-Water Tutorial problem : em.tpr

Dear Users I have been following the Lysozyme in Water tutorial by Dr. Lemkul step by step (GROMACS Version 4.6.5) and I must confess that I am a beginner. I am now stuck in Step 5 : Energy Minimization. I had performed the step :- *grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o

Re: [gmx-users] Lysozyme-Water Tutorial problem : em.tpr

On 8/8/14, 2:53 PM, Agnivo Gosai wrote: Dear Users I have been following the Lysozyme in Water tutorial by Dr. Lemkul step by step (GROMACS Version 4.6.5) and I must confess that I am a beginner. I am now stuck in Step 5 : Energy Minimization. I had performed the step :- *grompp -f

Re: [gmx-users] Can we set the number of pure PME nodes when using GPUCPU?

You can set the number of PME-only ranks with -npme. Whether it's useful is another matter :-) The CPU-based PME offload and the GPU-based PP offload do not combine very well. Mark On Fri, Aug 8, 2014 at 7:24 AM, Theodore Si sjyz...@gmail.com wrote: Hi, Can we set the number manually with

Re: [gmx-users] can we use AMBER12 FF?

You can find the supported force fields in share/gromacs/top, and they do not include AMBER12 Mark On Fri, Aug 8, 2014 at 8:44 AM, Albert mailmd2...@gmail.com wrote: Hello: I am just wondering can we use Amber12 FF in Gromacs now? thank you very much Albert -- Gromacs Users mailing

Re: [gmx-users] Charmm to gromacs

Thanks Justin for your response. I just manually inserted the input values only to that part of the script. The atom types I am interested in, they are not available in the charmm36. Since I have only few unusual atom types, I wish to do them manually and trying to figure out how it can

[gmx-users] Can I delete trr file?

Dear gmx users, I am new user of gromacs. Our calculations are running, but we have a problem that has not enough disk space. Therefore I need to delete some file that are unimportant for analysis. Is there any analysis use trr file? Can I delete trr file? Best regards,  Batsaikhan --