Re: [gmx-users] I have questions for tabulated bonded potentials

Dear Justin Lemkul, I got it. Thank you very much for your help. Best regards, Changwoon Jang On Tue, Aug 30, 2016 at 8:40 PM, Chang Woon Jang wrote: > Dear Justin, > > >Do you mean "Order of parameters"? If I would like to specify for > table_b1.xvg, I need to

Re: [gmx-users] I have questions for tabulated bonded potentials

Dear Justin, Do you mean "Order of parameters"? If I would like to specify for table_b1.xvg, I need to set 1 after 8. If I would like to specifiy for table_b2.xvg, I need to set 2 after 8. Am I right? Best regards, Changwoon Jang On Tue, Aug 30, 2016 at 8:35 PM, Chang Woon Jang

Re: [gmx-users] I have questions for tabulated bonded potentials

On 8/30/16 8:35 PM, Chang Woon Jang wrote: Dear Justin Lemkul, I have seen the 4.2.12 and Table 5.5. However, it does not show the specific example for several tabulated potentials in topol.top file. I created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg, table_a2.xvg ...

Re: [gmx-users] I have questions for tabulated bonded potentials

Dear Justin Lemkul, I have seen the 4.2.12 and Table 5.5. However, it does not show the specific example for several tabulated potentials in topol.top file. I created table_b1.xvg, table_b2.xvg ... table_b5.xvg, table_a1.xvg, table_a2.xvg ... table_a6.xvg, table_d1.xvg table_d4.xvg.

Re: [gmx-users] I have questions for tabulated bonded potentials

On 8/30/16 8:11 PM, Chang Woon Jang wrote: Dear Gromacs Users, From the above question, I think that I need to specify the each bonded interaction in topol.top file. Am I right? For example, [ bond ] 1 1 2 table_b1.xvg 2 2 3 table_b2.xvg 3 3 4 table_b3.xvg Is this right

Re: [gmx-users] I have questions for tabulated bonded potentials

Dear Gromacs Users, From the above question, I think that I need to specify the each bonded interaction in topol.top file. Am I right? For example, [ bond ] 1 1 2 table_b1.xvg 2 2 3 table_b2.xvg 3 3 4 table_b3.xvg Is this right format if I have several tabulated potential

[gmx-users] Normal Mode Analysis failing with no error message

Hi all I am trying to do a Normal Mode Analysis on a protein assembly with 1.05 million atoms without solvent or ions. I ma trying to do so using Gromacs 5.0.4 double precision using 1024 processor and up to 256 GB of RAM, but it always fails. I do not get any error message from Gromacs in

[gmx-users] I have questions for tabulated bonded potentials

Dear Gromacs Users, I have several bond, angle, dihedral potentials named table_b1.xvg, table_b2.xvg, table_b3.xvg ...table_a1.xvg, table_a2.xvg ... table_d1.xvg, table_d2.xvg, table_d3.xvg, table_d4.xvg. In my system, there are 6 types of beads (A, B, C, D, E, F). How can I assign each

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

Dear Justin, Search engine give a clue about using -nt options. However, how to choose the proper number for -nt option from the error message? Thank you. Best regards, Changwoon Jang On Tue, Aug 30, 2016 at 12:02 PM, Justin Lemkul wrote: > > > On 8/30/16 11:52 AM,

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

On 8/30/16 11:52 AM, Chang Woon Jang wrote: Dear Justin Lemkul, Thank you for your answers. The following is the error message after I run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd 2.5". Initializing Domain Decomposition on 8 ranks Dynamic load balancing:

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

Dear Justin Lemkul, Thank you for your answers. The following is the error message after I run " gmx mdrun -s topol.tpr -c confgout.gro -o traj.trr -x traj.xtc -rdd 2.5". Initializing Domain Decomposition on 8 ranks Dynamic load balancing: auto Will sort the charge groups at every domain

Re: [gmx-users] Assigning charges to Proline residues

On 8/30/16 11:28 AM, Dan Woodall wrote: Hello, I'm looking to define the charges on a 10 residue polypeptide using pdb2gmx. I want to have the N-terminus charged, and a proline at position 6 charged, but I can only find ways to assign charges to the amino acids that typically carry charges.

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

On 8/30/16 10:41 AM, Chang Woon Jang wrote: Dear Justin Lemkul, Thank you for your response. Yes, I use coarse-grained system (thermosetting polymer). I prepared the system from the equilibrated atomistic system. The atomistic system was equilibrated using OPLS-AA force filed under NPT and

[gmx-users] Assigning charges to Proline residues

Hello, I'm looking to define the charges on a 10 residue polypeptide using pdb2gmx. I want to have the N-terminus charged, and a proline at position 6 charged, but I can only find ways to assign charges to the amino acids that typically carry charges. Is there a way I can force the program to

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

Dear Justin Lemkul, Thank you for your response. Yes, I use coarse-grained system (thermosetting polymer). I prepared the system from the equilibrated atomistic system. The atomistic system was equilibrated using OPLS-AA force filed under NPT and NVT for almost 40 ns. The initial atomistic

Re: [gmx-users] Help with MD of water

Hi, There is a method in gromacs to insert water molecules into a box of size defined by you. Depending on the version of gromacs you have, it will be something like gmx insert-molecules. Dan On Tuesday, August 9, 2016, Omamuyovwi Akemu wrote: > Dear Gromacs Users,

Re: [gmx-users] evaluation of influence of pH on the stability of protein

On 8/29/16 3:10 PM, Mahboobeh Eslami wrote: Hi all Gmx usersI want to evaluate influence of pH on the stability of protein. can I use MD simulation for this goal? thanks Protonate the protein and any other relevant species in different forms characteristic of the dominant form at each

Re: [gmx-users] Fatal error: * of the *** bonded interactions could not be calculated because ...

On 8/29/16 6:02 PM, Chang Woon Jang wrote: Dear Gromacs Users, I have a Fatal error as follow. The error says -rdd option or -ddcheck. How can I properly use these options? Is the following command the proper use of these options? gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x

Re: [gmx-users] x,y,z components of forces on each atom

On 8/30/16 8:32 AM, Markus Kaukonen wrote: Dear All, I tried to get forces acting on every atom (fx, fy, fz, not the total force on atom). Is this somehow possible with standard gromacs 2016? Extract them from the .trr file with gmx traj -of. -Justin --

Re: [gmx-users] minimum distance between the protein and its mirror image

On 8/29/16 9:20 PM, OuyangYanhua wrote: The minimum protein-image distance is less than the value 2.0nm, such as t around 1.6nm above. Does it mean my simulation is failed in the box size set? Please read the first sentence of my previous reply. -Justin 在 2016年8月29日，下午8:58，Justin Lemkul

[gmx-users] x,y,z components of forces on each atom

Dear All, I tried to get forces acting on every atom (fx, fy, fz, not the total force on atom). Is this somehow possible with standard gromacs 2016? terveisin, Markus -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: www.helsinki.fi/kemia/svenskakemen/index_eng.html

Re: [gmx-users] Odd behaviour of editconf or VMD?

> > Hi, > > > > I am trying to solvate a small DNA molecule. Since I don't want so > > > > simulate more waters than what is really neccessary, I decided to try the > > dodecahdron and octahedron unit cells. > > > > After I added waters I went to examine the resulting structures in VMD > >

[gmx-users] shear flow

dear all I want to simulate a box with two walls. One of them is fixed and other is moving with steady velocity in a certain direction. I am going to produce a shear flow. If I constrain wall in two directions is enough? How can I produce fixed velocity in other direction? Thanks, Pari --

[gmx-users] evaluation of influence of pH on the stability of protein

On Monday, August 29, 2016 11:40 PM, Mahboobeh Eslami wrote: Hi all Gmx usersI want to evaluate influence of pH on the stability of  protein.  can I use MD simulation for this goal? thanks -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Odd behaviour of editconf or VMD?

Hi Jernej, This is simpler in two dimensions: Consider a hexagonal unit cell. Draw it, together with the surrounding copies (7 hexagons total). Now connect the central hexagon with the right horizontal neighbor, and with the 'northeast' neighbour. Connect these two neighbors with their other

[gmx-users] Odd behaviour of editconf or VMD?

Hi, I am trying to solvate a small DNA molecule. Since I don't want so simulate more waters than what is really neccessary, I decided to try the dodecahdron and octahedron unit cells. After I added waters I went to examine the resulting structures in VMD only to find that the octahedron and

Re: [gmx-users] X Amino Acids for Building CG Structure

Hi Elka, Methyl asparagine is not known by DSSP and is not availble in Martini. You're probably best off replacing it by asparagine: sed '/^ATOM/s/MEN/ASN/' 1HG0.pdb > out.pdb Cheers, Tsjerk On Fri, Aug 26, 2016 at 11:26 AM, Elka Firmanda wrote: > Hi, I just got "X"

Re: [gmx-users] QM/MM simulations (Mark Abraham)

Hi, Unless there are no atoms in the QM region, the QM energy should not be zero. Can you confirm that mdrun writes an input file (input.com)? and gaussian is executed? If not, has gromacs been compiled with QMMM support (GMX_QMMM_PROGRAM:STRING=gaussian)? Best, Gerrit Hi, Sadly, most