[gmx-users] DPOSRES and energy minimization

Is it possible to use position restraints: define = -DPOSRES during an energy minimization? I tried to do that but it looks like all atoms are moved during minimization: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include =

Re: [gmx-users] No Distribution?

@ Justin, Thanks. I fixed the index files like you suggested. I’m getting logical results now. All the best, On Nov 2, 2013, at 7:11 PM, Justin Lemkul wrote: > > > On 11/2/13 7:01 PM, Xu Dong Huang wrote: >> Should I perhaps make an edit in the index file for group 1 to be particle 1 >> a

Re: [gmx-users] No Distribution?

On 11/2/13 7:01 PM, Xu Dong Huang wrote: Should I perhaps make an edit in the index file for group 1 to be particle 1 and 2, and group 2 = particle 2 and 3? No. If you want three different distances, you need three groups, as I said in my previous message, and I even wrote the exact index

Re: [gmx-users] No Distribution?

Should I perhaps make an edit in the index file for group 1 to be particle 1 and 2, and group 2 = particle 2 and 3? On Nov 2, 2013, at 6:50 PM, Xu Dong Huang wrote: > @ Gromacs users, > > so I did g_dist , and I’m confused by a couple of things. 1) why is it asking > me for 2 groups? I have

Re: [gmx-users] No Distribution?

On 11/2/13 6:50 PM, Xu Dong Huang wrote: @ Gromacs users, so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1 23, and nothing else. 2) I just picked the same group twice, and the

Re: [gmx-users] No Distribution?

@ Gromacs users, so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1 23, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following Th

Re: [gmx-users] No Distribution?

On 11/2/13 6:29 PM, Xu Dong Huang wrote: Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 1&2, 1&3 and 2&3, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the fo

[gmx-users] No Distribution?

Dear All, My martini system has 3 particles in a chain, rest is martini water, and I’m only interested in the bond length distribution of particle 1&2, 1&3 and 2&3, and I execute the following: g_bond -f npt.xtc -n index.ndx -o bonds.xvg I get the following error: Total number of samples

Re: [gmx-users] energy minimization problem

On 11/2/13 3:38 PM, kiana moghaddam wrote: Hi GMX Users I 'm running MD Simulation for DNA-ligand interaction. I ran energy minimization with emtol=10, 100 and 250 in 1 steps (steepest descent followed by the conjugate gradient algorithm). The lowest value for energy obtained for emtol=

[gmx-users] energy minimization problem

Hi GMX Users I 'm running MD Simulation for DNA-ligand interaction. I ran energy minimization with emtol=10, 100 and 250 in 1 steps (steepest descent followed by the conjugate gradient algorithm). The lowest value for energy obtained for emtol=10.  I have some questions about energy minimiz

Re: [gmx-users] Gromacs 4.6 & 4.5.3 qualitative differences & 4.6 instability in polarizable force field vacuum/liquid mixture interface simulations

On 2013-11-02 18:38, ploetz wrote: Dear Gromacs Users, Please start a redmine.gromacs.org issue and assign it to me, but try to simplify the system as much as possible. You can cut and paste all the information to the redmine issue. I am trying to simulate a system consisting of a vacuum/co

[gmx-users] Gromacs 4.6 & 4.5.3 qualitative differences & 4.6 instability in polarizable force field vacuum/liquid mixture interface simulations

Dear Gromacs Users, I am trying to simulate a system consisting of a vacuum/condensed phase interface in which a 6x6x12nm condensed phase region is flanked on both ends (in the z-dimension) by a 6x6x12nm vacuum region to form overall box dimensions of 6x6x36 nm. The system is a binary liquid mixtu

Re: [gmx-users] Re: trjconv for pbc

On 11/2/13 12:25 PM, rankinb wrote: Here are the steps that I used: 1. trjconv -pbc whole -dump 37.875 2. trjconv -pbc nojump 3. trjconv -center 4. g_select to make an index containing the atoms of interest 5. trjconv to extract coordinates Regardless of whether step 1 is used or not, th

[gmx-users] Re: trjconv for pbc

Here are the steps that I used: 1. trjconv -pbc whole -dump 37.875 2. trjconv -pbc nojump 3. trjconv -center 4. g_select to make an index containing the atoms of interest 5. trjconv to extract coordinates Regardless of whether step 1 is used or not, the resulting coordination shell configura

Re: [gmx-users] g_lie and ligand only simulation

Ok thank you. I thought it was for protein-ligand-water that needs to be rerun without PME. Thanks Regards Kavya On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul wrote: > > > On 11/2/13 12:14 PM, Kavyashree M wrote: > >> Sir, >> >> Thank you. Should the ligand-water MD be done without PME? >> >>

Re: [gmx-users] g_lie and ligand only simulation

On 11/2/13 12:14 PM, Kavyashree M wrote: Sir, Thank you. Should the ligand-water MD be done without PME? I already answered this. Please read my previous reply again. -Justin Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul wrote: On 11/2/13 1:22 AM, Kavyash

Re: [gmx-users] g_lie and ligand only simulation

Sir, Thank you. Should the ligand-water MD be done without PME? Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul wrote: > > > On 11/2/13 1:22 AM, Kavyashree M wrote: > >> Dear Users, >> >> Its mentioned in the list that it would be >> wrong to use g_lie on a simulation w

[gmx-users] Re: trjconv for pbc

Here is a snapshot of what I was able to extract, if that helps. Blake PhD candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/trjconv-for-pbc-tp5012160p5012166.html Sent from the

Re: [gmx-users] Re: trjconv for pbc

On 11/2/13 11:23 AM, rankinb wrote: Tsjerk, Thanks for your reply. I have tried using the center option, but ran into similar problems. Here are the exact commands that I used: g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within 0.71 of group 13' -b 37.875 -e 37.875 -

Re: [gmx-users] g_lie and ligand only simulation

On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done wit

Re: [gmx-users] Re: RNA simulation (Justin Lemkul)

On 11/2/13 6:32 AM, Hossein Lanjanian wrote: Thank Justin for your help What forcefield is most suitable to study this case? The one that your careful study of the literature tells you is the most reliable. It's up to you to justify your choice, not what someone on the Internet tells you :

Re: [gmx-users] g_lie and ligand only simulation

On 11/2/13 1:00 AM, Kavyashree M wrote: Dear Gromacs users, I have a protein-ligand in water simulation (Gmx 4.5.3), for calculating free energy of ligand binding, a separate simulation of ligand in water simulation is required (which I read from the list). The question is the protein-ligand i

[gmx-users] Re: trjconv for pbc

Tsjerk, Thanks for your reply. I have tried using the center option, but ran into similar problems. Here are the exact commands that I used: g_select -f file.xtc -s file.tpr -n index.ndx -select 'group 14 and within 0.71 of group 13' -b 37.875 -e 37.875 -on index1 (where group 14 contains the w

Re: [gmx-users] trjconv for pbc

Hi Blake, Centering on the solute should help. Cheers, Tsjerk On Sat, Nov 2, 2013 at 3:55 PM, rankinb wrote: > Hi all, > > I am trying to use trjconv to remove PBC. More specifically, I would like > to extract the coordinates of all the water molecules within a certain > distance of a singl

[gmx-users] trjconv for pbc

Hi all, I am trying to use trjconv to remove PBC. More specifically, I would like to extract the coordinates of all the water molecules within a certain distance of a single solute molecule. However, I have been unsuccessful in doing so, even after following the guidelines on the GROMACS website

Re: [gmx-users] ligand problem

Hi, Parmbsc0 is extension of parm99 force-field for which HF/6-31G* was used for charge calculations. Therefore, HF/6-31G* should be used for the RESP calculations. With best regards, Rajendra -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] ligand problem

Hi gmx-users  I'm going to study the molecular dynamics of DNA-ligand interaction. I prepared the DNA topology by using the parmbsc0 force field and the ligand by the GAFF force field.  My question is: what level of theory (HF/6-31G* or B3lyp/6-31G*) is needed for RESP calculation? can someone h

[gmx-users] Re: RNA simulation (Justin Lemkul)

Thank Justin for your help What forcefield is most suitable to study this case? On Oct 31, 2013 1:56 PM, "Hossein Lanjanian" wrote: > Hi > > I'm going to study the molecular dynamics of an RNA(which has stem-loop > structure) by comparison the native RNA structure and it's mutant to find > the c