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Related to velocities in gro files after editing
- satnamphysics
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10 years 9 months ago #1769
by satnamphysics
Related to velocities in gro files after editing was created by satnamphysics
Hi
I want to discuss one problem related to the velocities in the gro file. When we use editconf we lost the velocities in the gro or pdb format. When we run simulation we use gen_vel option in .mdp file . It generate velocities according to temperature given . After simulation we get trr file. To visualize whole phenomena we use VMD and we load trr file and coordinate file(.gro) . But in that file there are no initial velocities . So we can not visualize. Kindly tell me how to do...I shall be thankful to you for this...
I want to discuss one problem related to the velocities in the gro file. When we use editconf we lost the velocities in the gro or pdb format. When we run simulation we use gen_vel option in .mdp file . It generate velocities according to temperature given . After simulation we get trr file. To visualize whole phenomena we use VMD and we load trr file and coordinate file(.gro) . But in that file there are no initial velocities . So we can not visualize. Kindly tell me how to do...I shall be thankful to you for this...
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- djurre
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10 years 9 months ago #1770
by djurre
Replied by djurre on topic Related to velocities in gro files after editing
There are a few options:
-Most of things you can do with editconf, you can also do with trjconv and this is capable of writing out velocities. But this may be to late since you already did the simulation.
-Are you sure you need the velocities at every frame? This is generally not information one would look at, especially not in VMD. I for one didn't even know it was possible to load them. This all the more true, since dynamics are very hard to interpret in CG/Martini.
-You could get a gro with velocities from the trajectory (trjconv -dump 0).
-Most of things you can do with editconf, you can also do with trjconv and this is capable of writing out velocities. But this may be to late since you already did the simulation.
-Are you sure you need the velocities at every frame? This is generally not information one would look at, especially not in VMD. I for one didn't even know it was possible to load them. This all the more true, since dynamics are very hard to interpret in CG/Martini.
-You could get a gro with velocities from the trajectory (trjconv -dump 0).
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- xavier
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10 years 9 months ago #1771
by xavier
It is not clear to me what you are trying to do!
You want to visualise the velocities in VMD? This might be a topic to discuss with the VMD people!
Replied by xavier on topic Related to velocities in gro files after editing
satnamphysics wrote: Hi
I want to discuss one problem related to the velocities in the gro file. When we use editconf we lost the velocities in the gro or pdb format. When we run simulation we use gen_vel option in .mdp file . It generate velocities according to temperature given . After simulation we get trr file. To visualize whole phenomena we use VMD and we load trr file and coordinate file(.gro) . But in that file there are no initial velocities . So we can not visualize. Kindly tell me how to do...I shall be thankful to you for this...
It is not clear to me what you are trying to do!
You want to visualise the velocities in VMD? This might be a topic to discuss with the VMD people!
Please Log in or Create an account to join the conversation.
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