normal How to set desired mass to a given bead?

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2 years 1 week ago #7176 by yogi@martini
How to set desired mass to a given bead? was created by yogi@martini
Dear all,

I would like to assign desired mass to a martini bead to get accurate density profile for the CG bilayer. One way is I edited martini_v2.1.itp to set desired mass but unfortunately my lipid have P4 bead type whose mass I assigned 59 amu (I calculated from atomic structure), I got reasonable density profile for lipid which is close to atomistic results. But, since water molecules are also P4 type, water density got reduced obviously. What should I do? Please help.

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2 years 1 week ago #7177 by peterkroon
Replied by peterkroon on topic How to set desired mass to a given bead?
Change it in the ITP of your molecule (e.g. dopc.itp). Consult the Gromacs manual for the syntax.

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2 years 4 days ago #7181 by yogi@martini
Replied by yogi@martini on topic How to set desired mass to a given bead?
Dear Peterkroon, thanks for the reply. You mean, if we do not mention mass in our .itp file, Gromacs will take default values (72 amu) from martini force field.

Thanks.

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2 years 3 days ago #7184 by riccardo
Replied by riccardo on topic How to set desired mass to a given bead?
Yes, if you don't provide masses in the itp file of your molecule (e.g., dopc.itp) the masses specified for each particular particle (e.g., P4) will be taken from the Martini force field definition (e.g., martini_v2.1.itp). Vice versa, if you *do* specify masses for the different beads in the molecule itp file (as suggested by Peter), those will be used.

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1 year 11 months ago #7192 by yogi@martini
Replied by yogi@martini on topic How to set desired mass to a given bead?
Thank you Riccardo and Peterkroon. It worked!

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