I have taken new server and created custom dns ns1.domain.com and ns2.domain.com and assigned ip addresses.
I have transfered all accounts of old server to new server. my old server name server was ns3.domain.com and ns4.domain.com now if i change the ip of ns3 and ns4 domain at registrar with ns1 and ns2 domains ip. Is my all domain of old server will resolve on new server correctly or i have to do something extra on new server.
Changing the IP of ns3 and ns4 at the registrar will get you 90% of the way there, that should be enough to point your sites at the new server. This is called changing child nameservers by a lot of registrars, so I'll call it that.
If you want the switchover to go faster, I'd edit the zone files (/var/named/*) so they give nameserver IPs pointing to the new server as well. You may get away with just editing the zone for domain.com (ie /var/named/domain.com.db).
In the longer term, the delegated nameservers (at the registrar) should agree with the nameserver records returned by a query on the domain. At the moment the nameserver records returned will be ns1 and ns2 so you'll want to switch those over in the zone files (again in /var/named). This shouldn't affect your switchover but it does on very rare occasions block some antique versions of Bind from being able to resolve those domains with differing nameservers, so you'll want to fix it.